From 636721d5c6f2cc53ea3cf0690401c0304c017cbe Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 14:06:37 -0400 Subject: [PATCH 01/24] Fix careers links --- content/careers/2021-07-euro-bioimaging/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/careers/2021-07-euro-bioimaging/index.md b/content/careers/2021-07-euro-bioimaging/index.md index ad5956ed0a..a2e0c71701 100644 --- a/content/careers/2021-07-euro-bioimaging/index.md +++ b/content/careers/2021-07-euro-bioimaging/index.md @@ -2,7 +2,7 @@ title: "Image Data Specialist" date: "2021-07-27" closes: "2021-08-31" -summary: "Support the Image Data Services of the [European research infrastructure Euro-BioImaging ERIC](www.eurobioimaging.eu). Develop modular, shareable, open, and FAIR workflows, integrated in Galaxy for submitting large image data sets to the BioImage Archive." +summary: "Support the Image Data Services of the [European research infrastructure Euro-BioImaging ERIC](https://www.eurobioimaging.eu/). Develop modular, shareable, open, and FAIR workflows, integrated in Galaxy for submitting large image data sets to the BioImage Archive." continent: EU location: "EMBL Heidelberg, Heidelberg, Germany" image: "/src/images/logos/euro-bioimaging-wide.png" From 1c43c6de16500bfe68faa8f4be2a899b86f96bcd Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 14:06:47 -0400 Subject: [PATCH 02/24] Fix jxtx links --- content/jxtx/index.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/content/jxtx/index.md b/content/jxtx/index.md index 4b7f2e3937..53d9a346d8 100644 --- a/content/jxtx/index.md +++ b/content/jxtx/index.md @@ -23,7 +23,11 @@ title: 'James Peter Taylor | 1979 - 2020'
-[James Taylor](/src/jxtx/james.jpg) +
+ +![James Taylor](./james.jpg) + +
*A note to James, a year after his passing.* From ce36c281db42579e2ad2855818bee95ae07f40b8 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 14:58:50 -0400 Subject: [PATCH 03/24] Move sv-wtih-ont to sv-with-ont --- .../index.md | 2 +- .../sv-with-ont-workshop.png | Bin .../sv-with-ont.pdf | Bin 3 files changed, 1 insertion(+), 1 deletion(-) rename content/events/{2021-01-sv-wtih-ont => 2021-01-sv-with-ont}/index.md (85%) rename content/events/{2021-01-sv-wtih-ont => 2021-01-sv-with-ont}/sv-with-ont-workshop.png (100%) rename content/events/{2021-01-sv-wtih-ont => 2021-01-sv-with-ont}/sv-with-ont.pdf (100%) diff --git a/content/events/2021-01-sv-wtih-ont/index.md b/content/events/2021-01-sv-with-ont/index.md similarity index 85% rename from content/events/2021-01-sv-wtih-ont/index.md rename to content/events/2021-01-sv-with-ont/index.md index 3abaacd52f..b4913ef916 100644 --- a/content/events/2021-01-sv-wtih-ont/index.md +++ b/content/events/2021-01-sv-with-ont/index.md @@ -6,7 +6,7 @@ tease: "A GalaxyPro Webinar" continent: GL location: "GalaxyWorks, Online, Global" location_url: "https://galaxyworks.io/webinars/" -external_url: "/events/2021-01-sv-wtih-ont/sv-with-ont.pdf" +external_url: "/events/2021-01-sv-with-ont/sv-with-ont.pdf" gtn: false contact: "Nathan Roach, Michael Alonge" tags: [ webinar ] diff --git a/content/events/2021-01-sv-wtih-ont/sv-with-ont-workshop.png b/content/events/2021-01-sv-with-ont/sv-with-ont-workshop.png similarity index 100% rename from content/events/2021-01-sv-wtih-ont/sv-with-ont-workshop.png rename to content/events/2021-01-sv-with-ont/sv-with-ont-workshop.png diff --git a/content/events/2021-01-sv-wtih-ont/sv-with-ont.pdf b/content/events/2021-01-sv-with-ont/sv-with-ont.pdf similarity index 100% rename from content/events/2021-01-sv-wtih-ont/sv-with-ont.pdf rename to content/events/2021-01-sv-with-ont/sv-with-ont.pdf From e443bdfd92d5ea486bdf03dab8c7a64a6925956a Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 16:36:43 -0400 Subject: [PATCH 04/24] Fix people name links across the site. --- .../index.md | 2 +- .../dev-news-briefs/2011-04-08/index.md | 2 +- .../dev-news-briefs/2011-11-18/index.md | 2 +- .../dev-news-briefs/2012-10-05/index.md | 2 +- .../dev-news-briefs/2012-12-03/index.md | 4 +- .../dev-news-briefs/2015-01-13/index.md | 40 +- .../archive/dev-news-briefs/2015-03/index.md | 20 +- .../blog/2015-07-mysql-2-postgresql/index.md | 2 +- content/blog/2017-10-5000-pubs/index.md | 2 +- content/blog/2017-10-a-blog-is-born/index.md | 2 +- .../2018-11-cotm-saskia-hiltemann/index.md | 2 +- content/blog/2019-07-galaxy-twitter/index.md | 2 +- .../blog/2019-07-looking-for-galaxy/index.md | 2 +- content/blog/2020-08-10k-pubs/index.md | 2 +- content/citing-galaxy/index.md | 20 +- content/cloudman/openstack/index.md | 2 +- content/cloudman/team/index.md | 6 +- .../community/galaxy-admins/future/index.md | 2 +- .../galaxy-admins/meetups/2013-01-16/index.md | 4 +- 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content/news/galaxy-at-asms2013/index.md | 2 +- content/news/galaxy-at-pag2012/index.md | 4 +- .../galaxy-cite-u-like-paper1000/index.md | 2 +- .../news/galaxy-current-protocols/index.md | 4 +- content/news/galaxy-czars-first-call/index.md | 2 +- content/news/galaxy-czars-survey/index.md | 2 +- .../news/galaxy-deployment-catalog/index.md | 2 +- .../galaxy-events-pageand-calendar/index.md | 2 +- .../news/galaxy-gmod-biocuration2013/index.md | 2 +- content/news/galaxy-google-calendars/index.md | 2 +- .../news/galaxy-ismb-eccb-bosc2011/index.md | 2 +- .../galaxy-linked-in-group-created/index.md | 2 +- content/news/galaxy-on-mobile/index.md | 2 +- content/news/galaxy-pag2012/index.md | 4 +- .../galaxy-project-grant-support/index.md | 2 +- content/news/galaxy-project-openings/index.md | 2 +- .../news/galaxy-tour-de-france2012/index.md | 4 +- .../galaxy-workshops-in-south-africa/index.md | 2 +- .../gcc2012-abstract-submission-open/index.md | 2 +- .../gcc2012-registration-is-open/index.md | 2 +- .../news/gcc2012-registration-open/index.md | 2 +- content/news/gcc2012-scheduled/index.md | 2 +- content/news/gcc2014-hackathon/index.md | 2 +- .../gcc2015-data-wrangling-hackathon/index.md | 2 +- .../news/gcc2015-registration-open/index.md | 2 +- content/news/gcc2016-call-for-host/index.md | 2 +- content/news/gcc2017-call-for-host/index.md | 2 +- content/news/gcc2018-call-for-host/index.md | 2 +- content/news/gtn-joins-goblet/index.md | 6 +- .../ismb2011-slides-now-available/index.md | 2 +- .../news/iuc-collections-codefest/index.md | 6 +- .../jan2012-distribution-news-brief/index.md | 2 +- .../index.md | 2 +- .../news/january2012-galaxy-events/index.md | 8 +- .../news/jhu-apl-bioinformaticist/index.md | 2 +- .../index.md | 2 +- .../liste-de-diffusion-galaxy-france/index.md | 2 +- .../index.md | 2 +- .../index.md | 2 +- .../new-galaxy-announce-mailing-list/index.md | 2 +- .../new-galaxy-group-cite-u-like/index.md | 2 +- .../nov2011-distribution-news-brief/index.md | 2 +- .../news/november2011-galaxy-events/index.md | 12 +- .../oct2011-distribution-news-brief/index.md | 2 +- .../news/october2011-galaxy-events/index.md | 8 +- content/news/poweredby-galaxy/index.md | 2 +- content/news/s-g2014-report/index.md | 4 +- .../index.md | 2 +- .../news/september2011-galaxy-events/index.md | 6 +- .../south-africa-workshop-tour2013/index.md | 2 +- .../updated-galaxy-project.org-site/index.md | 2 +- .../watchthe-gcc2011-talks-online/index.md | 2 +- .../index.md | 2 +- content/news/workshop-zagreb201503/index.md | 2 +- content/people/dave-clements/index.md | 10 +- content/people/delphine-lariviere/index.md | 2 +- content/people/fubar/index.md | 2 +- content/people/tori-r/index.md | 2 +- .../toolshed/contributions/2015-04/index.md | 2 +- content/use/basic-sequence/index.md | 2 +- content/use/blast/index.md | 2 +- content/use/ewas-galaxy/index.md | 2 +- content/use/exome-seq/index.md | 2 +- content/use/g-onramp/index.md | 2 +- content/use/galaxy-test/index.md | 2 +- content/use/graphclust/index.md | 2 +- content/use/hic-explorer/index.md | 2 +- content/use/imaging/index.md | 2 +- content/use/metaproteomics-gateway/index.md | 2 +- content/use/proteogenomics-gateway/index.md | 2 +- content/use/quantp/index.md | 2 +- content/use/usegalaxy-au/index.md | 2 +- content/use/usegalaxy-eu/index.md | 2 +- content/use/usegalaxy-org/index.md | 2 +- 422 files changed, 1487 insertions(+), 1487 deletions(-) diff --git a/content/admin/tools/external-display-applications-tutorial/index.md b/content/admin/tools/external-display-applications-tutorial/index.md index c910c4ebdb..645f40c954 100644 --- a/content/admin/tools/external-display-applications-tutorial/index.md +++ b/content/admin/tools/external-display-applications-tutorial/index.md @@ -13,7 +13,7 @@ There are many services available that allow users to upload their own data for ## Citation -If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/src/people/dan/index.md), [John Chilton](/src/people/john-chilton/index.md), and [Nate Coraor](/src/people/nate/index.md). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x * * * diff --git a/content/archive/dev-news-briefs/2011-04-08/index.md b/content/archive/dev-news-briefs/2011-04-08/index.md index 15499ae8b4..9c411f7108 100644 --- a/content/archive/dev-news-briefs/2011-04-08/index.md +++ b/content/archive/dev-news-briefs/2011-04-08/index.md @@ -121,7 +121,7 @@ The target folders select list is filtered to include only valid folders to whic ### Community Tools (Tool Shed) * Tuning: Clarified what is being searched in the **Tool Shed**. -* New ***ClustalW*** wrapper (see http://www.clustal.org) for protein/dna multiple alignments based on the Galaxy *ClustalW* wrapper posted by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) [in an email on the developer list](http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html) +* New ***ClustalW*** wrapper (see http://www.clustal.org) for protein/dna multiple alignments based on the Galaxy *ClustalW* wrapper posted by [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) [in an email on the developer list](http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html) * New *Weblogo3* wrapper ([http://weblogo.berkeley.edu](http://weblogo.berkeley.edu)) that creates sequence logos from *FASTA* data such as the output from a *ClustalW* alignment. ### Data Libraries diff --git a/content/archive/dev-news-briefs/2011-11-18/index.md b/content/archive/dev-news-briefs/2011-11-18/index.md index 22750252e5..1b13245fd7 100644 --- a/content/archive/dev-news-briefs/2011-11-18/index.md +++ b/content/archive/dev-news-briefs/2011-11-18/index.md @@ -30,7 +30,7 @@ Some things will be the same as in previous years, but we are also using feedbac Please reserve July 25-27 on your calendars! -[Dave Clements](/src/people/dave-clements/index.md) and Neil Bahroos +[Dave Clements](/people/dave-clements/) and Neil Bahroos ### Upcoming Workshops and Presentations diff --git a/content/archive/dev-news-briefs/2012-10-05/index.md b/content/archive/dev-news-briefs/2012-10-05/index.md index 76cbc44ce1..d64e0e55ab 100644 --- a/content/archive/dev-news-briefs/2012-10-05/index.md +++ b/content/archive/dev-news-briefs/2012-10-05/index.md @@ -109,7 +109,7 @@ The following sections of the tool shed wiki have been updated to more thoroughl 2. Apply styles when displaying the long description when viewing a tool shed repository. -3. Merged in jmchilton/galaxy-central-toolshed-hg-urls, see *[pull request 69](http://bitbucket.org/galaxy/galaxy-central/pull-request/69)* contributed by [John Chilton](/src/people/john-chilton/index.md). +3. Merged in jmchilton/galaxy-central-toolshed-hg-urls, see *[pull request 69](http://bitbucket.org/galaxy/galaxy-central/pull-request/69)* contributed by [John Chilton](/people/john-chilton/). ### New Galaxy fixes and features included in this Galaxy release diff --git a/content/archive/dev-news-briefs/2012-12-03/index.md b/content/archive/dev-news-briefs/2012-12-03/index.md index 29c938026d..5fbdfd6ce1 100644 --- a/content/archive/dev-news-briefs/2012-12-03/index.md +++ b/content/archive/dev-news-briefs/2012-12-03/index.md @@ -182,8 +182,8 @@ All Galaxy instance maintainers are *strongly encouraged* to run the latest rele
2013 Galaxy Community Conference (GCC2013)
* [Training Day Topic Nominations](/src/events/gcc2013/training-day/index.md) for [GCC2013](/src/events/gcc2013/index.md) will open in December. Start thinking of ideas now! -* Slides and Screencast from [November GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2012-11-14/index.md) are online. The next [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/index.md) will be on [January 16](/src/community/galaxy-admins/meetups/2013-01-16/index.md) and feature [John Chilton](/src/people/john-chilton/index.md) discussing "Deploying Galaxy on OpenStack with CloudBioLinux & CloudMan" -* [A short "Getting started with JGalaxy" document (with screenshots)](http://bit.ly/SkW2yU), by [John Chilton](/src/people/john-chilton/index.md) +* Slides and Screencast from [November GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2012-11-14/index.md) are online. The next [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/index.md) will be on [January 16](/src/community/galaxy-admins/meetups/2013-01-16/index.md) and feature [John Chilton](/people/john-chilton/) discussing "Deploying Galaxy on OpenStack with CloudBioLinux & CloudMan" +* [A short "Getting started with JGalaxy" document (with screenshots)](http://bit.ly/SkW2yU), by [John Chilton](/people/john-chilton/) * [Batch Workflow starting using the Galaxy API : Practical Example by Geert Vandeweyer](http://bit.ly/TjTj6X)
diff --git a/content/archive/dev-news-briefs/2015-01-13/index.md b/content/archive/dev-news-briefs/2015-01-13/index.md index 72e6abe8e4..0050e11369 100644 --- a/content/archive/dev-news-briefs/2015-01-13/index.md +++ b/content/archive/dev-news-briefs/2015-01-13/index.md @@ -71,7 +71,7 @@ Galaxy’s mobile interface, in addition to being vulnerable to XSS attacks, has ## IPython Integration -Thanks to the awesome work of community members [Björn Grüning](/src/people/bjoern-gruening/index.md) and [Helena Rasche](/src/people/helena-rasche/index.md), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. +Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/index.md) and [Helena Rasche](/src/people/helena-rasche/), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. ## Tool Form Upgrade (for Beta Testing) @@ -83,28 +83,28 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Updated Admin Tool Panel with options to load and watch directories of Tools and to trigger auto-reload upon update of any tool. [https://trello.com/c/fXGdYmzo](https://trello.com/c/fXGdYmzo) 1. Fixed bug in Sentry where it was not generated a URL for `history_contents`. [https://trello.com/c/5d6j4X5y](https://trello.com/c/5d6j4X5y) 1. Added a configurable [Google Analytics](http://www.google.com/analytics) tracking tag to Galaxy and Tool Shed forms. Requires configuration modifications for full functionality, see ticket. [https://trello.com/c/R3agjM9U](https://trello.com/c/R3agjM9U) -1. Added an API call to collect History Dataset job metrics. Update will let an API user view the id of the job that produced a History’s Dataset. Thanks to [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/mhmRhxIZ](https://trello.com/c/mhmRhxIZ) +1. Added an API call to collect History Dataset job metrics. Update will let an API user view the id of the job that produced a History’s Dataset. Thanks to [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/mhmRhxIZ](https://trello.com/c/mhmRhxIZ) 1. Updated Job Command line abstraction class to better mask internal values. See ticket for details. [https://trello.com/c/IlSdD0qV](https://trello.com/c/IlSdD0qV) 1. Enhanced job scheduling through new process that resubmits jobs terminated due to memory constraints. [https://trello.com/c/7dJIHzKd](https://trello.com/c/7dJIHzKd) 1. Enhanced client security. Contains a pair of changes aimed at protected clients by preventing [Clickjacking](https://www.owasp.org/index.php/Clickjacking) and informing browsers to not send session cookies issues over HTTPS to HTTP URLs by using [using SecureFlag](https://www.owasp.org/index.php/SecureFlag). [https://trello.com/c/Gt98iH7u](https://trello.com/c/Gt98iH7u) -1. Added [RPy](http://sourceforge.net/projects/rpy/) requirement to the `ngs_simulation` tool. Contributed by [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/kojo4KR2](https://trello.com/c/kojo4KR2) +1. Added [RPy](http://sourceforge.net/projects/rpy/) requirement to the `ngs_simulation` tool. Contributed by [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/kojo4KR2](https://trello.com/c/kojo4KR2) 1. Updated to allow Background and Plugin Driven Scheduling of Workflows. API call details included in tickets. [https://trello.com/c/wiND0YQh](https://trello.com/c/wiND0YQh) [https://trello.com/c/SX2ghmtM](https://trello.com/c/SX2ghmtM) 1. Enhancement to configuration that permits the resolution of relative paths in tool data configuration and .loc files. The string `${__HERE__`} will be expanded out to the directory the file (XML configuration or loc) currently resides in. Ticket includes details/use cases/dependencies. [https://trello.com/c/5VQOWgld](https://trello.com/c/5VQOWgld) -1. Improved handling of Report applications. Will discover and utilize proper configuration file. Thank you for testing by [Helena Rasche](/src/people/helena-rasche/index.md). [https://trello.com/c/aRQglAkf](https://trello.com/c/aRQglAkf) [https://trello.com/c/SOe8W2U6](https://trello.com/c/SOe8W2U6) [https://trello.com/c/SOe8W2U6](https://trello.com/c/SOe8W2U6) +1. Improved handling of Report applications. Will discover and utilize proper configuration file. Thank you for testing by [Helena Rasche](/people/helena-rasche/). [https://trello.com/c/aRQglAkf](https://trello.com/c/aRQglAkf) [https://trello.com/c/SOe8W2U6](https://trello.com/c/SOe8W2U6) [https://trello.com/c/SOe8W2U6](https://trello.com/c/SOe8W2U6) 1. Added a javascript validation for username and email changes. A user account was deactivated upon an email address update when no prior activation token existed, requiring account activation, but no notice was given to the user. Now, if no token present (legacy auto-validation), the email must be verified and upon login, the email to do so is sent. Plus minor tunings. [https://trello.com/c/WTSZtxuD](https://trello.com/c/WTSZtxuD) [https://trello.com/c/HJsfz3no](https://trello.com/c/HJsfz3no) 1. Added blank string for `host_url` to tooltip rendering when the value is unavailable. Avoids an occasional issue that comes up in the Workflow editor. Thank you Kyle Ellrott. [https://trello.com/c/g5xNIYGS](https://trello.com/c/g5xNIYGS) -1. Included enhancements to the "Convert delimiters" and "velvetg" tools. Please see ticket for the changesets included. Thanks to [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/4cDu8T4I](https://trello.com/c/4cDu8T4I) -1. Expanded configuration options to permit a dynamic external proxy manager (`dynamic_proxy_external_proxy`), which is required for certain server type’s to have correct functionality/URL paths. Contributed by [Helena Rasche](/src/people/helena-rasche/index.md). [https://trello.com/c/C7wtcdvd](https://trello.com/c/C7wtcdvd) +1. Included enhancements to the "Convert delimiters" and "velvetg" tools. Please see ticket for the changesets included. Thanks to [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/4cDu8T4I](https://trello.com/c/4cDu8T4I) +1. Expanded configuration options to permit a dynamic external proxy manager (`dynamic_proxy_external_proxy`), which is required for certain server type’s to have correct functionality/URL paths. Contributed by [Helena Rasche](/people/helena-rasche/). [https://trello.com/c/C7wtcdvd](https://trello.com/c/C7wtcdvd) 1. Updated the `tool_conf.xml.sample` file as the initial phase of [Galaxy’s](http://galaxyproject.org) tool revision plans for 2015. [https://trello.com/c/soeyuJfV](https://trello.com/c/soeyuJfV) -1. Implemented a way of creating a [Tool Shed](http://usegalaxy.org/toolsehd) repository revisions through an API tarball upload. Overall goal is to simplify tool loads. Please see the ticket for full details. Thank you [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/rvO8CijI](https://trello.com/c/rvO8CijI) +1. Implemented a way of creating a [Tool Shed](http://usegalaxy.org/toolsehd) repository revisions through an API tarball upload. Overall goal is to simplify tool loads. Please see the ticket for full details. Thank you [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/rvO8CijI](https://trello.com/c/rvO8CijI) 1. Included new API method ` /api/tool_data` to allow for the interactive interrogation of the `tool-data` tables on a server. Authored by Kyle Ellrott. [https://trello.com/c/zf6Rni64](https://trello.com/c/zf6Rni64) -1. Improved the `docstring` of previously added Dataset type detection (sniff) functions. Thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/UFjkigva](https://trello.com/c/UFjkigva) +1. Improved the `docstring` of previously added Dataset type detection (sniff) functions. Thanks to [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/UFjkigva](https://trello.com/c/UFjkigva) 1. Added [.xlsx](http://filext.com/file-extension/XLSX) as a new datatype. This enables proper identification and labeling of the (primarily) Excel data upon Upload. Thank you Hunter Moseley. [https://trello.com/c/qxGGQ1Ls](https://trello.com/c/qxGGQ1Ls) -1. Added `.cbx` as a new datatype. This is used/produced by recent versions of the [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/manual) RNA-Seq analysis tool set. Contributed by [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/WBWxACyr](https://trello.com/c/WBWxACyr) -1. Added `.owl` and `.obo` as new datatypes. This facilities data use in the recently created [Ontology Toolkit](https://github.com/galaxyproject/tools-iuc/pull/6) wrappers. Design and testing from [Björn Grüning](/src/people/bjoern-gruening/index.md), Erick Antezana, and Peter Cock on behalf of the [IUC](https://wiki.galaxyproject.org/IUC). [https://trello.com/c/4t96N2eV](https://trello.com/c/4t96N2eV) +1. Added `.cbx` as a new datatype. This is used/produced by recent versions of the [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/manual) RNA-Seq analysis tool set. Contributed by [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/WBWxACyr](https://trello.com/c/WBWxACyr) +1. Added `.owl` and `.obo` as new datatypes. This facilities data use in the recently created [Ontology Toolkit](https://github.com/galaxyproject/tools-iuc/pull/6) wrappers. Design and testing from [Björn Grüning](/people/bjoern-gruening/), Erick Antezana, and Peter Cock on behalf of the [IUC](https://wiki.galaxyproject.org/IUC). [https://trello.com/c/4t96N2eV](https://trello.com/c/4t96N2eV) 1. Updated [Docker](http://www.docker.com) to run with 'auto-remove' by default (`—rm`} flag). Containers are automatically removed, which prevents a collection of old work containers from building up. Thanks Kyle Ellrott. [https://trello.com/c/uSyg8OYN](https://trello.com/c/uSyg8OYN) 1. Updated [Docker](http://www.docker.com) to run with 'set user' by default (`docker_set_user = true`}). This change updates the ownership of commands and any results to be non-root. Thanks again to Kyle Ellrott. [https://trello.com/c/0FO0UOe7](https://trello.com/c/0FO0UOe7) -1. Updated [Docker](http://www.docker.com) to run with the `-u $USER` argument. Thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/A3VjbvMG](https://trello.com/c/A3VjbvMG) +1. Updated [Docker](http://www.docker.com) to run with the `-u $USER` argument. Thanks to [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/A3VjbvMG](https://trello.com/c/A3VjbvMG) 1. Added `tool_library_dir` to `tool_conf` parser (`tool_dir` was already added). For `tool_library_dir`, the parser scans the child directories of the given directory, and loads the .xml files inside of them. This permits the loading of all the .xml tool definitions within a the same base directory, included nested directories. [https://trello.com/c/OJelgFPu](https://trello.com/c/OJelgFPu) 1. Allow Model objects to be loaded when they have problematic [JSON](http://www.json.org) values. Now, when such a value is encountered, it is substitute with None. [https://trello.com/c/9lvIKGXa](https://trello.com/c/9lvIKGXa) 1. Changed the [JSON](http://www.json.org) custom type to be a `large blob` type when [MySQL](http://www.mysql.com) is used. Upgrading migrates the update. [https://trello.com/c/RbW6pOd2](https://trello.com/c/RbW6pOd2) [https://trello.com/c/qhGD4sIk](https://trello.com/c/qhGD4sIk) @@ -120,7 +120,7 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Improved `DatasetMatcher` to now check if a Dataset’s `hda` is of the correct format before attempting to perform filtering. This ensures that the correct metadata attributes are intact, with the goal of clarifying job failure reasons (as some attributes may not exist for an unexpected format). [https://trello.com/c/wKuW6o1R](https://trello.com/c/wKuW6o1R) 1. Improved handling in the function `DynamicOptions AdditionalValueFilter` when Dataset columns have not been assigned. Logic now interprets a data’s `value` instead of failing due to a missing/unassigned `name` (column label) metadata attribute. [https://trello.com/c/kPFaKDlv](https://trello.com/c/kPFaKDlv) 1. Improved handling of the Slurm job `CANCELLED` state. This improves error reporting, e.g. by clearly stating when a job fails because it exceeds memory quotas versus being cancel by the administrator for other reasons. [https://trello.com/c/GA29VWGL](https://trello.com/c/GA29VWGL) -1. Hide the `GALAXY` env variable in `updateucsc.sh.sample`. This enables it to be set externally when calling the script. Useful in docker containers. Contributed by [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/rkjT8COY](https://trello.com/c/rkjT8COY) [https://trello.com/c/Uu1fDBw2](https://trello.com/c/Uu1fDBw2) +1. Hide the `GALAXY` env variable in `updateucsc.sh.sample`. This enables it to be set externally when calling the script. Useful in docker containers. Contributed by [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/rkjT8COY](https://trello.com/c/rkjT8COY) [https://trello.com/c/Uu1fDBw2](https://trello.com/c/Uu1fDBw2) 1. Relocated `job_lock` from the queue to the `JobManager` itself. This fixes `NoopQueue` from not having `job_lock` errors when viewed in the UI under Admin → Jobs. [https://trello.com/c/iHlVTdMX](https://trello.com/c/iHlVTdMX) 1. Removed r3 instance types due to issues with dependencies that resulted in launch failures. [https://trello.com/c/NeqbeLMD](https://trello.com/c/NeqbeLMD) 1. Added flexibility for `tool data table` configuration in the Install and Test Framework. [https://trello.com/c/oKZPySe2](https://trello.com/c/oKZPySe2) @@ -133,29 +133,29 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Resolved issue where Pages with embedded Visualization were causing a UI error. [https://trello.com/c/fZRdzMoI](https://trello.com/c/fZRdzMoI) 1. Corrected issue where installing repositories with many tools causes Galaxy to throw errors in the admin interface. [https://trello.com/c/Hv5iIweU](https://trello.com/c/Hv5iIweU) 1. Corrected `lib/galaxy/config.py`. A missing comma on openid configuration locations has been replaced and the resulting error no longer occurs. Reported by @scholtalbers. [https://trello.com/c/AwZwAx4l](https://trello.com/c/AwZwAx4l) -1. Corrected `package_picard_1_56_0` so that it no longer contains `Picard v. 1.122.0`. Discovered by [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/jKJRjf9N](https://trello.com/c/jKJRjf9N) +1. Corrected `package_picard_1_56_0` so that it no longer contains `Picard v. 1.122.0`. Discovered by [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/jKJRjf9N](https://trello.com/c/jKJRjf9N) 1. Finalized a bug fix for over escaping implemented in prior changeset c2bed0a. [https://trello.com/c/godTRTgY](https://trello.com/c/godTRTgY) [https://trello.com/c/pAGxM1mb](https://trello.com/c/pAGxM1mb) -1. Fixed a variable name associated with data folders that was causing a `NameError` issue. Thank you [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/lXgZR2Yb](https://trello.com/c/lXgZR2Yb) -1. Corrected a bug in Internet Explorer (IE) configuration parsing. Thank you [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/p49eQLPx](https://trello.com/c/p49eQLPx) +1. Fixed a variable name associated with data folders that was causing a `NameError` issue. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/lXgZR2Yb](https://trello.com/c/lXgZR2Yb) +1. Corrected a bug in Internet Explorer (IE) configuration parsing. Thank you [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/p49eQLPx](https://trello.com/c/p49eQLPx) 1. Fixed an improper redirect during user password reset. [https://trello.com/c/ROONezok](https://trello.com/c/ROONezok) 1. Fixed Workflow import to correctly set the `uuid`. Contributed by Kyle Ellrott. [https://trello.com/c/4UP6Gfo9](https://trello.com/c/4UP6Gfo9) -1. Corrected a few small bugs in docs and pylint. See ticket/changesets for details. Contributed by [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/HVm9vKl2](https://trello.com/c/HVm9vKl2) +1. Corrected a few small bugs in docs and pylint. See ticket/changesets for details. Contributed by [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/HVm9vKl2](https://trello.com/c/HVm9vKl2) 1. Corrected a boolean parameter handling issue that occurred during a Workflow’s runtime execution. ’’Incorporating this fix is critical for proper Workflow execution.’’. The problem manifested as certain tool parameters executing »in the reverse state« when used within Workflows (exclusively, and never when tools were executed directly outside of Workflows). A tool »re-run« form will reveal the issue and various failure errors are known to have resulted. If a prior successful Workflow now fails, and your instance as not yet included in this changeset yet, the issue could likely be the root cause of Workflow tool errors. The problem impacted the [Main](/src/main/index.md) public Galaxy instance at [http://usegalaxy.org](http://usegalaxy.org) for a short time window in November. The fix was applied to the public instance and added to the Stable branch under [latest_2014.10.06](/src/archive/dev-news-briefs/2014-10-06/index.md) upon discovery/resolution, at a priority, during this same time frame. Reported by Andrea Pinna. [https://trello.com/c/zdHaxzSn](https://trello.com/c/zdHaxzSn) [https://trello.com/c/sXUwBJgb](https://trello.com/c/sXUwBJgb) 1. Fixed changeset 04a072e to now use the correct `MAKO` method in the masthead. [https://trello.com/c/ZSMVriGJ](https://trello.com/c/ZSMVriGJ) 1. Composite Datatype uploads no longer problematic by assuming groups have a UUID field. [https://trello.com/c/GbZwGPmt](https://trello.com/c/GbZwGPmt) -1. Fixed passing nested parameter replacements to the Workflow run API. Discovered by [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/WtFpviiw](https://trello.com/c/WtFpviiw) +1. Fixed passing nested parameter replacements to the Workflow run API. Discovered by [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/WtFpviiw](https://trello.com/c/WtFpviiw) 1. Fixed Pulsar's default HTTP transport to automatically load. Impacts behavior of `urllib` changes with respect of content length of `mmap` data after loading. [https://trello.com/c/Aq0PK81c](https://trello.com/c/Aq0PK81c) 1. Fixed composite Datatypes issue related to renaming individual parts of paired Datasets. [https://trello.com/c/ExOMfxtT](https://trello.com/c/ExOMfxtT) 1. Fixed issue where Dataset download links were being incorrectly populated by regenerating `dataset-model` URLs upon fetching (even when silent). Plus a corrections for cases where the `to_ext` value was missing. [https://trello.com/c/ngLd7M4u](https://trello.com/c/ngLd7M4u) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) 1. Fix Slurm job post-mortem for »clusters« functionality added to `slurm-drmaa` (and currently in use on [http://usegalaxy.org](http://usegalaxy.org)). [https://trello.com/c/OuNEdZLc](https://trello.com/c/OuNEdZLc) -1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md) & [Björn Grüning](/src/people/bjoern-gruening/index.md). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) -1. Fixed import bug for `run_reports.sh`. Thank you [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [https://trello.com/c/ZmTmQTZl](https://trello.com/c/ZmTmQTZl) +1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/people/nicola-soranzo/index.md) & [Björn Grüning](/src/people/bjoern-gruening/). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) +1. Fixed import bug for `run_reports.sh`. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/ZmTmQTZl](https://trello.com/c/ZmTmQTZl) 1. Fixed a parameter parsing issue in the Data Libraries API (recently introduced while refactoring Data Managers). [https://trello.com/c/1ZTlAVlT](https://trello.com/c/1ZTlAVlT) 1. Corrected a temporary issue where Import was omitted from the original release of `latest_2014.10.06`. [https://trello.com/c/iJwFduar](https://trello.com/c/iJwFduar) # News and Community -1. We would like to send a special acknowledgement along with a huge **Thank YOU!!** (or as our own [Dave Clements](/src/people/dave-clements/index.md) often states informally, "Hugs!") to our *Intergalactic Utilities Commission* members. Our project most definitely would not be the same without the *IUC's* unwavering and dedicated support, contributions, and suggestions throughout the years. Everyone in the Galaxy community benefits directly, in a multitude of ways, that are too far reaching to list out fully in this quick note. *Curious* about who is involved and the key role this community-driven group has in improving and maintaining the [Tool Shed](https://wiki.galaxyproject.org/ToolShed) and their owned/reviewed [Repositories](http://usegalaxy.org) (in addition to other important areas)? Learn more about the members and future/active/prior projects and goals [here...](https://wiki.galaxyproject.org/IUC). +1. We would like to send a special acknowledgement along with a huge **Thank YOU!!** (or as our own [Dave Clements](/people/dave-clements/) often states informally, "Hugs!") to our *Intergalactic Utilities Commission* members. Our project most definitely would not be the same without the *IUC's* unwavering and dedicated support, contributions, and suggestions throughout the years. Everyone in the Galaxy community benefits directly, in a multitude of ways, that are too far reaching to list out fully in this quick note. *Curious* about who is involved and the key role this community-driven group has in improving and maintaining the [Tool Shed](https://wiki.galaxyproject.org/ToolShed) and their owned/reviewed [Repositories](http://usegalaxy.org) (in addition to other important areas)? Learn more about the members and future/active/prior projects and goals [here...](https://wiki.galaxyproject.org/IUC). 1. Explore the latest [Galaxy Project](http://galaxyproject.org) news from our team that covers recent Events, Publications, New Tools, and much more in our monthly project reports published in our wiki under [Galaxy Updates](http://wiki.galaxyproject.org/GalaxyUpdates). 1. [Tool Shed Contributions](https://wiki.galaxyproject.org/ToolShed/Contributions). This is a brand-new area previously included directly in the *[Galaxy Updates](http://wiki.galaxyproject.org/GalaxyUpdates)* news letters. Watch as this area develops as we work to summarize new repository updates in a concise and organized format. Feedback about how you would like to see this evolve (including general interest) is welcome. We will be posting a comment/feedback post at [Galaxy Biostar](https://biostar.usegalaxy.org/) to provide an opportunity to for our community to discuss. A summary will be added to [Trello](https://wiki.galaxyproject.org/Issues) once feedback is gathered for review and action. (A link to that post will be updated and added right here in this wiki within the next week - is truly a *brand-new* endeavor to break this out as a distinct wiki resource!!). 1. If you are new to Galaxy or wish to connect with our project more in 2015, these key links can help keep you updated about our activities and updates in real time (or at your own pace). Galaxy is a community project we would like to remind all about of the resources and venues available for news and support. Most reading our News Briefs are familiar with [Development](https://wiki.galaxyproject.org/Develop), [Cloud](https://wiki.galaxyproject.org/Cloud), [Local](https://wiki.galaxyproject.org/Admin/GetGalaxy), and other deployment resources such as [Admin](https://wiki.galaxyproject.org/Admin) plus [Tool](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax) and [Tool Repository](https://wiki.galaxyproject.org/ToolShed) documenation, but below is a short list of even more places to visit and get connected: diff --git a/content/archive/dev-news-briefs/2015-03/index.md b/content/archive/dev-news-briefs/2015-03/index.md index 68d67acf89..7ef54eb416 100644 --- a/content/archive/dev-news-briefs/2015-03/index.md +++ b/content/archive/dev-news-briefs/2015-03/index.md @@ -81,7 +81,7 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. [Mercurial](http://mercurial.selenic.com) egg updated to version (3.2.4). [9A9uIav0](https://trello.com/c/9A9uIav0) [NUqyskst](https://trello.com/c/NUqyskst) 1. [SQLAlchemy](http://www.sqlalchemy.org) upgrade to version 0.9.8. [zGLtSgPW](https://trello.com/c/zGLtSgPW) 1. An invalid API key will now always return a »403« error. Triggers: API key is not found, is expired, or is not associated with an active account. [n59kZhXk](https://trello.com/c/n59kZhXk) -1. Python PEP-8 fixes and API documentation enhancements for Libraries API. Thanks to [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [MD4iUtzk](https://trello.com/c/MD4iUtzk) +1. Python PEP-8 fixes and API documentation enhancements for Libraries API. Thanks to [Nicola Soranzo](/people/nicola-soranzo/). [MD4iUtzk](https://trello.com/c/MD4iUtzk) 1. Moved the vast majority of the test-data out of `GALAXY_ROOT` (remaining tools excluded). [kcYI9DnK](https://trello.com/c/kcYI9DnK) [xd7Uri9l](https://trello.com/c/xd7Uri9l) 1. New options that permits tools to access their `$REPOSITORY_INSTALL_DIR` location via `PATH`. [0pgF5PBQ](https://trello.com/c/0pgF5PBQ) 1. To preserve the original deployment state, a new option to disable runtime egg fetching was created (a configurable environment variable - see ticket for details). [lthRjVZq](https://trello.com/c/lthRjVZq) @@ -92,9 +92,9 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. Expanded on Base, History, and HDA managers to provide a consistent facade for common model operations. [3A8nocpN](https://trello.com/c/3A8nocpN) 1. Upgraded [SQLAlchemy](http://www.sqlalchemy.org) to incorporate two major revisions in this release. [XbZwEuxx](https://trello.com/c/XbZwEuxx) 1. Removed use of the elementtree package and move to lxml.etree. [JJDxFdzK](https://trello.com/c/JJDxFdzK) -1. Stopped aborted restart when `stop_daemon()` fails. Thank you [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [1nlG2OmX](https://trello.com/c/1nlG2OmX) -1. Merged `rolling_restart.sh` in `run.sh` by adding a new `—wait` parameter and other enhancements. Thank you [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [QNKSMf2B](https://trello.com/c/QNKSMf2B) [S3WLFpGL](https://trello.com/c/S3WLFpGL) [jx0F2RKy](https://trello.com/c/jx0F2RKy) -1. Enhancements to `galaxy.ini` and `integrated_tool_panel.xml` documentation. Contributed by [Nicola Soranzo](/src/people/nicola-soranzo/index.md). [4idoVDY8](https://trello.com/c/4idoVDY8) +1. Stopped aborted restart when `stop_daemon()` fails. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [1nlG2OmX](https://trello.com/c/1nlG2OmX) +1. Merged `rolling_restart.sh` in `run.sh` by adding a new `—wait` parameter and other enhancements. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [QNKSMf2B](https://trello.com/c/QNKSMf2B) [S3WLFpGL](https://trello.com/c/S3WLFpGL) [jx0F2RKy](https://trello.com/c/jx0F2RKy) +1. Enhancements to `galaxy.ini` and `integrated_tool_panel.xml` documentation. Contributed by [Nicola Soranzo](/people/nicola-soranzo/). [4idoVDY8](https://trello.com/c/4idoVDY8) 1. New configuration option to isolate tool commands in their own shell. [kyS9dF0s](https://trello.com/c/kyS9dF0s) 1. Added a new configuration, `template_cache_path`, to reports_wsgi.ini.sample. Thank you Trevor Wennblom. [5vJ4EsDI](https://trello.com/c/5vJ4EsDI) 1. Provide [NGINX](http://nginx.org/en) packages with the upload module. [C3g6Ko8K](https://trello.com/c/C3g6Ko8K) @@ -103,7 +103,7 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. Restructured `mvc/ui.js`. [HnnBFJy0](https://trello.com/c/HnnBFJy0) 1. Improved use of a SELECT statement to reliably retrieve table column names. Thank you James Johnson. [oYkjj4T3](https://trello.com/c/oYkjj4T3) 1. Enhanced a method to use first component of X-Forwarded-{For,Host,Scheme} when redirecting to the Galaxy browser. [BmbtnSon](https://trello.com/c/BmbtnSon) [BmbtnSon](https://trello.com/c/BmbtnSon) -1. Migrated `shed_tool_conf.xml` into /config. Contributed by [Nitesh Turaga](/src/people/nitesh-turaga/index.md). [6olcQrhR](https://trello.com/c/6olcQrhR) +1. Migrated `shed_tool_conf.xml` into /config. Contributed by [Nitesh Turaga](/people/nitesh-turaga/). [6olcQrhR](https://trello.com/c/6olcQrhR) 1. Made installation of tool repositories more robust by setting time to "Epoch" instead of throwing server error when `repository_metadata.time_last_tested` is unset. [o09VBhr1](https://trello.com/c/o09VBhr1) 1. Change to allow anonymous users (those not logged into a Galaxy account) to view Pages with embedded Histories. [9Om6Odj2](https://trello.com/c/9Om6Odj2) 1. The GET /api/jobs request/response functionality has been expanded. Details in ticket. Thank you Thomas McGowan. [H0Bvd737](https://trello.com/c/H0Bvd737) @@ -111,7 +111,7 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. Moved `blastdb_p.loc.sample` to the NCBI BLAST Tool Shed repository. Thanks to Lance Parsons. [lpZNmEzj](https://trello.com/c/lpZNmEzj) 1. Clearer error messages where parameter validation fails. Thanks to Peter Cock. [dRaX5reV](https://trello.com/c/dRaX5reV) 1. Added `pkg_resources` to load required Mako packages. Thanks to Lance Parsons. [JdxJ11U0](https://trello.com/c/JdxJ11U0) -1. Updated the Dockerfile template to the latest version our Galaxy Docker Container (updated at Galaxy release). Thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md). [Z45ZZ9C2](https://trello.com/c/Z45ZZ9C2) +1. Updated the Dockerfile template to the latest version our Galaxy Docker Container (updated at Galaxy release). Thanks to [Björn Grüning](/people/bjoern-gruening/). [Z45ZZ9C2](https://trello.com/c/Z45ZZ9C2) 1. Added a new API method to remove items from tool data tables. Thanks to Anthony Bretaud. [51JsMj0b](https://trello.com/c/51JsMj0b) 1. Create attribute »optional« for data column parameters. A compliment to »force_select«. [G5YtpQZK](https://trello.com/c/G5YtpQZK) 1. Enhanced the `collect_primary_datasets()` method to allow assignment of the defined output parameter for 3rd-party tools that manage tool outputs internally. [pncHLXdw](https://trello.com/c/pncHLXdw) @@ -133,7 +133,7 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy * Implementation of Dataset Collections »list of pairs«. Additional work is in-progress (see ticket). [8hEO00xj](https://trello.com/c/8hEO00xj) * Dataset Collections updated to permit »Drag & Drop« functionality (»copy datasets« is still an option). [Zmy8aiFP](https://trello.com/c/Zmy8aiFP) 1. New [ZebrafishMine](http://www.zebrafishmine.org) Data Source tool. [u5OlE4kZ](https://trello.com/c/u5OlE4kZ) -1. New datatypes. Thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md). +1. New datatypes. Thanks to [Björn Grüning](/people/bjoern-gruening/). * Added [SnpEff](http://snpeff.sourceforge.net) datatypes. [accZ8KdI](https://trello.com/c/accZ8KdI) * Added `CompressedArchive` as a new datatype that does not uncompress during data upload. [1xtvpWil](https://trello.com/c/1xtvpWil) * Added Arff datatype. [fdVfagbS](https://trello.com/c/fdVfagbS) @@ -151,13 +151,13 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. Workflow steps are now assigned UUIDs. [4U9e1och](https://trello.com/c/4U9e1och) 1. Updated the Workflow API by replacing preferred usage terminology (s/usage/invocation). [XNInq5KH](https://trello.com/c/XNInq5KH) 1. Tuning for History panel functions: Dataset search, multi-select Datasets to perform batch operations, related database modifications. [D4nLl5Ky](https://trello.com/c/D4nLl5Ky) -1. To enhance sharing of a History or Page, the forms now accept user IDs. Contributed by [Helena Rasche](/src/people/helena-rasche/index.md). [qzYtnG4T](https://trello.com/c/qzYtnG4T) [DCjT4KdQ](https://trello.com/c/DCjT4KdQ) +1. To enhance sharing of a History or Page, the forms now accept user IDs. Contributed by [Helena Rasche](/people/helena-rasche/). [qzYtnG4T](https://trello.com/c/qzYtnG4T) [DCjT4KdQ](https://trello.com/c/DCjT4KdQ) 1. Load the »Available Genomes« list from data tables for visualizations (Trackster). Thanks to Anthony Bretaudeau. [x8LMSD7Z](https://trello.com/c/x8LMSD7Z) 1. The History »Options« menu has been updated to better compliment other recent UI changes. [EEsM0abM](https://trello.com/c/EEsM0abM) 1. Several improvements to the History list view. [ltNMDNbZ](https://trello.com/c/ltNMDNbZ) 1. New [Fetch Genome](http://toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta) Data Manager updated to create the metadata needed by Trackster. [IKdX0vX5](https://trello.com/c/IKdX0vX5) 1. Addressed »multipart-upload« by using [Swift](https://swiftstack.com/openstack-swift) as an object storage backend. Thank you Charles Hsu. [U4kJBMk9](https://trello.com/c/U4kJBMk9) -1. Added [Planemo](http://https://github.com/galaxyproject/planemo) test file to Tool Shed upload »blacklist«. Thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md). [0Z1tfTVU](https://trello.com/c/0Z1tfTVU) +1. Added [Planemo](http://https://github.com/galaxyproject/planemo) test file to Tool Shed upload »blacklist«. Thanks to [Björn Grüning](/people/bjoern-gruening/). [0Z1tfTVU](https://trello.com/c/0Z1tfTVU) 1. Added tool tests functions to assert properties about command, standard output, and standard error. [kNgOADAF](https://trello.com/c/kNgOADAF) # Fixed @@ -215,7 +215,7 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy 1. Various low-vulnerability-level security fixes. [U6yj2pPr](https://trello.com/c/U6yj2pPr) 1. Galaxy logs no longer leak database connection information. [VjEqTxlT](https://trello.com/c/VjEqTxlT) 1. The email for resetting an account password is now a link. [SKjU40t6](https://trello.com/c/SKjU40t6) -1. New »shared secret« between Galaxy and upstream proxies, thereby preventing a specific potential impersonation attack. Thank you [Helena Rasche](/src/people/helena-rasche/index.md). [jTHrXHol](https://trello.com/c/jTHrXHol) +1. New »shared secret« between Galaxy and upstream proxies, thereby preventing a specific potential impersonation attack. Thank you [Helena Rasche](/people/helena-rasche/). [jTHrXHol](https://trello.com/c/jTHrXHol) # Upgrades diff --git a/content/blog/2015-07-mysql-2-postgresql/index.md b/content/blog/2015-07-mysql-2-postgresql/index.md index f481d29426..c7aaafbe28 100644 --- a/content/blog/2015-07-mysql-2-postgresql/index.md +++ b/content/blog/2015-07-mysql-2-postgresql/index.md @@ -203,4 +203,4 @@ I first tested the transition process with our development server. Although, we As the final step, I had to change the database setting in the "galaxy.ini" (well, "universe_wsgi.ini" for our old instance) and "reports_wsgi.ini" files, and restart the server. -I am sure there are better and easier ways to do this, but the process worked for me. Feel free to contact [me](/src/people/hansrudolf-hotz/index.md), if you have any questions or want to do such a migration for your Galaxy server as well. +I am sure there are better and easier ways to do this, but the process worked for me. Feel free to contact [me](/people/hansrudolf-hotz/), if you have any questions or want to do such a migration for your Galaxy server as well. diff --git a/content/blog/2017-10-5000-pubs/index.md b/content/blog/2017-10-5000-pubs/index.md index 088fe9e5be..57082a985d 100644 --- a/content/blog/2017-10-5000-pubs/index.md +++ b/content/blog/2017-10-5000-pubs/index.md @@ -441,7 +441,7 @@ If [current trends continue](#publications-per-year) we'll hit 10,000 publicatio *Thanks for using Galaxy,* -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) ---- diff --git a/content/blog/2017-10-a-blog-is-born/index.md b/content/blog/2017-10-a-blog-is-born/index.md index d251f11e2a..ad09400e10 100644 --- a/content/blog/2017-10-a-blog-is-born/index.md +++ b/content/blog/2017-10-a-blog-is-born/index.md @@ -10,7 +10,7 @@ Today we launch the new *[Galactic Blog](/src/blog/index.md)*. The *Galactic Blog* is a place for longer-form posts that are relevant to Galaxy. (See [Galaxy News](/src/news/index.md) for shorter-form items.) -**Our very first post is about the [ELIXIR Galaxy Community](/src/blog/2017-10-05-elixir-galaxy-community/index.md) and was written by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/src/people/bjoern-gruening/index.md).** +**Our very first post is about the [ELIXIR Galaxy Community](/src/blog/2017-10-05-elixir-galaxy-community/index.md) and was written by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/people/bjoern-gruening/).** The *Galactic Blog* replaces the former *Community Log* and includes all content from it, which is why, even though the blog is new, it includes entries back to 2013. diff --git a/content/blog/2018-11-cotm-saskia-hiltemann/index.md b/content/blog/2018-11-cotm-saskia-hiltemann/index.md index f65a1ebf0c..520a77a2d4 100644 --- a/content/blog/2018-11-cotm-saskia-hiltemann/index.md +++ b/content/blog/2018-11-cotm-saskia-hiltemann/index.md @@ -48,7 +48,7 @@ My (biologist) supervisor always likes to describe his ideal view of bioinformat Thanks for the fun question :) CTF stands for "Capture The Flag" and these are online hacking events that usually last anywhere from a day to a couple of weeks, and basically consist of a series of computer security challenges or puzzles in which your goal is to obtain a specific hidden string of text. This could be a web service that has been intentionally left vulnerable to SQL injections, or an executable that can be manipulated into unintended behaviour, or it might involve the breaking of insecure encryption schemes. Very often they will include real-world scenarios based on recently discovered vulnerabilities. It is a great way to learn about a broad set of computer science and security topics, but also to learn about the potential vulnerabilities in any tools and program you will write in your professional life. I usually participate in these events together with Helena Rasche, but anybody is welcome to join our team! (no experience needed, there are always challenges of varying difficulty levels) :) -Inspired by these CTF competitions, [Helena](/src/people/helena-rasche) and I also created a [Galaxy CTF event at GCC2017](https://sched.co/BCVY), which was great fun to create and hopefully also a fun way to learn more about Galaxy features and internals for the people who participated, and we hope to organize another Galaxy CTF at [GCC2019](/src/events/gcc2019/index.md), so come check it out! +Inspired by these CTF competitions, [Helena](/people/helena-rasche) and I also created a [Galaxy CTF event at GCC2017](https://sched.co/BCVY), which was great fun to create and hopefully also a fun way to learn more about Galaxy features and internals for the people who participated, and we hope to organize another Galaxy CTF at [GCC2019](/src/events/gcc2019/), so come check it out! Thanks for the interview! diff --git a/content/blog/2019-07-galaxy-twitter/index.md b/content/blog/2019-07-galaxy-twitter/index.md index df17279721..4f784a039b 100644 --- a/content/blog/2019-07-galaxy-twitter/index.md +++ b/content/blog/2019-07-galaxy-twitter/index.md @@ -106,4 +106,4 @@ We recommend [TweetDeck](https://tweetdeck.twitter.com/) for using Twitter. Twe See you on Twitter, -[Dave Clements](/src/people/dave-clements/index.md), [Martin Cech](/src/people/marten/index.md), [Mo Heydarian](/src/people/mo-heydarian/index.md), [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) and Nicola Soranzo +[Dave Clements](/people/dave-clements/index.md), [Martin Cech](/people/marten/index.md), [Mo Heydarian](/src/people/mo-heydarian/), [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) and Nicola Soranzo diff --git a/content/blog/2019-07-looking-for-galaxy/index.md b/content/blog/2019-07-looking-for-galaxy/index.md index e9b56e9d2b..7aaf893a72 100644 --- a/content/blog/2019-07-looking-for-galaxy/index.md +++ b/content/blog/2019-07-looking-for-galaxy/index.md @@ -36,7 +36,7 @@ The search further classifies results by where they are found and what they are The **Galaxy Publication Search** tab searches the [Galaxy Publication Library](https://www.zotero.org/groups/1732893/galaxy) using Zotero's built in search. It will show you publications relevant to your search. (It's not integrated into the Google search because Google doesn't want to search collections of material available elsewhere on the web.) Happy searching,
-[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) * Or the *infinitely* more interesting [*Galaxie 500*](https://en.wikipedia.org/wiki/Ford_Galaxie) (which was also my very first car). diff --git a/content/blog/2020-08-10k-pubs/index.md b/content/blog/2020-08-10k-pubs/index.md index c1adef5a5a..1523555516 100644 --- a/content/blog/2020-08-10k-pubs/index.md +++ b/content/blog/2020-08-10k-pubs/index.md @@ -641,7 +641,7 @@ Galaxy has had an interesting journey over the past 15 years, and the Galaxy Pub *Thanks for using Galaxy (and for saying that you are using Galaxy!),* -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) ---- diff --git a/content/citing-galaxy/index.md b/content/citing-galaxy/index.md index 7aed6ebea4..ce7d8edcdc 100644 --- a/content/citing-galaxy/index.md +++ b/content/citing-galaxy/index.md @@ -40,7 +40,7 @@ Some excellent examples (*emphasis added*): If you use, extend or reference Galaxy in your published work, please cite this publication: -* [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Vahid Jalili](/src/people/vahid-jalili/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Daniel Blankenberg](/src/people/dan/index.md). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 This and other references are also [available in GitHub](https://github.com/galaxyproject/galaxy/blob/dev/CITATION) as a [CITATION file](http://software-carpentry.org/blog/2013/09/introducing-citation-files.html). @@ -50,41 +50,41 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## Application Programming Interface (API) -* Clare Sloggett, Nuwan Goonasekera and [Enis Afgan](/src/people/enis-afgan/index.md). **[BioBlend: automating pipeline analyses within Galaxy and CloudMan](https://academic.oup.com/bioinformatics/article/29/13/1685/185761/BioBlend-automating-pipeline-analyses-within)**. *Bioinformatics* (2013) 29(13): 1685-1686 doi:10.1093/bioinformatics/btt199 +* Clare Sloggett, Nuwan Goonasekera and [Enis Afgan](/people/enis-afgan/). **[BioBlend: automating pipeline analyses within Galaxy and CloudMan](https://academic.oup.com/bioinformatics/article/29/13/1685/185761/BioBlend-automating-pipeline-analyses-within)**. *Bioinformatics* (2013) 29(13): 1685-1686 doi:10.1093/bioinformatics/btt199 ## Cloud -* [Enis Afgan](/src/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/index.md), Nuwan Goonasekera. +* [Enis Afgan](/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. **[CloudLaunch: Discover and deploy cloud applications](https://doi.org/10.1016/j.future.2018.04.037)**, *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 ## Data Managers -* [Daniel Blankenberg](/src/people/dan/index.md), James E. Johnson, The [Galaxy Team](/src/galaxy-team/index.md), [James Taylor](/src/people/james-taylor/index.md) and [Anton Nekrutenko](/src/people/anton/index.md). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 +* [Daniel Blankenberg](/people/dan/index.md), James E. Johnson, The [Galaxy Team](/src/galaxy-team/index.md), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 ## DataSource Tools -* [Daniel Blankenberg](/src/people/dan/index.md), [Nate Coraor](/src/people/nate/index.md), [Gregory Von Kuster](/src/people/greg_vonkuster/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and The [Galaxy Team](/src/galaxy-team/index.md). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. +* [Daniel Blankenberg](/people/dan/index.md), [Nate Coraor](/people/nate/index.md), [Gregory Von Kuster](/people/greg_vonkuster/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. ## External Display Applications -* [Daniel Blankenberg](/src/people/dan/index.md), [John Chilton](/src/people/john-chilton/index.md), and [Nate Coraor](/src/people/nate/index.md). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +* [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x ## Interactive Environments -* [Björn Grüning](/src/people/bjoern-gruening/index.md), [Helena Rasche](/src/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/src/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/src/people/john-chilton/index.md), [Nate Coraor](/src/people/nate/index.md), Rolf Backofen, [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 +* [Björn Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 ## Reproducibility -* [Björn Grüning](/src/people/bjoern-gruening/index.md), [John Chilton](/src/people/john-chilton/index.md), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/people/james-taylor/index.md). +* [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/people/john-chilton/index.md), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). **[Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014)**, *Cell Systems*, Volume 6, Issue 6, 2018, Pages 631-635, ISSN 2405-4712, doi:10.1016/j.cels.2018.03.014. ## ToolShed -* [Daniel Blankenberg](/src/people/dan/index.md), [Gregory Von Kuster](/src/people/greg_vonkuster/index.md), [Emil Bouvier](/src/people/dave-bouvier/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Enis Afgan](/src/people/enis-afgan/index.md), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/index.md), [James Taylor](/src/people/james-taylor/index.md) and [Anton Nekrutenko](/src/people/anton/index.md). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 +* [Daniel Blankenberg](/people/dan/index.md), [Gregory Von Kuster](/people/greg_vonkuster/index.md), [Emil Bouvier](/people/dave-bouvier/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 ## Training & Education -* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/src/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/index.md), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/index.md), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 ### Online Education diff --git a/content/cloudman/openstack/index.md b/content/cloudman/openstack/index.md index 8899769e89..ba5ebf3042 100644 --- a/content/cloudman/openstack/index.md +++ b/content/cloudman/openstack/index.md @@ -2,4 +2,4 @@ Details on running [CloudMan](/src/cloudman/index.md) on OpenStack-based cloud infrastructures. This is an active area of development for the [CloudMan Team](/src/cloudman/team/index.md). -[John Chilton](/src/people/john-chilton/index.md) has made available [a set of scripts and config files](https://github.com/jmchilton/cloudman_openstack_bootstrap) he uses to setup customized CloudMan instances on OpenStack. They do not represent a turn-key solution and would require significant modification, but it is a potential place to start looking for ideas on this topic. +[John Chilton](/people/john-chilton/) has made available [a set of scripts and config files](https://github.com/jmchilton/cloudman_openstack_bootstrap) he uses to setup customized CloudMan instances on OpenStack. They do not represent a turn-key solution and would require significant modification, but it is a potential place to start looking for ideas on this topic. diff --git a/content/cloudman/team/index.md b/content/cloudman/team/index.md index 8dc8636dfb..f51cc0f02c 100644 --- a/content/cloudman/team/index.md +++ b/content/cloudman/team/index.md @@ -6,9 +6,9 @@ - - + + - +

Enis Afgan
RBI
Dannon Baker
Johns Hopkins
Enis Afgan
RBI
Dannon Baker
Johns Hopkins
Tomislav Lipic
RBI
James Taylor
Johns Hopkins
James Taylor
Johns Hopkins
diff --git a/content/community/galaxy-admins/future/index.md b/content/community/galaxy-admins/future/index.md index a7a31181b2..ef0a02d8ec 100644 --- a/content/community/galaxy-admins/future/index.md +++ b/content/community/galaxy-admins/future/index.md @@ -56,7 +56,7 @@ The GalaxyAdmins group has been hiatus for a while. Though, the discussion about ## Leadership -When Srinivas took over for Ann in fall 2012, he agreed to be the *interim* leader of the group. Beginning 2015, [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) took over the leadership. +When Srinivas took over for Ann in fall 2012, he agreed to be the *interim* leader of the group. Beginning 2015, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) took over the leadership. ### Leadership Model diff --git a/content/community/galaxy-admins/meetups/2013-01-16/index.md b/content/community/galaxy-admins/meetups/2013-01-16/index.md index 0324619692..931e845d6d 100644 --- a/content/community/galaxy-admins/meetups/2013-01-16/index.md +++ b/content/community/galaxy-admins/meetups/2013-01-16/index.md @@ -6,7 +6,7 @@ The January 2013 [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) was held Wednesday, January 16, 2013 at 10am US central time. [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." -[Greg Von Kuster](/src/people/greg_vonkuster/index.md) also gave a Galaxy Project update. +[Greg Von Kuster](/people/greg_vonkuster/) also gave a Galaxy Project update. @@ -23,7 +23,7 @@ The January 2013 [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013 - + diff --git a/content/community/galaxy-admins/meetups/2013-03-20/index.md b/content/community/galaxy-admins/meetups/2013-03-20/index.md index 59fb485fe2..0afb413ec4 100644 --- a/content/community/galaxy-admins/meetups/2013-03-20/index.md +++ b/content/community/galaxy-admins/meetups/2013-03-20/index.md @@ -17,7 +17,7 @@ - + diff --git a/content/community/galaxy-admins/meetups/2013-05-15/index.md b/content/community/galaxy-admins/meetups/2013-05-15/index.md index 0c4d7182f3..a716a96276 100644 --- a/content/community/galaxy-admins/meetups/2013-05-15/index.md +++ b/content/community/galaxy-admins/meetups/2013-05-15/index.md @@ -19,7 +19,7 @@ - + @@ -34,7 +34,7 @@ Andrew Warren of the [Cyberinfrastructure Division](http://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division) of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech talked about their experience deploying Galaxy for [Pathogen Portal](http://pathogenportal.org), a highly customized Galaxy installation, and also about the group's objectives and future plans. -[Dannon Baker](/src/people/dannon-baker/index.md) brought the group up to speed on what's happening in the Galaxy project. +[Dannon Baker](/people/dannon-baker/) brought the group up to speed on what's happening in the Galaxy project.

diff --git a/content/community/galaxy-admins/meetups/2013-11-20/index.md b/content/community/galaxy-admins/meetups/2013-11-20/index.md index 7c37368cb3..a96933dd43 100644 --- a/content/community/galaxy-admins/meetups/2013-11-20/index.md +++ b/content/community/galaxy-admins/meetups/2013-11-20/index.md @@ -19,7 +19,7 @@ - + @@ -31,7 +31,7 @@
Dave and Srinivas will lead a discussion following up on the issues that were raised at the [GCC2013 GalaxyAdmins Birds-of-a-Feather session](/src/events/gcc2013/bof/galaxy-admins/index.md). -[Nate Coraor](/src/people/nate/index.md) will also discuss the recent move of [usegalaxy.org](http://usegalaxy.org) from Penn State to TACC. +[Nate Coraor](/people/nate/) will also discuss the recent move of [usegalaxy.org](http://usegalaxy.org) from Penn State to TACC. ## GCC2013 Followup diff --git a/content/community/galaxy-admins/meetups/2015-02-19/index.md b/content/community/galaxy-admins/meetups/2015-02-19/index.md index 62bace1aa9..70facd57f1 100644 --- a/content/community/galaxy-admins/meetups/2015-02-19/index.md +++ b/content/community/galaxy-admins/meetups/2015-02-19/index.md @@ -20,7 +20,7 @@ - + @@ -33,7 +33,7 @@ # GalaxyAdmins is Back! -Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Thanks to the efforts of [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) *is back.* Starting in February 2015, we will resume our bi-monthly web meetups. +Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Thanks to the efforts of [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/) *is back.* Starting in February 2015, we will resume our bi-monthly web meetups. *[GalaxyAdmins](/src/community/galaxy-admins/index.md)* is a discussion group for Galaxy community members who are responsible for Galaxy installations. @@ -43,7 +43,7 @@ The lead presentation will summarize the [Galaxy Community Questionnaires](/src/ ## Galaxy Project Update: Gravity -[Nate Coraor](/src/people/nate/index.md) will also introduce *[Gravity](https://github.com/galaxyproject/gravity/blob/master/README.rst)*: +[Nate Coraor](/people/nate/) will also introduce *[Gravity](https://github.com/galaxyproject/gravity/blob/master/README.rst)*:
diff --git a/content/community/galaxy-admins/meetups/2015-04-16/index.md b/content/community/galaxy-admins/meetups/2015-04-16/index.md index 6c9aa72ebe..680a9d292f 100644 --- a/content/community/galaxy-admins/meetups/2015-04-16/index.md +++ b/content/community/galaxy-admins/meetups/2015-04-16/index.md @@ -20,7 +20,7 @@
- + @@ -41,7 +41,7 @@ ## Galaxy Project Update: Galaxy's new tool form support -[Sam Guerler](/src/people/guerler/index.md) of the [Galaxy Team](/src/galaxy-team/index.md) will discuss recent work to update Galaxy's tool forms. +[Sam Guerler](/people/guerler/index.md) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work to update Galaxy's tool forms. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/2015-06-18/index.md b/content/community/galaxy-admins/meetups/2015-06-18/index.md index 1041047eba..abdadf4264 100644 --- a/content/community/galaxy-admins/meetups/2015-06-18/index.md +++ b/content/community/galaxy-admins/meetups/2015-06-18/index.md @@ -20,7 +20,7 @@ - + @@ -44,7 +44,7 @@ deploying Galaxy and developing tools within the [Bioinformatics Core Facility](
[[Planemo
-[John Chilton](/src/people/john-chilton/index.md) will also give an update on recent and upcoming work on [Planemo](https://github.com/galaxyproject/planemo), a set of command-line utilities to assist in building and publishing Galaxy tools. +[John Chilton](/people/john-chilton/) will also give an update on recent and upcoming work on [Planemo](https://github.com/galaxyproject/planemo), a set of command-line utilities to assist in building and publishing Galaxy tools. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/2015-08-20/index.md b/content/community/galaxy-admins/meetups/2015-08-20/index.md index 4fa89ec6b5..fc265aa8d4 100644 --- a/content/community/galaxy-admins/meetups/2015-08-20/index.md +++ b/content/community/galaxy-admins/meetups/2015-08-20/index.md @@ -20,7 +20,7 @@ - + @@ -45,7 +45,7 @@ ## Adding transparency and automation into the Galaxy tool installation process -[Enis Afgan](/src/people/enis-afgan/index.md) of the [Galaxy Team](/src/galaxy-team/index.md) will discuss recent work on *[Adding transparency and automation into the Galaxy tool installation process](https://github.com/afgane/ansible-tools)* via Ansible. The talk will discuss process of unifying the tool installation approach within the Galaxy project and how it can be used by anyone to to install potentially hundreds of tools in an automated fashion. +[Enis Afgan](/people/enis-afgan/index.md) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work on *[Adding transparency and automation into the Galaxy tool installation process](https://github.com/afgane/ansible-tools)* via Ansible. The talk will discuss process of unifying the tool installation approach within the Galaxy project and how it can be used by anyone to to install potentially hundreds of tools in an automated fashion. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/2016-02-18/index.md b/content/community/galaxy-admins/meetups/2016-02-18/index.md index 607ef42523..8ac0d11867 100644 --- a/content/community/galaxy-admins/meetups/2016-02-18/index.md +++ b/content/community/galaxy-admins/meetups/2016-02-18/index.md @@ -18,7 +18,7 @@ - + diff --git a/content/community/galaxy-admins/meetups/2016-04-21/index.md b/content/community/galaxy-admins/meetups/2016-04-21/index.md index 8706c3b824..5b3bcfc368 100644 --- a/content/community/galaxy-admins/meetups/2016-04-21/index.md +++ b/content/community/galaxy-admins/meetups/2016-04-21/index.md @@ -19,7 +19,7 @@ - + @@ -42,7 +42,7 @@ The app has been in development for over a year at the University of Oslo as part of [Claus Børnich's masters thesis](https://www.duo.uio.no/handle/10852/44701) and is described in - Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/src/people/marten/index.md), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 + Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/people/marten/), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 A [user manual](https://github.com/Tarostar/QMLGalaxyPortal/raw/master/GalaxyPortalUserGuide.pdf), additional information, and the full source are [available on GitHub](https://github.com/Tarostar/QMLGalaxyPortal). @@ -51,7 +51,7 @@ Galaxy Portal is provided free of charge. ## Tool Development Developments -[Galaxy Team](/src/galaxy-team/index.md) member [John Chilton](/src/people/john-chilton/index.md) will discuss recent tool development developments including Conda, tool version profiles, and Planemo enhancements. +[Galaxy Team](/src/galaxy-team/index.md) member [John Chilton](/people/john-chilton/) will discuss recent tool development developments including Conda, tool version profiles, and Planemo enhancements. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/2016-06-16/index.md b/content/community/galaxy-admins/meetups/2016-06-16/index.md index d004954b6b..09b1a35619 100644 --- a/content/community/galaxy-admins/meetups/2016-06-16/index.md +++ b/content/community/galaxy-admins/meetups/2016-06-16/index.md @@ -18,7 +18,7 @@ - + diff --git a/content/community/galaxy-admins/meetups/2016-12-15/index.md b/content/community/galaxy-admins/meetups/2016-12-15/index.md index 260437e27b..ccd2c96700 100644 --- a/content/community/galaxy-admins/meetups/2016-12-15/index.md +++ b/content/community/galaxy-admins/meetups/2016-12-15/index.md @@ -11,8 +11,8 @@ tease: 'GalaxyAdmins December 2016 Meetup' | ---- | ---- | | **Date** | 15 December 2016 | | **Time** | [5 pm Central European Time](http://bit.ly/2h2QOsT). See [your local time](http://bit.ly/2h2QOsT) | -| **Topic 1** | *Galaxy Training Materials: Community creation, curation, and use*, [Björn Grüning](/src/people/bjoern-gruening/index.md) and Bérénice Batut, University of Freiburg | -| **Topic 2** | *The new Galaxy Hub: Community creation, curation, and use*, [Dannon Baker](/src/people/dannon-baker/index.md), Johns Hopkins University | +| **Topic 1** | *Galaxy Training Materials: Community creation, curation, and use*, [Björn Grüning](/people/bjoern-gruening/) and Bérénice Batut, University of Freiburg | +| **Topic 2** | *The new Galaxy Hub: Community creation, curation, and use*, [Dannon Baker](/people/dannon-baker/), Johns Hopkins University | | **Links** | [Video](https://connect.johnshopkins.edu/p7ek9bf4ez0/) | *[GalaxyAdmins](/src/community/galaxy-admins/index.md)* is a discussion group for Galaxy community members who are responsible for Galaxy installations. diff --git a/content/community/galaxy-admins/meetups/2017-02-16/index.md b/content/community/galaxy-admins/meetups/2017-02-16/index.md index 6744bfa570..a0f7db2d89 100644 --- a/content/community/galaxy-admins/meetups/2017-02-16/index.md +++ b/content/community/galaxy-admins/meetups/2017-02-16/index.md @@ -12,7 +12,7 @@ tease: 'GalaxyAdmins February 2017 Meetup' | **Date** | 16 February 2017 | | **Time** | [9:30 pm India Standard Time](http://bit.ly/2kPgfSF). See [your local time](http://bit.ly/2kPgfSF) | | **Topic** | *CloudLaunch* | -| **Presenters** | Nuwan Goonesekera and [Enis Afgan](/src/people/enis-afgan/index.md) | +| **Presenters** | Nuwan Goonesekera and [Enis Afgan](/people/enis-afgan/) | | **Links** | **[Video](https://connect.johnshopkins.edu/p8t92n1zw9q)** | *[GalaxyAdmins](/src/community/galaxy-admins/index.md)* is a discussion group for Galaxy community members who are responsible for Galaxy installations. diff --git a/content/community/galaxy-admins/meetups/index.md b/content/community/galaxy-admins/meetups/index.md index 875989fbca..34abee0a13 100644 --- a/content/community/galaxy-admins/meetups/index.md +++ b/content/community/galaxy-admins/meetups/index.md @@ -19,7 +19,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m **2017** * [2017-02-16 Web Meetup](/src/community/galaxy-admins/meetups/2017-02-16/index.md) - * Nuwan Goonesekera and [Enis Afgan](/src/people/enis-afgan/index.md) talk about the [new CloudLaunch](https://beta.launch.usegalaxy.org). + * Nuwan Goonesekera and [Enis Afgan](/people/enis-afgan/) talk about the [new CloudLaunch](https://beta.launch.usegalaxy.org). **2016** @@ -32,7 +32,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * [2016-06-16 Web Meetup](/src/community/galaxy-admins/meetups/2016-06-16/index.md) * [Evan Bollig](https://www.msi.umn.edu/staff/evan) and [JJ Johnson](https://www.msi.umn.edu/staff/jj) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) will present *Galaxy in Production at the University of Minnesota*. * [2016-04-21 Web Meetup](/src/community/galaxy-admins/meetups/2016-04-21/index.md) - * [Ivar Grytten](http://www.mn.uio.no/ifi/english/people/aca/ivargry/) and [Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/) of the [University of Oslo](http://www.uio.no/) discussed [The Galaxy Portal: Accessing Galaxy from Mobile Devices](http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinformatics.btw042.full) and [John Chilton](/src/people/john-chilton/index.md) presented [Tool Development Developments](http://planemo.readthedocs.org/en/latest/galaxy_changelog.html). + * [Ivar Grytten](http://www.mn.uio.no/ifi/english/people/aca/ivargry/) and [Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/) of the [University of Oslo](http://www.uio.no/) discussed [The Galaxy Portal: Accessing Galaxy from Mobile Devices](http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinformatics.btw042.full) and [John Chilton](/people/john-chilton/) presented [Tool Development Developments](http://planemo.readthedocs.org/en/latest/galaxy_changelog.html). * [2016-02-18 Web Meetup](/src/community/galaxy-admins/meetups/2016-02-18/index.md) * Marius van den Beek will talk about *Ansible*, and Nate Coraor about *Python Wheels in Galaxy* @@ -46,7 +46,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * [2015-06-18 Web Meetup](/src/community/galaxy-admins/meetups/2015-06-18/index.md) * Peter Briggs will talk about *Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester* * [2015-04-16 Web Meetup](/src/community/galaxy-admins/meetups/2015-04-16/index.md) - * Carrie Ganote talks about Galaxy tweaks and customizations at Indiana University, and [Aysam Guerler](/src/people/guerler/index.md) talks about new tool forms. + * Carrie Ganote talks about Galaxy tweaks and customizations at Indiana University, and [Aysam Guerler](/people/guerler/) talks about new tool forms. * [2015-02-19 Web Meetup](/src/community/galaxy-admins/meetups/2015-02-19/index.md) * Fall 2014 Galaxy Questionnaires Summary, Galaxy Project Update, GalaxyAdmins direction @@ -62,11 +62,11 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * 2013/06/30-2013/07/02: [Future of GalaxyAdmins BoF](/src/events/gcc2013/bof/galaxy-admins/index.md) at [GCC2013](/src/events/gcc2013/index.md) * Meet in person at [GCC2013](/src/events/gcc2013/index.md) to discuss [the future of GalaxyAdmins](/src/community/galaxy-admins/future/index.md). * [2013-05-15 Web Meetup](/src/community/galaxy-admins/meetups/2013-05-15/index.md) - * Andrew Warren of the [Cyberinfrastructure Division](http://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division) of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech talked about their [Galaxy deployment](http://rnaseq.pathogenportal.org/) at [Pathogen Portal](http://pathogenportal.org), a highly customized Galaxy installation, and also about the group's objectives and future plans. [DannonBaker](/src/people/dannon-baker/index.md) did the Galaxy Project update on this call. + * Andrew Warren of the [Cyberinfrastructure Division](http://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division) of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech talked about their [Galaxy deployment](http://rnaseq.pathogenportal.org/) at [Pathogen Portal](http://pathogenportal.org), a highly customized Galaxy installation, and also about the group's objectives and future plans. [DannonBaker](/people/dannon-baker/) did the Galaxy Project update on this call. * [2013-03-20 Web Meetup](/src/community/galaxy-admins/meetups/2013-03-20/index.md) - * [Hailiang Leon Mei](mailto:hailiang DOT mei AT nbic DOT nl) discuss NBIC's recent experiences deploying the [NBIC Galaxy](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/). [Dan Blankenberg](/src/people/dan/index.md) discusses the new release policy and upcoming *Data Manager* features. + * [Hailiang Leon Mei](mailto:hailiang DOT mei AT nbic DOT nl) discuss NBIC's recent experiences deploying the [NBIC Galaxy](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/). [Dan Blankenberg](/people/dan/) discusses the new release policy and upcoming *Data Manager* features. * [2013-01-16 Web Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) - * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/src/people/greg_vonkuster/index.md) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/index.md) + * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/people/greg_vonkuster/index.md) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/) **2012** diff --git a/content/develop/gsoc/2015-ideas/index.md b/content/develop/gsoc/2015-ideas/index.md index 1a4a1b26f7..0f1a9be8c6 100644 --- a/content/develop/gsoc/2015-ideas/index.md +++ b/content/develop/gsoc/2015-ideas/index.md @@ -32,7 +32,7 @@ Galaxy supports running jobs in Docker containers for running jobs on a single n **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy and/or Kubernetes, bioinformatics knowledge -**Possible Mentors** Kyle Ellrott, [John Chilton](/src/people/john-chilton/index.md), [Dannon Baker](/src/people/dannon-baker/index.md) +**Possible Mentors** Kyle Ellrott, [John Chilton](/people/john-chilton/index.md), [Dannon Baker](/src/people/dannon-baker/) ## GA4GH Container and Workflows Integration @@ -53,7 +53,7 @@ The [Global Alliance for Genomics Health](http://genomicsandhealth.org/) (GA4GH) **Potentially Helpful Skills** Familiarity with Galaxy and/or other Workflow Management Systems -**Possible Mentors** [John Chilton](/src/people/john-chilton/index.md), [Daniel Blankenberg](/src/people/dan/index.md) +**Possible Mentors** [John Chilton](/people/john-chilton/index.md), [Daniel Blankenberg](/src/people/dan/) ## Docker Swarm and Compose @@ -75,7 +75,7 @@ By making complex applications easier to deploy and doing so reproducibly, the o **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy, Docker, and/or Fig, bioinformatics knowledge -**Possible Mentors** [John Chilton](/src/people/john-chilton/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Dannon Baker](/src/people/dannon-baker/index.md) +**Possible Mentors** [John Chilton](/people/john-chilton/index.md), [Björn Grüning](/people/bjoern-gruening/), [Dannon Baker](/src/people/dannon-baker/) ## Fostering Bioconductor Collaborations @@ -92,7 +92,7 @@ The [RGalaxy](http://www.bioconductor.org/packages/release/bioc/html/RGalaxy.htm * Implement automated scripts (for use with cron jobs or CI tools such as Jenkins or Buildbot) to automate the release and publication of such artifacts. * Build and publish workflows demonstrating these tools with actual data. -**Possible Mentors** [Nitesh Turaga](/src/people/nitesh-turaga/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), Daniel Blankenberg +**Possible Mentors** [Nitesh Turaga](/people/nitesh-turaga/index.md), [Björn Grüning](/src/people/bjoern-gruening/), Daniel Blankenberg **Required Skills** Python programming @@ -134,7 +134,7 @@ Implement Galaxy [data providers](/src/data-providers/index.md) and [visualizati * Allow visualization from additional programs (e.g. ProtK). * Allow visualization of additional input types (e.g. MGF, mztab). -**Possible Mentors** [Ira Cooke](https://github.com/iracooke), [John Chilton](/src/people/john-chilton/index.md) +**Possible Mentors** [Ira Cooke](https://github.com/iracooke), [John Chilton](/people/john-chilton/) **Required Skills** Python and JavaScript programming @@ -157,7 +157,7 @@ The Galaxy proteomics community maintains Galaxy tools for [building PeptideShak * Create a generic framework for quickly building out Galaxy IEs for Desktop applications. * Enable two way communication between PeptideShaker and Galaxy - by allowing exporting files from PeptideShaker directly back into Galaxy. -**Possible Mentors** [Marc Vaudel](http://compomics.com/people/marc-vaudel/), [Björn Grüning](/src/people/bjoern-gruening/index.md) +**Possible Mentors** [Marc Vaudel](http://compomics.com/people/marc-vaudel/), [Björn Grüning](/people/bjoern-gruening/) **Required Skills** Java programming @@ -180,7 +180,7 @@ The Galaxy application implements the notion of an Object Store - a pluggable fi **Potentially Helpful Skills** Familiarity with Galaxy and/or object store APIs, familiarity with cloud computing concepts -**Possible Mentors** [Enis Afgan](/src/people/enis-afgan/index.md) +**Possible Mentors** [Enis Afgan](/people/enis-afgan/) ## Integrate bcbio-nextgen Pipelines into Galaxy @@ -200,7 +200,7 @@ For smaller jobs - it should be possible to build traditional Galaxy tools to ru * Develop a generic framework for translating bcbio-nextgen pipelines into Galaxy and Common Workflow Language tools to ease future integration efforts. * Extend Galaxy's job running mechanism to allow it to collect provenance information from bcbio-nextgen about intermediate files and analysis steps, modify the bcbio-nextgen tools to produce this metadata. -**Possible Mentors** [Rory Kirchner](https://github.com/roryk), [Brad Chapman](https://github.com/chapmanb), [John Chilton](/src/people/john-chilton/index.md) +**Possible Mentors** [Rory Kirchner](https://github.com/roryk), [Brad Chapman](https://github.com/chapmanb), [John Chilton](/people/john-chilton/) **Required Skills** Python programming, Highly motivate and independent problem solver @@ -244,7 +244,7 @@ Once familiar with pages - there are at least two paths this project could diver **Potentially Helpful Skills** Familiarity with Galaxy and IPython -**Possible Mentors** [Carl Eberhard](/src/people/carl-eberhard/index.md), [Martin Cech](/src/people/marten/index.md) +**Possible Mentors** [Carl Eberhard](/people/carl-eberhard/index.md), [Martin Cech](/src/people/marten/) ## Easier or More Robust History Imports and Exports @@ -266,7 +266,7 @@ that can be pasted into an import the history from another Galaxy instance. * Split this process in pieces to allow tracking/resuming the transfers. * Rework the API and UI to provide pleasant progress bar tracking progress and estimating time remaining. -**Possible Mentors** [Martin Cech](/src/people/marten/index.md), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/src/people/dan/index.md) +**Possible Mentors** [Martin Cech](/people/marten/index.md), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/src/people/dan/) **Required Skills** Python programming @@ -303,7 +303,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Convert Galaxy to run on Python 3. * Once all dependencies are upgraded, package Galaxy for [Debian Med](https://www.debian.org/devel/debian-med/). -**Possible Mentors** [Nate Coraor](/src/people/nate/index.md), [Tim Booth](https://github.com/tbooth), [John Chilton](/src/people/john-chilton/index.md) +**Possible Mentors** [Nate Coraor](/people/nate/index.md), [Tim Booth](https://github.com/tbooth), [John Chilton](/src/people/john-chilton/) **Required Skills:** * Knowledge of DPKG, BASH scripting, Makefiles, and the layout of files on a standard Linux filesystem (/etc, /var, /usr, ...) @@ -326,7 +326,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Integrate the authentication mechanism with [Globus Nexus](https://www.globus.org/platform/services). -**Possible Mentors** [Martin Cech](/src/people/marten/index.md), [Enis Afgan](/src/people/enis-afgan/index.md), [Nitesh Turaga](/src/people/nitesh-turaga/index.md) +**Possible Mentors** [Martin Cech](/people/marten/index.md), [Enis Afgan](/people/enis-afgan/), [Nitesh Turaga](/src/people/nitesh-turaga/) **Required Skills** Python Programming @@ -352,7 +352,7 @@ This approach could also be used with reference genomes, and published histories * Extend this ability to include reference genomes, published histories, workflows, pages, and visualizations * Improve Galaxy's tool-search for single-instance use-case as well, using the API and lunr (as an example approach) -**Possible Mentors** [Martin Cech](/src/people/marten/index.md), Dannon Baker, Daniel Blankenberg +**Possible Mentors** [Martin Cech](/people/marten/), Dannon Baker, Daniel Blankenberg **Required Skills** Python programming @@ -371,7 +371,7 @@ Recently Interactive Environments (IEs) were developed for Galaxy. These consist * Unit test framework for IEs to ensure the proxy works ([some progress](https://github.com/hexylena/vagrant-galaxy-casperjs) exists but it's not very generic). -**Possible Mentors** [Helena Rasche](/src/people/helena-rasche/index.md), [John Chilton](/src/people/john-chilton/index.md) +**Possible Mentors** [Helena Rasche](/people/helena-rasche/index.md), [John Chilton](/src/people/john-chilton/) **Required Skills** Docker, NodeJS diff --git a/content/develop/resources-tools/index.md b/content/develop/resources-tools/index.md index d4a52481d6..19057f0b21 100644 --- a/content/develop/resources-tools/index.md +++ b/content/develop/resources-tools/index.md @@ -20,6 +20,6 @@ * Popular tool repositories on [github](https://github.com/) to contribute to and serve as best practice examples: * [tools-iuc](https://github.com/galaxyproject/tools-iuc) - A collection of tools developed and maintained by the the Intergalactic Utilities Commission (the IUC). ([Contributing to tools-iuc](https://github.com/galaxyproject/tools-devteam/blob/master/CONTRIBUTING.md)) * [tools-devteam](https://github.com/galaxyproject/tools-devteam) - A collection of tools developed and maintained by the 'devteam'. ([Contributing to tools-devteam](https://github.com/galaxyproject/tools-devteam/blob/master/CONTRIBUTING.md)) - * [Bjoern's Galaxy Tools](https://github.com/bgruening/galaxytools) - A collection of tools developed and maintained by [BjoernGruening](/src/people/bjoern-gruening/index.md). ([Contributing to galaxytools](https://github.com/bgruening/galaxytools/blob/master/CONTRIBUTING.md)) + * [Bjoern's Galaxy Tools](https://github.com/bgruening/galaxytools) - A collection of tools developed and maintained by [BjoernGruening](/people/bjoern-gruening/). ([Contributing to galaxytools](https://github.com/bgruening/galaxytools/blob/master/CONTRIBUTING.md)) * [galaxy_blast](https://github.com/peterjc/galaxy_blast) - A best practice set of tools wrapping NCBI BLAST+ and related applications maintained by Peter Cock. ([Contributing to the BLAST+ tools](https://github.com/peterjc/galaxy_blast/blob/master/CONTRIBUTING.md)) * [GalaxyP Tools](https://github.com/galaxyproteomics/tools-galaxyp) - A collection of tools for proteomics maintained by the GalaxyP team. diff --git a/content/events/2017-09-bgu/index.md b/content/events/2017-09-bgu/index.md index 70c1cbae8f..7c3f511101 100644 --- a/content/events/2017-09-bgu/index.md +++ b/content/events/2017-09-bgu/index.md @@ -18,7 +18,7 @@ September 7th **GALAXY – a tool for analyzing NGS data: introduction** -[Anton Nekrutenko](/src/people/anton/index.md), PhD (Penn State University) +[Anton Nekrutenko](/people/anton/), PhD (Penn State University) The workshop will take place in Building 38, computer room, ground floor (unless indicated differently) diff --git a/content/events/2017-genome-informatics/index.md b/content/events/2017-genome-informatics/index.md index 955e95bcbc..180931ca07 100644 --- a/content/events/2017-genome-informatics/index.md +++ b/content/events/2017-genome-informatics/index.md @@ -16,9 +16,9 @@ Galaxy will be featured in talks and posters at the [2017 Genome Informatics](ht | Day | Time | Topic | Presenter | | ---- | :----: | ---- | ---- | -| Thursday Nov 2 | 1:30pm | P29: Choosing the best of all worlds—à la carte access to extant and emergent best-practice metagenomic pipelines | [Dan Blankenberg](/src/people/dan/index.md) | +| Thursday Nov 2 | 1:30pm | P29: Choosing the best of all worlds—à la carte access to extant and emergent best-practice metagenomic pipelines | [Dan Blankenberg](/people/dan/) | | | 1:30pm | P46: GDCWebApp—Filtering, extracting, and converting genomic and clinical data from the Genomic Data Commons Portal | Fabio Cumbo | | | 1:30pm | P48: Streamlining the installation of thousands of bioinformatics software packages with Bioconda | Ryan Dale | -| | 1:30pm | P90: Hybrid assembly of small genomes in Galaxy | [Dephine Laviviere](/src/people/delphine-lariviere/index.md) | -| | 9:00pm | Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter | [Anton Nekrutenko](/src/people/anton/index.md) | -| Friday Nov 3 | 5:30pm | P192: Quality assessment and large-scale integration of chromosome conformation capture datasets | [James Taylor](/src/people/james-taylor/index.md) | +| | 1:30pm | P90: Hybrid assembly of small genomes in Galaxy | [Dephine Laviviere](/people/delphine-lariviere/) | +| | 9:00pm | Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter | [Anton Nekrutenko](/people/anton/) | +| Friday Nov 3 | 5:30pm | P192: Quality assessment and large-scale integration of chromosome conformation capture datasets | [James Taylor](/people/james-taylor/) | diff --git a/content/events/2017-ismb-bosc/index.md b/content/events/2017-ismb-bosc/index.md index 178cc66316..d45d08482c 100644 --- a/content/events/2017-ismb-bosc/index.md +++ b/content/events/2017-ismb-bosc/index.md @@ -19,7 +19,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | -| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Bjorn Gruning](/src/people/bjoern-gruening/index.md) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | +| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | ## 22 July, Saturday @@ -27,9 +27,9 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | | 12:08 | Discovery and visualisation of homologous genes and gene families using Galaxy | Anil S. Thanki | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1189), [Video](https://youtu.be/xE8uIXE05I4) | -| 15:00 | The backbone of research reproducibility: sustainable and flexible tool deployment | [Bjorn Gruning](/src/people/bjoern-gruening/index.md) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1203), [Video](https://youtu.be/zTne29-GU_E) | -| 15:28 | A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms | [John Chilton](/src/people/john-chilton/index.md) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](http://jmchilton.github.io/writing/bosc2017slides/biocontainers.html#1), [Video](https://youtu.be/OqzS4I-HSzs) | -| 16:30 | [TT03: Supporting highly scalable scientific data analysis with Galaxy](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/technologytrack.php) | [James Taylor](/src/people/james-taylor/index.md) | Terrace 1 | [Slides](https://speakerdeck.com/jxtx/ismb-2017-supporting-highly-scalable-scientific-data-analysis-with-galaxy) | +| 15:00 | The backbone of research reproducibility: sustainable and flexible tool deployment | [Bjorn Gruning](/people/bjoern-gruening/) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1203), [Video](https://youtu.be/zTne29-GU_E) | +| 15:28 | A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms | [John Chilton](/people/john-chilton/) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](http://jmchilton.github.io/writing/bosc2017slides/biocontainers.html#1), [Video](https://youtu.be/OqzS4I-HSzs) | +| 16:30 | [TT03: Supporting highly scalable scientific data analysis with Galaxy](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/technologytrack.php) | [James Taylor](/people/james-taylor/) | Terrace 1 | [Slides](https://speakerdeck.com/jxtx/ismb-2017-supporting-highly-scalable-scientific-data-analysis-with-galaxy) | | 18:00 | [A-113: SIAMCAT - Statistical Inference of Associations between Microbial Communities And host phenoTypes](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B#A-113) | Konrad Zych | BOSC, Congress Foyer, Level 2 | | | 18:00 | [A-149: Discovery and visualisation of homologous genes and gene families using Galaxy](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B#A-149) | Anil Thanki | BOSC, Congress Foyer, Level 2 | [Poster](https://doi.org/10.7490/f1000research.1114431.1) | | 18:00 | [A-161: EDAM - The ontology of bioinformatics operations, types of data, topics, and data formats (2017 update)](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B#A-161) | Hervé Ménager | BOSC, Congress Foyer, Level 2 | [Poster](https://f1000research.com/posters/6-1181) @@ -41,7 +41,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | | 11:04 | Building an open, collaborative, online infrastructure for bioinformatics training | Bérénice Batut | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://bebatut-slides.github.io/bosc_07_17/#/1), [Video](https://youtu.be/ZL7xTqCaRsI) | -| 11:30 | Recent object formation in the core of Galaxy | [Martin Čech](/src/people/marten/index.md) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1207), [Video](https://youtu.be/_EWWMAW0x1s) | +| 11:30 | Recent object formation in the core of Galaxy | [Martin Čech](/people/marten/) | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1207), [Video](https://youtu.be/_EWWMAW0x1s) | | 11:45 | ToolDog - generating tool descriptors from the ELIXIR tool registry | Kenzo-Hugo Hillion | Meeting Hall IV, [BOSC](https://www.open-bio.org/w/index.php?title=BOSC_2017_Schedule) | [Slides](https://f1000research.com/slides/6-1194), [Video](https://youtu.be/_CXeyTsBfWg) | | 18:00 | [A-166: Scaling Bioinformatics Training: An ELIXIR, GOBLET & Galaxy Training Network Collaboration](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=F#A-166) | Bérénice Batut | Congress Foyer, Level 2 | [Poster](https://f1000research.com/posters/6-1218) | | 18:00 | [A-170: ELIXIR-SI eLearning platform as a new tool in bioinformatics (teaching)](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=F#A-170) | Andrej Kastrin | Congress Foyer, Level 2 | | @@ -51,16 +51,16 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | -| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Bjorn Gruning](/src/people/bjoern-gruening/index.md), [James Taylor](/src/people/james-taylor/index.md) | Meeting Hall V | | +| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Bjorn Gruning](/src/people/bjoern-gruening/), [James Taylor](/src/people/james-taylor/) | Meeting Hall V | | | 18:00 | [B-079: Development of a bioinformatics pipeline for the routine analysis of viral whole genome sequencing data](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=H#B-079) | Qiang Fu | Congress Foyer, Level 2 | [Poster]( https://depot.galaxyproject.org/hub/attachments/documents/posters/2017_ismb_viral_wgs_fu.pdf) | | 18:00 | [B-365: Comparison of open source (galaxy based) and commercial pipelines for RNA-Seq data analysis](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=P#B-365) | Slave Trajanoski | Congress Foyer, Level 2 | [Poster](https://depot.galaxyproject.org/hub/attachments/documents/posters/ismb2017-trajanoski.pdf) | -| 20:00 | [Galaxy Community Dinner](http://bit.ly/gxyismb2017bdinner) | [Martin Čech](/src/people/marten/index.md) | [VYŠEHRADSKÝ RESTAURANT KANDELÁBR](http://bit.ly/gxyismb2017bdinner) | | +| 20:00 | [Galaxy Community Dinner](http://bit.ly/gxyismb2017bdinner) | [Martin Čech](/people/marten/) | [VYŠEHRADSKÝ RESTAURANT KANDELÁBR](http://bit.ly/gxyismb2017bdinner) | | ## 25 July, Tuesday | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | -| 10:20 | [TT24: Galaxy Interactive Environments: Combining the computational power of Galaxy with the analytical flexibility of Jupyter](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/technologytrack.php) | [Anton Nekrutenko](/src/people/anton/index.md) | Terrace 1 | [Slides (as video)](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2017-ismb-adhoc-analytics-nekrutenko.mp4) | +| 10:20 | [TT24: Galaxy Interactive Environments: Combining the computational power of Galaxy with the analytical flexibility of Jupyter](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/technologytrack.php) | [Anton Nekrutenko](/people/anton/) | Terrace 1 | [Slides (as video)](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2017-ismb-adhoc-analytics-nekrutenko.mp4) | | 13:00 | [B-018: MINTIA : Metagenomic INsertT Bioinformatic Annotation in Galaxy](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=H#B-018) | Christophe Klopp | Congress Foyer, Level 2 | | diff --git a/content/events/2017-sacnas/index.md b/content/events/2017-sacnas/index.md index e648476177..c4ab76e5ce 100644 --- a/content/events/2017-sacnas/index.md +++ b/content/events/2017-sacnas/index.md @@ -105,7 +105,7 @@ Want to do data analysis and don’t know where to start? [CyVerse](http://www. - [Amanda Cooksey](http://www.cyverse.org/amanda-cooksey), CyVerse and the University of Arizona - [Joslynn Lee](https://www.hhmi.org/developing-scientists/meet-our-team), Howard Hughes Medical Institute and University of Maryland Baltimore County, joslynnlee@gmail.com -- [Dave Clements](/src/people/dave-clements/index.md), Galaxy Project and Johns Hopkins University, clements@galaxyproject.org +- [Dave Clements](/people/dave-clements/), Galaxy Project and Johns Hopkins University, clements@galaxyproject.org ## Session 1 : CyVerse diff --git a/content/events/2018-01-csusm-workshop/index.md b/content/events/2018-01-csusm-workshop/index.md index 6b1845dfde..b11021c955 100644 --- a/content/events/2018-01-csusm-workshop/index.md +++ b/content/events/2018-01-csusm-workshop/index.md @@ -49,4 +49,4 @@ This workshop is generously supported by the [College of Science & Mathematics ( ## Questions -Contact [Arun Sethuraman](http://www.csusm.edu/biology/directory.html#asethuraman) or [Dave Clements](/src/people/dave-clements/index.md). +Contact [Arun Sethuraman](http://www.csusm.edu/biology/directory.html#asethuraman) or [Dave Clements](/people/dave-clements/). diff --git a/content/events/2018-csh-bds/index.md b/content/events/2018-csh-bds/index.md index c91ecc9d6e..ffb66f8e6f 100644 --- a/content/events/2018-csh-bds/index.md +++ b/content/events/2018-csh-bds/index.md @@ -15,9 +15,9 @@ Galaxy will be featured several presentations at the [Cold Spring Harbor 2018 Bi | Date | Time | Topic | Contact | | ---- | :----: | ---- | ---- | ---- | ---- | -| **November 8** | 4:00 PM | P25: Scaling scalable infrastructure to analysis tools | [Daniel J Blankenberg](/src/people/dan/index.md) | +| **November 8** | 4:00 PM | P25: Scaling scalable infrastructure to analysis tools | [Daniel J Blankenberg](/people/dan/) | | **November 8** | 4:00 PM | P29: JBrowse Connect—Launch analysis tasks from the browser | [Scott Cain](http://gmod.org/wiki/User:Scott) | -| **November 8** | 4:00 PM | P34: Accessible and scalable machine learning for biomedical data analysis | [Jeremy Goecks](/src/people/jeremy-goecks/index.md) | -| **November 8** | 4:00 PM | P57: Galaxy at scale—Automated analysis of thousands of single cell transcriptomes | [Mo Heydarian](/src/people/mo-heydarian/index.md) | -| **November 8** | 4:00 PM | P75: Bacterial genomic at large scale with Galaxy - a Tn-SEQ example | [Delphine Lariviere](/src/people/delphine-lariviere/index.md) | -| **November 8** | 7:30 PM | Can UI handle 10x datasets where X > 3? Yes, it can! | [Anton Nekrutenko](/src/people/anton/index.md) | +| **November 8** | 4:00 PM | P34: Accessible and scalable machine learning for biomedical data analysis | [Jeremy Goecks](/people/jeremy-goecks/) | +| **November 8** | 4:00 PM | P57: Galaxy at scale—Automated analysis of thousands of single cell transcriptomes | [Mo Heydarian](/people/mo-heydarian/) | +| **November 8** | 4:00 PM | P75: Bacterial genomic at large scale with Galaxy - a Tn-SEQ example | [Delphine Lariviere](/people/delphine-lariviere/) | +| **November 8** | 7:30 PM | Can UI handle 10x datasets where X > 3? Yes, it can! | [Anton Nekrutenko](/people/anton/) | diff --git a/content/events/2018-europe-dev/index.md b/content/events/2018-europe-dev/index.md index 26e3063fa4..5331a928f2 100644 --- a/content/events/2018-europe-dev/index.md +++ b/content/events/2018-europe-dev/index.md @@ -39,8 +39,8 @@ We will meet at 19 in Bertholdsbrunnen | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:45 - 10:00 | ARRIVAL | | | -| 10:00 - 10:20 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | Welcome and short introduction into the Galaxy Project | [slides](https://depot.galaxyproject.org/hub/attachments/events/2018-europe-dev/EGD_SG2018T_intro_Monday.pdf) | -| 10:20 - 10:50 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | [State of the Galaxy Project - priorities, plans, and community (from a European perspective)](https://docs.google.com/presentation/d/1cqFtHus4TIFsD56tBSGvgdICx56AVnzwTWuJI1z4rE4/edit?usp=sharing) | [slides](https://docs.google.com/presentation/d/1cqFtHus4TIFsD56tBSGvgdICx56AVnzwTWuJI1z4rE4/edit?usp=sharing) | +| 10:00 - 10:20 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Welcome and short introduction into the Galaxy Project | [slides](https://depot.galaxyproject.org/hub/attachments/events/2018-europe-dev/EGD_SG2018T_intro_Monday.pdf) | +| 10:20 - 10:50 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | [State of the Galaxy Project - priorities, plans, and community (from a European perspective)](https://docs.google.com/presentation/d/1cqFtHus4TIFsD56tBSGvgdICx56AVnzwTWuJI1z4rE4/edit?usp=sharing) | [slides](https://docs.google.com/presentation/d/1cqFtHus4TIFsD56tBSGvgdICx56AVnzwTWuJI1z4rE4/edit?usp=sharing) | | 10:50 - 11:20 | Coffee Break | | | | 11:20 - 11:45 | Matthias Bernt ([UFZ](http://www.ufz.de/)) | *Establishing a Galaxy Server and building a Galaxy User Community from scratch. A field report from the UFZ Leipzig* | [slides](https://depot.galaxyproject.org/hub/attachments/events/2018-europe-dev/egd-bernt.pdf) | | 11:45 - 12:20 | Geoffrey Nelson ([Harvard Medical School](https://hms.harvard.edu/)) | *Refinery: a data management, analysis, and visualization platform using the Galaxy workbench* (plus Demo) | [slides](https://github.com/refinery-platform/refinery-platform/blob/gh-pages/presentations/EGD18.pdf) | @@ -52,7 +52,7 @@ We will meet at 19 in Bertholdsbrunnen | 15:40 - 16:05 | Krzysztof Poterlowicz ([University of Bradford](https://bradford.ac.uk/external/)) | [*EWAS tool development / Training / Elixir-CNV community*](https://galaxyproject.org/events/2018-europe-dev/abstracts/#krzysztof-poterlowicz) | [slides](https://github.com/kpoterlowicz/presentations/blob/master/EuropeanGalaxyDays18_Poterlowicz.pdf) | | 16:05 - 16:30 | Bérénice Batut ([University of Freiburg](http://www.uni-freiburg.de/)) | *RNA-Seq data analysis in Galaxy: lessons learned and what next?* | [slides](http://bebatut.fr/talks/18/11_19_egd/#/1) | | 16:30 - 16:55 | Mehmet Tekman ([University of Freiburg](http://www.uni-freiburg.de/)) | *Single Cell in Galaxy, from pre-processing to analysis* | [slides](https://docs.google.com/presentation/d/1uLub5IfCjhMr52R8spCRdkk4yAvKyx2M7z9JmLrqVwM/edit?usp=sharing) | -| 16:55 - 17:00 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md)| concluding remarks | | +| 16:55 - 17:00 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/)| concluding remarks | | | 17:00 | ...going to the pub | | | @@ -62,7 +62,7 @@ We will meet at 19 in Bertholdsbrunnen | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | -| 9:30 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | Welcome and organization for the day | | +| 9:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Welcome and organization for the day | | | 9:30 - 09:55 | Marius van den Beek ([Institut Curie](https://institut-curie.org/)), John Chilton ([Penn State](http://www.bx.psu.edu/)) | [*Travelling with warp-speed, an update on Galaxy workflows*](https://galaxyproject.org/events/2018-europe-dev/abstracts/#marius-van-den-beek-john-chilton) | [slides](https://docs.google.com/presentation/d/1iGCKLNI9gwfpNL__yADhK97ucLtZ1Cy62_EJGNPlKPI/edit#slide=id.p) | | 09:55 - 10:20 | Nicola Soranzo ([Earlham Institute](http://www.earlham.ac.uk/)) | *Beta Python 3 support for Galaxy in release 18.09, at last!* | [slides](https://docs.google.com/presentation/d/1txmwpDK3CG7eCsJXPOpHaNuGEzJ6-hBX6Iq-HJZb0pY/edit?usp=sharing) | | 10:20 - 10:45 | Musumba Awori ([Goethe University of Frankfurt](http://www.goethe-university-frankfurt.de)) | *Draft genome of a bacterium (Xenorhabdus griffiniae XN45) isolated from Kenyan Steinernema nematodes reveals its potential synthesis of a spectrum of specialised metabolites* | [slides](https://prezi.com/view/VrIGwwQPPEd6VtnN2qf4/) | @@ -75,7 +75,7 @@ We will meet at 19 in Bertholdsbrunnen | 13:45 - 14:10 | Nikolay Vazov ([UiO](https://www.usit.uio.no/)) | [*Two customizations in Galaxy*](https://galaxyproject.org/events/2018-europe-dev/abstracts/#nikolay-vazov) | [slides](https://drive.google.com/open?id=1Hdi9cV49FJ7eL4XrnJXs5kNIs68y4HJ3) | | 14:10 - 14:35 | Yvan Le Bras ([Muséum national d’histoire naturelle](https://www.mnhn.fr/)) | [*GalaxyE, a new vision of workflow oriented Biodiversity research?*](https://galaxyproject.org/events/2018-europe-dev/abstracts/#yvan-le-bras) | | | 14:35 - 15:00 | Anup Kumar ([University of Freiburg](http://www.uni-freiburg.de/)) | *Machine learning with Galaxy* | [slides](https://github.com/anuprulez/issues/raw/master/EuropeanGalaxyDays18_AnupKumar.pdf) | -| 15:00 - 15:10 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md)| end of official part | | +| 15:00 - 15:10 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/)| end of official part | | | 15:10 - 15:40 | Coffee Break | | | | 15:40 - .... | informal gathering for hacking, discussions, etc...and finally going to the pub again | | | | @@ -132,5 +132,5 @@ http://www.vag-freiburg.de/fahrplan-linien/netzplaene/liniennetzplan.html ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) (hrh@fmi.ch) or [Björn Grüning](/src/people/bjoern-gruening/index.md) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/src/people/jeanfrancois-dufayard/index.md) (jean-francois.dufayard@cirad.fr) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) (hrh@fmi.ch) or [Björn Grüning](/people/bjoern-gruening/) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/src/people/jeanfrancois-dufayard/) (jean-francois.dufayard@cirad.fr) diff --git a/content/events/2018-genome-informatics/index.md b/content/events/2018-genome-informatics/index.md index beac6b6322..872f14eff8 100644 --- a/content/events/2018-genome-informatics/index.md +++ b/content/events/2018-genome-informatics/index.md @@ -17,6 +17,6 @@ Galaxy will be featured at the [2018 Genome Informatics](https://coursesandconfe | Topic | Presenter | | ---- | ---- | | [P46: JBrowse Connect: Launch Analysis Tasks from the Browser](https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics-Aug-18-V4.pdf#page=162) | Ian Holmes | -| [P60: Transposon Insertion Sequencing (TnSeq) in Galaxy](https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics-Aug-18-V4.pdf#page=176) | [Delphine Larivière](/src/people/delphine-lariviere/index.md) | +| [P60: Transposon Insertion Sequencing (TnSeq) in Galaxy](https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics-Aug-18-V4.pdf#page=176) | [Delphine Larivière](/people/delphine-lariviere/) | | [P93: Genome analysis of Pantoea ananatis strain MHSD5 on web-based platform](https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics-Aug-18-V4.pdf#page=209) | Mahloro Hope Serepa-Dlamini | | [P100: Characterising and visualising gene families with GeneSeqToFamily and Aequatus](https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics-Aug-18-V4.pdf#page=216) | Anil S. Thanki | diff --git a/content/events/2018-pag/index.md b/content/events/2018-pag/index.md index 3c43f440b0..4e35e343ca 100644 --- a/content/events/2018-pag/index.md +++ b/content/events/2018-pag/index.md @@ -20,7 +20,7 @@ Galaxy was at [Plant and Animal Genome XXVI (PAG 2018)](http://www.intlpag.org/) | **Thursday, January 11** | All day | [Tripal Hackathon](https://docs.google.com/document/d/1klQwUqaT_KxPKIfGYy_3rtGnOMVhJxEoD9dZ4PGc4yg/edit) | Pre-conference | [Register](https://docs.google.com/document/d/1klQwUqaT_KxPKIfGYy_3rtGnOMVhJxEoD9dZ4PGc4yg/edit) | [Meg Staton](https://ag.tennessee.edu/EPP/Pages/Dr.MegStaton.aspx), [Ethy Cannon](mailto:ekcannon@iastate.edu) | | | All day | [GMOD 2018 PAG Hackathon](http://gmod.org/wiki/2018_PAG_Hackathon) | Pre-conference, Brittany Room | [Register](https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260) | [Scott Cain](http://gmod.org/wiki/User:Scott) | | **Friday, January 12** | All day | [Tripal User Meeting](https://docs.google.com/document/d/1klQwUqaT_KxPKIfGYy_3rtGnOMVhJxEoD9dZ4PGc4yg/edit) | Pre-conference | [Register](https://docs.google.com/document/d/1klQwUqaT_KxPKIfGYy_3rtGnOMVhJxEoD9dZ4PGc4yg/edit) | [Meg Staton](https://ag.tennessee.edu/EPP/Pages/Dr.MegStaton.aspx), [Ethy Cannon](mailto:ekcannon@iastate.edu) | -| | 9:00-5:00 | [Introduction to Galaxy Workshop](/src/events/2018-01-csusm-workshop/index.md) | Pre-conference workshop, [California State University San Marcos](https://www.csusm.edu/) | [Register](http://bit.ly/gxy-csusm-2018-reg)| [Dave Clements](/src/people/dave-clements/index.md), [Arun Sethuraman](http://www.csusm.edu/biology/directory.html#asethuraman) | +| | 9:00-5:00 | [Introduction to Galaxy Workshop](/src/events/2018-01-csusm-workshop/index.md) | Pre-conference workshop, [California State University San Marcos](https://www.csusm.edu/) | [Register](http://bit.ly/gxy-csusm-2018-reg)| [Dave Clements](/people/dave-clements/), [Arun Sethuraman](http://www.csusm.edu/biology/directory.html#asethuraman) | | **Saturday, January 13** | 10:40-10:57 | [MiCloud and BioDocklets: A Plug and Play, on-Premises Bioinformatics Cloud, Providing Seamless, Single-Step Execution of NGS Pipelines](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28434) | [Workshop: Interoperability and Federation Across Bioinformatic Platforms and Resources](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4820), California Room | [Paper](https://academic.oup.com/gigascience/article/6/8/1/3894236), [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-micloud-biodocklets-krampis.pdf) | Konstantinos Krampis | | | 11:10-11:30 | [James Hutton Institute Informatics Visualization Software](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/27875) | [Workshop: Connecting Crop Phenotype and Genotype Data](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4765), Golden Ballroom | | Iain Milne | | | 12:00-12:10 | [IRRI's Pipeline for Integrating Genotype and Phenotype Data for Enhanced Product Development](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28560) | [Workshop: Connecting Crop Phenotype and Genotype Data](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4765), Golden Ballroom | | Joshua Cobb | @@ -41,11 +41,11 @@ Galaxy was at [Plant and Animal Genome XXVI (PAG 2018)](http://www.intlpag.org/) | **Tuesday, January 16** | 11:00-11:15 | [C19: Efficiency, Design, and Analytical Improvements in Cartogratree, a Web-Framework for Association Mapping and Landscape Genomics in Forest Trees](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28855) | [Digital Tools and Resources Session 3](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/5104), California Room | | Taylor Falk | | | 12:00-12:15 | [C23: RepeatExplorer Galaxy Server for in-Depth Characterization of Repetitive Sequences in Next-Generation Sequencing Data](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/30509) | [Digital Tools and Resources Session 3](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/5104), California Room | | Petr Novak | | | 12:15-12:35 | [The GOBII Project: Transforming Breeding through Genomic Data Management and Decision Support](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28316) | [Workshop: Genomics-Assisted Breeding](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4805), Town and Country Room | | Elizabeth Jones | -| | 4:00-4:20 | [Galaxy: Introduction and ecosystem](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28292) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-galaxy-intro-eco.pdf) | [Dave Clements](/src/people/dave-clements/index.md) | -| | 4:20-5:30 | [Using Galaxy for Genome Annotation](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28294) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | [Slides](https://speakerdeck.com/jgoecks/pag-2018-galaxy-workshop-g-onramp) | [Jeremy Goecks](/src/people/jeremy-goecks/index.md) | +| | 4:00-4:20 | [Galaxy: Introduction and ecosystem](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28292) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-galaxy-intro-eco.pdf) | [Dave Clements](/people/dave-clements/) | +| | 4:20-5:30 | [Using Galaxy for Genome Annotation](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28294) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | [Slides](https://speakerdeck.com/jgoecks/pag-2018-galaxy-workshop-g-onramp) | [Jeremy Goecks](/people/jeremy-goecks/) | | | 5:30-5:50 | [South Green, a Hitchhiker’s Guide to Galaxy](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29236) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | [Slides](https://drive.google.com/file/d/13LUb-IKSsLjhYs2cRUIcSn8ILZHqbLkk/view) | [Marilyne Summo](https://scholar.google.fr/citations?user=4Pqy2aYAAAAJ&hl=fr) | | | 5:50-6:10 | [Building a Bridge from the Tripal Community Database to Galaxy](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28295) | [Workshop: Galaxy: An Open Platform for Data Analysis and Integration](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4796), California Room | | [Margaret Staton](http://gst.tennessee.edu/people/meg-staton/) | | **Wednesday, January 17** | 10:30-10:45 | [C25: PiRATE: A Pipeline to Retrieve and Annotate Transposable Elements of Non-Model Organisms](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29148) | [Digital Tools and Resources Session 4](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/5105), California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-jérémy-berthelier-PiRATE.pdf) | Jérémy Berthelier | -| | 11:05-11:25 | [Galaxy Community Update](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31525) | [Workshop: GMOD](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4806), Pacific Salon 4-5 | [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-gmod-galaxy-community-update.pdf) | [Dave Clements](/src/people/dave-clements/index.md) | +| | 11:05-11:25 | [Galaxy Community Update](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31525) | [Workshop: GMOD](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4806), Pacific Salon 4-5 | [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2018-pag-gmod-galaxy-community-update.pdf) | [Dave Clements](/people/dave-clements/) | | | 11:25-11:45 | [G-OnRamp: Collaborative Eukaryotic Genome Annotations with Galaxy and Apollo](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31526) | [Workshop: GMOD](https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4806), Pacific Salon 4-5 | [Slides](https://wustl.app.box.com/s/ubt03ku69suoe8reprcxf3qkeykhmntx) | Luke Sargent | diff --git a/content/events/2018-sacnas/index.md b/content/events/2018-sacnas/index.md index efb776b292..bc1ba90862 100644 --- a/content/events/2018-sacnas/index.md +++ b/content/events/2018-sacnas/index.md @@ -103,7 +103,7 @@ Want to do data analysis and don’t know where to start? [CyVerse](http://www. **Instructors** - [Blake Joyce](http://www.cyverse.org/blake-joyce), CyVerse and the University of Arizona -- [Dave Clements](/src/people/dave-clements/index.md), Galaxy Project and Johns Hopkins University, clements@galaxyproject.org +- [Dave Clements](/people/dave-clements/), Galaxy Project and Johns Hopkins University, clements@galaxyproject.org - [Joslynn Lee](https://www.hhmi.org/developing-scientists/meet-our-team), Howard Hughes Medical Institute and University of Maryland Baltimore County, joslynnlee@gmail.com ## Session 1 : CyVerse diff --git a/content/events/2019-04-bioit/index.md b/content/events/2019-04-bioit/index.md index bb4373ba2c..22914abd18 100644 --- a/content/events/2019-04-bioit/index.md +++ b/content/events/2019-04-bioit/index.md @@ -10,7 +10,7 @@ external_url: image: /src/events/2019-04-bioit/bioitworld19.png gtn: false contact: "Presenters" -contact_url: "/src/people/jeremy-goecks/index.md" +contact_url: "/people/jeremy-goecks/" tags: [ cofest ] --- @@ -21,5 +21,5 @@ Going to [BioIT World 2019](https://www.bio-itworldexpo.com/)? Galaxy is there | Mon 4/15 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 4:15 | Hackathon Report Outs: Integrating Globus into Galaxy to Enable FAIRifying Data | Track 6: FAIR Data | Globus Genomics | -| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/src/people/enis-afgan/index.md) & [Vahid Jalili](/src/people/vahid-jalili/index.md) | -| Thu 4/18 | 10:40 | [Longitudinal and Context Visualization for Precision Oncology](http://www.giiconference.com/chi653337/data-visualization.shtml) | Track 8: Data Visualization & Exploration Tools | [Jeremy Goecks](/src/people/jeremy-goecks/index.md) | +| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/people/enis-afgan/index.md) & [Vahid Jalili](/src/people/vahid-jalili/) | +| Thu 4/18 | 10:40 | [Longitudinal and Context Visualization for Precision Oncology](http://www.giiconference.com/chi653337/data-visualization.shtml) | Track 8: Data Visualization & Exploration Tools | [Jeremy Goecks](/people/jeremy-goecks/) | diff --git a/content/events/2019-09-gateways/index.md b/content/events/2019-09-gateways/index.md index 0093b2b450..023d97083c 100644 --- a/content/events/2019-09-gateways/index.md +++ b/content/events/2019-09-gateways/index.md @@ -17,11 +17,11 @@ There are several Galaxy related presentations at [Gateways 2019](https://scienc | Date | When | Topic | Where | Presenter | | ---- | ----: | ---- | ---- | ---- | | Tues Sept 24 | 8:30 | [Workshop on Research Objects 2019 (RO2019)](https://researchobject.github.io/ro2019/) | Cockatoo Room ([Part of E-Science](https://sched.co/UuQL)) | Frederik Coppens | -| | 9:00 | [Keynote - Galaxy: from Genomic Science Gateway to Global Community](https://sched.co/RaHj) ([Slides](https://speakerdeck.com/jxtx/galaxy-dot-dot-dot-from-genomic-data-science-gateway-to-global-community), [Video](https://youtu.be/GBYhmq-CJuE)) | Kon Tiki Room | [James Taylor](/src/people/james-taylor/index.md) | -| | 4:15 | [Plenary Panel: Effective Checklists for Developers and Researchers to Gather Requirements for Science Gateways](https://sched.co/RaIM) ([Video](https://www.youtube.com/watch?v=iQHX_y7_Ghw)) | Kon Tiki Room | Sandra Gesing, Marlon Pierce, Maytal Dahan, Shawn Rice, Kyle Chard, Mark Miller, [Dave Clements](/src/people/dave-clements/index.md) | +| | 9:00 | [Keynote - Galaxy: from Genomic Science Gateway to Global Community](https://sched.co/RaHj) ([Slides](https://speakerdeck.com/jxtx/galaxy-dot-dot-dot-from-genomic-data-science-gateway-to-global-community), [Video](https://youtu.be/GBYhmq-CJuE)) | Kon Tiki Room | [James Taylor](/people/james-taylor/) | +| | 4:15 | [Plenary Panel: Effective Checklists for Developers and Researchers to Gather Requirements for Science Gateways](https://sched.co/RaIM) ([Video](https://www.youtube.com/watch?v=iQHX_y7_Ghw)) | Kon Tiki Room | Sandra Gesing, Marlon Pierce, Maytal Dahan, Shawn Rice, Kyle Chard, Mark Miller, [Dave Clements](/people/dave-clements/) | ## Find out more -Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/src/people/mo-heydarian/index.md) or [Dave Clements](/src/people/dave-clements/index.md). +Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/people/mo-heydarian/index.md) or [Dave Clements](/src/people/dave-clements/). diff --git a/content/events/2019-09-incob/index.md b/content/events/2019-09-incob/index.md index f48a2ed773..0e187a46f9 100644 --- a/content/events/2019-09-incob/index.md +++ b/content/events/2019-09-incob/index.md @@ -20,8 +20,8 @@ Galaxy, and especially the [Galaxy Australia community](https://www.embl-abr.org | ---- | ---: | --- | --- | | Tue | 2:00-2:15 | [Galaxy Australia - a truly national open-source bioinformatics platform](https://depot.galaxyproject.org/hub/attachments/events/2019-09-incob/galaxy-australia-open.pdf) | [Gareth Price](https://qfab.org/team-member/dr-gareth-price) | | | 3:00-3:15 | [EpiMOLAS: An Intuitive Web-based Framework for Genome-Wide DNA Methylation Analysis](https://www.slideshare.net/daniel0523/epimolas-an-intuitive-webbased-framework-for-genomewide-dna-methylation-analysis) | Sheng-Yao Su | -| Wed | 1:30-5:00 | [Workshop : An introduction to the Galaxy platform for computational biology – with real-world hands-on demonstration](http://bit.ly/galaxyincob19) | [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), [Dave Clements](/src/people/dave-clements/index.md) | -| Thu | 11:00-12:00 | [Building a regional Galaxy Community and Platform](#building-a-regional-galaxy-community-and-platform) | [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), [Dave Clements](/src/people/dave-clements/index.md) | +| Wed | 1:30-5:00 | [Workshop : An introduction to the Galaxy platform for computational biology – with real-world hands-on demonstration](http://bit.ly/galaxyincob19) | [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), [Dave Clements](/people/dave-clements/) | +| Thu | 11:00-12:00 | [Building a regional Galaxy Community and Platform](#building-a-regional-galaxy-community-and-platform) | [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), [Dave Clements](/people/dave-clements/) | ## Building a regional Galaxy Community and Platform @@ -33,7 +33,7 @@ Several regional communities and resources already exist in the Galaxy ecosystem This breakout features three short talks to introduce the Galaxy regional community landscape: -* [Global Galaxy communities and services](https://depot.galaxyproject.org/hub/attachments/events/2019-09-incob/global-galaxy-communities.pdf), [Dave Clements](/src/people/dave-clements/index.md), Galaxy Project, [Johns Hopkins University](https://jhu.edu/) +* [Global Galaxy communities and services](https://depot.galaxyproject.org/hub/attachments/events/2019-09-incob/global-galaxy-communities.pdf), [Dave Clements](/people/dave-clements/), Galaxy Project, [Johns Hopkins University](https://jhu.edu/) * [Galaxy Australia as a usegalaxy.* public service](https://depot.galaxyproject.org/hub/attachments/events/2019-09-incob/galaxy-australia-open.pdf), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), Galaxy Australia, [QFAB Bioinformatics](https://qfab.org/), Brisbane * [Future Galaxy developments for distributed data access](https://depot.galaxyproject.org/hub/attachments/events/2019-09-incob/future-galaxy-developments-for-distributed-data-access.pdf), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), Galaxy Australia, [University of Melbourne](https://www.unimelb.edu.au/) @@ -52,4 +52,4 @@ The session will conclude with a commitment to grow a community of interested pa Galaxy is a widely used and deployed open-source platform that integrates thousands of analysis tools, and supports data integration and analysis, workflow creation, data visualization, and sharing and publishing your analyses and pipelines. Galaxy is also *a global community* of researchers, programmers, trainers, and users all doing and supporting data intensive research. Interested? Then we hope to see you at INCOB.
-[Dave Clements](/src/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/index.md) +[Dave Clements](/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) diff --git a/content/events/2019-11-biohackathon-europe/index.md b/content/events/2019-11-biohackathon-europe/index.md index 22e690397a..764bdf2948 100644 --- a/content/events/2019-11-biohackathon-europe/index.md +++ b/content/events/2019-11-biohackathon-europe/index.md @@ -31,13 +31,13 @@ tags: [ cofest ] Galaxy will be featured at [BioHackathon-Europe 2019](https://www.biohackathon-europe.org/index.html) as a prominent part of many of [this year's selected projects](https://www.biohackathon-europe.org/projects): * **[Interoperable Workflows for Communities](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/1)** - * Organizers: Frederik Coppens, [Björn Grüning](/src/people/bjoern-gruening/index.md), Marek Suchánek, Rob Hooft + * Organizers: Frederik Coppens, [Björn Grüning](/people/bjoern-gruening/), Marek Suchánek, Rob Hooft * **[Improve the support of Common Workflow Language in Galaxy](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/3)** - * Organizers: Hervé Ménager, [John Chilton](/src/people/john-chilton/index.md), Michael Crusoe + * Organizers: Hervé Ménager, [John Chilton](/people/john-chilton/), Michael Crusoe * **[Towards seamless Galaxy and InterMine integration: Enhanced region analysis](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/7)** * Organizers: Yo Yehudi * **[Scalable delivery of FAIR training in Life Sciences using Galaxy and the Carpentries training material](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/8)** - * Organizers: [Helena Rasche](/src/people/helena-rasche/index.md), Saskia Hiltemann, Bérénice Batut + * Organizers: [Helena Rasche](/people/helena-rasche/), Saskia Hiltemann, Bérénice Batut * **[Development of a Pulsar toolkit](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/17)** * Organizers: Gianmauro Cuccuru, Marco Antonio Tangaro * **[Updating the Galaksio workflow management interface for Galaxy and migrating it to Vue.js](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/19)** @@ -45,7 +45,7 @@ Galaxy will be featured at [BioHackathon-Europe 2019](https://www.biohackathon-e * **[A graph database of Galaxy tool interoperability](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/30)** * Organizers: Wolfgang Maier, Jon Ison * **[Bioconda and Biocontainers helpdesk](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/31)** - * Organizers: [Björn Grüning](/src/people/bjoern-gruening/index.md), Devon Ryan + * Organizers: [Björn Grüning](/people/bjoern-gruening/), Devon Ryan Join us to learn from and work with experts of the Open Source Life Science community, and discuss the future of the [ELIXIR Galaxy community](https://elixir-europe.org/communities/galaxy) and enjoy the great food and venue. diff --git a/content/events/2019-admin-training/index.md b/content/events/2019-admin-training/index.md index bab27a1a95..d8205f8213 100644 --- a/content/events/2019-admin-training/index.md +++ b/content/events/2019-admin-training/index.md @@ -74,8 +74,8 @@ All participants should bring a wifi-enabled laptop with We currently have five confirmed (and highly experienced!) instructors: -* [Martin Čech](/src/people/marten/index.md), software engineer for the Galaxy Project and frequent sys admin for usegalaxy.org. -* [Nate Coraor](/src/people/nate/index.md), lead sysadmin of Galaxy Main (https://usegalaxy.org) and a software engineer for the Galaxy Project +* [Martin Čech](/people/marten/), software engineer for the Galaxy Project and frequent sys admin for usegalaxy.org. +* [Nate Coraor](/people/nate/), lead sysadmin of Galaxy Main (https://usegalaxy.org) and a software engineer for the Galaxy Project * [John Chilton](/src/people/john-chilton/), software engineer for the Galaxy Project working on both the front and back ends, with an emphasis on scalability. * [Simon Gladman](https://github.com/Slugger70), administrator of Galaxy Australia (https://usegalaxy.org.au), University of Melbourne * [Helena Rasche](https://github.com/hexylena), lead sysadmin of Galaxy Europe (https://usegalaxy.eu), software engineer and cloud administrator for University of Freiburg/de.NBI Project Freiburg branch diff --git a/content/events/2019-asmcue/index.md b/content/events/2019-asmcue/index.md index bb0507502a..cf4e5dec36 100644 --- a/content/events/2019-asmcue/index.md +++ b/content/events/2019-asmcue/index.md @@ -12,7 +12,7 @@ image: "/src/events/2019-asmcue/asmcue-2019.jpg" gtn: true --- -[Mo Heydarian](/src/people/mo-heydarian/index.md) of the Galaxy Project will present two sessions at the [2019 ASM Conference for Undergraduate Educators (ASMCUE)](https://www.asm.org/Events/ASM-Conference-for-Undergraduate-Educators/Home) +[Mo Heydarian](/people/mo-heydarian/) of the Galaxy Project will present two sessions at the [2019 ASM Conference for Undergraduate Educators (ASMCUE)](https://www.asm.org/Events/ASM-Conference-for-Undergraduate-Educators/Home) | Day | Time | Topic | Where | | ---- | ---- | ---- | ---- | diff --git a/content/events/2019-genome-informatics/index.md b/content/events/2019-genome-informatics/index.md index f7d5a718d7..a656385f94 100644 --- a/content/events/2019-genome-informatics/index.md +++ b/content/events/2019-genome-informatics/index.md @@ -16,6 +16,6 @@ Galaxy will be featured at the [2019 Genome Informatics](https://meetings.cshl.e | Day | Time | Topic | Presenter | | ---- | :----: | ---- | ---- | -| Thursday, November 7 | 2-3:30pm | P24: An integrative environment for microbiome analysis and visualization | [Dan Blankenberg](/src/people/dan/index.md) | -| | 2-3:30pm | P88: Devising best practices for the analysis of transposon insertion sequencing data | [Delphine Larivière](/src/people/delphine-lariviere/index.md) | -| | 4-5:30pm | P178: Inverting the model of genomic data sharing and analysis with the NHGRI Analysis, Visualization, and Informatics Lab-Space (AnVIL) | [James Taylor](/src/people/james-taylor/index.md) | +| Thursday, November 7 | 2-3:30pm | P24: An integrative environment for microbiome analysis and visualization | [Dan Blankenberg](/people/dan/) | +| | 2-3:30pm | P88: Devising best practices for the analysis of transposon insertion sequencing data | [Delphine Larivière](/people/delphine-lariviere/) | +| | 4-5:30pm | P178: Inverting the model of genomic data sharing and analysis with the NHGRI Analysis, Visualization, and Informatics Lab-Space (AnVIL) | [James Taylor](/people/james-taylor/) | diff --git a/content/events/2019-sacnas/index.md b/content/events/2019-sacnas/index.md index a6b53f74fb..f6e1e06727 100644 --- a/content/events/2019-sacnas/index.md +++ b/content/events/2019-sacnas/index.md @@ -56,8 +56,8 @@ The goals of this workshop are to ## Instructors -- [Dave Clements](/src/people/dave-clements/index.md), [Galaxy Project](/src/index.md) and [Johns Hopkins University](http://jhu.edu) -- [Mo Heydarian](/src/people/mo-heydarian/index.md), [Galaxy Project](/src/index.md) and [Johns Hopkins University](http://jhu.edu) +- [Dave Clements](/people/dave-clements/index.md), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) +- [Mo Heydarian](/people/mo-heydarian/index.md), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) ## Registration diff --git a/content/events/2020-03-admin/index.md b/content/events/2020-03-admin/index.md index d92e7c6e47..16399a3d07 100644 --- a/content/events/2020-03-admin/index.md +++ b/content/events/2020-03-admin/index.md @@ -81,7 +81,7 @@ Space is available on a first come, first served basis. Rates depend on your org We currently have these confirmed (and highly experienced!) instructors: -* [Nate Coraor](/src/people/nate/index.md), lead sysadmin of [usegalaxy.org](https://usegalaxy.org), a software engineer for the Galaxy Project, ... +* [Nate Coraor](/people/nate/), lead sysadmin of [usegalaxy.org](https://usegalaxy.org), a software engineer for the Galaxy Project, ... * [Saskia Hiltemann](https://github.com/shiltemann), administrator of [Galaxian](https://bioinf-galaxian.erasmusmc.nl/galaxy/) the Galaxy server hosted by Erasmus MC, longtime tool developer, co-founder of the Galaxy Training Network, ... * [Helena Rasche](https://github.com/hexylena), managed and setup much of the [Galaxy Europe](https://usegalaxy.eu) and [CPT Galaxy](https://cpt.tamu.edu/galaxy-pub/) infrastructure, ... * [Nicola Soranzo](https://www.earlham.ac.uk/nicola-soranzo), Galaxy Platform Development Officer at the [Earlham Institute](https://www.earlham.ac.uk/), Intergalactic Utilities Commission member, ... diff --git a/content/events/2020-abrf/index.md b/content/events/2020-abrf/index.md index a81161656d..a7b622867e 100644 --- a/content/events/2020-abrf/index.md +++ b/content/events/2020-abrf/index.md @@ -27,13 +27,13 @@ The day focuses on two topics: # SW4a: Single Cell RNA-Seq and Visualization Using the Galaxy Workbench (AM)
-[](https://www.researchgate.net/profile/Mehmet_Tekman)   [](/src/people/dave-clements/index.md) +[](https://www.researchgate.net/profile/Mehmet_Tekman)   [](/src/people/dave-clements/)
**Instructors:** * [Mehmet Tekman](https://www.researchgate.net/profile/Mehmet_Tekman), [University of Freiburg](https://www.uni-freiburg.de/?set_language=en) -* [Dave Clements](/src/people/dave-clements/index.md), [Johns Hopkins University](https://www.jhu.edu/) +* [Dave Clements](/people/dave-clements/), [Johns Hopkins University](https://www.jhu.edu/) Due to technological advances, single cell RNA-seq (scRNA-seq) analysis has emerged as the new frontier of biomedical research. As scRNA-seq technology evolves and generates increasingly complex data, the need for scalable, flexible, and accessible analysis options remains critical to researchers. The Galaxy workbench (galaxyproject.org) offers a solution. Galaxy has been used for genomic data analysis for over a decade and includes many tools required for scRNA-seq analysis – offering a multitude of analysis options. @@ -107,4 +107,4 @@ The [Association of Biomolecular Resource Facilities 2020 Conference (ABRF 2020) We hope to see you Palm Springs, -[Pratik](https://www.researchgate.net/profile/Pratik_Jagtap2), [Tim](https://cbs.umn.edu/contacts/timothy-j-griffin), [Saskia](https://www.researchgate.net/profile/Saskia_Hiltemann), [Subina](https://www.researchgate.net/profile/Subina_Mehta), [Mehmet](https://www.researchgate.net/profile/Mehmet_Tekman), and [Dave C](/src/people/dave-clements/index.md) +[Pratik](https://www.researchgate.net/profile/Pratik_Jagtap2), [Tim](https://cbs.umn.edu/contacts/timothy-j-griffin), [Saskia](https://www.researchgate.net/profile/Saskia_Hiltemann), [Subina](https://www.researchgate.net/profile/Subina_Mehta), [Mehmet](https://www.researchgate.net/profile/Mehmet_Tekman), and [Dave C](/people/dave-clements/) diff --git a/content/events/2020-pag/index.md b/content/events/2020-pag/index.md index b993477946..a77df0739a 100644 --- a/content/events/2020-pag/index.md +++ b/content/events/2020-pag/index.md @@ -17,22 +17,22 @@ In addition, there was be a [GMOD Codefest](http://gmod.org/wiki/Codefest_2020) | Date | Time | Topic | Session | Links | Contact | | ---- | :----: | ---- | ---- | ---- | ---- | -| **Thursday, January 9** | 9:00-5:00 | [GMOD Codefest 2020](http://gmod.org/wiki/Codefest_2020) | Pre-PAG | [Add your ideas](https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing) | [Scott Cain](http://gmod.org/wiki/User:Scott), [Dave Clements](/src/people/dave-clements/index.md) | -| **Friday, January 10** | 9:00-5:00 | [GMOD Codefest 2020](http://gmod.org/wiki/Codefest_2020) | Pre-PAG | [Add your ideas](https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing) | [Scott Cain](http://gmod.org/wiki/User:Scott), [Dave Clements](/src/people/dave-clements/index.md) | +| **Thursday, January 9** | 9:00-5:00 | [GMOD Codefest 2020](http://gmod.org/wiki/Codefest_2020) | Pre-PAG | [Add your ideas](https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing) | [Scott Cain](http://gmod.org/wiki/User:Scott), [Dave Clements](/people/dave-clements/) | +| **Friday, January 10** | 9:00-5:00 | [GMOD Codefest 2020](http://gmod.org/wiki/Codefest_2020) | Pre-PAG | [Add your ideas](https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing) | [Scott Cain](http://gmod.org/wiki/User:Scott), [Dave Clements](/people/dave-clements/) | | **Saturday, January 11** | 1:30-1:50 | [Quick and Easy Genome Annotation Editing with Apollo](https://plan.core-apps.com/pag_2020/abstract/a885a36a840d339cf200206aaf8055c9) | [Digital Tools and Resources Session 1](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb051890), California Room | [Slides](https://www.slideshare.net/nathandunneugene/digital-resources-quick-and-easy-genome-annotation-editing-with-apollo) | [Nathan Dunn](http://www.berkeleybop.org/people/nathan-dunn/) | | | 2:30-2:50 | [TreeGenes and CartograTree: Tools for Forest Tree Genomics](https://plan.core-apps.com/pag_2020/event/d60310dad9818605b937c0137958c9ce) | [Digital Tools and Resources Session 1](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb051890), California Room | | [Emily Grau](http://plantcompgenomics.com/people-emily-grau/) | -| | 4:20-4:40 | **[Galaxy As an Educational Tool and Community Resource for Undergraduate Training](https://plan.core-apps.com/pag_2020/event/60658e794c2a6d06f3aa20dcfb5fc100)** | [Teaching Genetics, Genomics, Biotechnology, and Bioinformatics](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb0303c8), Pacific Salon 6-7 (2nd Floor) | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-gtn-slides.pdf) | [Mo Heydarian](/src/people/mo-heydarian/index.md) | +| | 4:20-4:40 | **[Galaxy As an Educational Tool and Community Resource for Undergraduate Training](https://plan.core-apps.com/pag_2020/event/60658e794c2a6d06f3aa20dcfb5fc100)** | [Teaching Genetics, Genomics, Biotechnology, and Bioinformatics](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb0303c8), Pacific Salon 6-7 (2nd Floor) | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-gtn-slides.pdf) | [Mo Heydarian](/people/mo-heydarian/) | | **Sunday, January 12** | 8:30-8:50 | [Using Genome Browsers Constructed by G-OnRamp to Provide Students with a Course-Based Undergraduate Research Experience in Genome Annotation](https://plan.core-apps.com/pag_2020/event/60658e794c2a6d06f3aa20dcfb6074c8) | [Resources and Programs for Undergraduate Education in Genomics](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb03ffae), Terrace Room - Handlery Hotel | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-g-onramp-slides.pdf) | [Wilson Leung](https://biology.wustl.edu/people/wilson-leung) | | | 10:00-10:30| [Submission, Archival and Visualisation of Single-Cell Sequencing Data](https://plan.core-apps.com/pag_2020/abstract/9d8fed59-9c8d-4dfd-b39c-e0eb32cddc34) | [Genome annotation resources at the EBI](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb064c91), California Room | | [Nancy George](https://www.ebi.ac.uk/about/people/nancy-george) | | | 5:28-5:35 | **[Tapping into the Tripal Galaxy: Association Mapping Studies on Forest Trees with Cartogratree](https://plan.core-apps.com/pag_2020/event/d58894cb3c5f7a1019a50c969c5b7535)** | [Tripal Database Network and Initiatives](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb054ce2), California Room | | [Nic Herndon](https://myweb.ecu.edu/herndonn19/) | | **Monday, January 13** | 10:00-11:30 | [P138: The Genomics Education Partnership: Introducing Undergraduates to Research by Engaging Them in Genome Annotation](https://plan.core-apps.com/pag_2020/abstract/c36ea450c35dad0021dfc0a90dfda528) | Poster Session - Even numbers | | [Sarah Elgin](https://en.wikipedia.org/wiki/Sarah_Elgin) | -| | | **[P142: Galaxy: A Global Platform & Community for Life Science Data Integration & Analysis](https://plan.core-apps.com/pag_2020/abstract/d58894cb3c5f7a1019a50c969c59cd70)** | Poster Session - Even numbers | [Poster](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-galaxy-poster.pdf) | [Dave Clements](/src/people/dave-clements/index.md) | +| | | **[P142: Galaxy: A Global Platform & Community for Life Science Data Integration & Analysis](https://plan.core-apps.com/pag_2020/abstract/d58894cb3c5f7a1019a50c969c59cd70)** | Poster Session - Even numbers | [Poster](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-galaxy-poster.pdf) | [Dave Clements](/people/dave-clements/) | | | | [P616: TreeGenes and CartograTree: Tools for Forest Tree Genomics](https://plan.core-apps.com/pag_2020/abstract/0bc8b133f1593865d26b54a355e9327f) | Poster Session - Even numbers | | [Emily Grau](http://plantcompgenomics.com/people-emily-grau/) | | | 3:00-4:30 | [P137: Using Genome Browsers Constructed by G-OnRamp to Provide Students with a Course-Based Undergraduate Research Experience in Genome Annotation](https://plan.core-apps.com/pag_2020/abstract/c36ea450c35dad0021dfc0a90dfd70ac) | Poster Session - Odd numbers | [Poster](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-galaxy-poster.pdf) | [Wilson Leung](https://biology.wustl.edu/people/wilson-leung) | -| | | **[P141: The Galaxy Training Network: A Community Based Training Resource](https://plan.core-apps.com/pag_2020/abstract/d58894cb3c5f7a1019a50c969c59b001)** | Poster Session - Odd numbers | [Poster](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-gtn-poster.pdf) | [Mo Heydarian](/src/people/mo-heydarian/index.md) | +| | | **[P141: The Galaxy Training Network: A Community Based Training Resource](https://plan.core-apps.com/pag_2020/abstract/d58894cb3c5f7a1019a50c969c59b001)** | Poster Session - Odd numbers | [Poster](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-gtn-poster.pdf) | [Mo Heydarian](/people/mo-heydarian/) | | | | [P561: Submission, Archival and Visualisation of Single-Cell Sequencing Data](https://plan.core-apps.com/pag_2020/abstract/66342fa357793c308766316c381c3cc0) | Poster Session - Odd numbers | | [Nancy George](https://www.ebi.ac.uk/about/people/nancy-george) | | | 6:20-6:40 | [National Center for Genome Analysis Support (NCGAS): Genomics and other Science in the NSF-Funded Jetstream Cloud](https://plan.core-apps.com/pag_2020/event/113c3cf6f8416ef27402b60534ad197d) | [Cloud Computing for Genomics Data Analysis](https://plan.core-apps.com/pag_2020/event/91d41f080d91bca973636b572e642935), Pacific Salon 2 | | [Thomas G. Doak](https://ncgas.org/Tom-staff-page.php) | | | 7:13-7:25 | [Eukaryotic Pathogen, Vector & Host Informatics Resources (VEuPathDB) - a Merged International Approach Towards Achieving Sustainability](https://plan.core-apps.com/pag_2020/event/06b15a6d8bf3d42e3dbaf3d39ebad5d7) | [Data Resource Sustainability and Funding](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb048f4a), East 1 | | [Jessica Kissinger](http://mango.ctegd.uga.edu/jkissingLab/) | -| **Tuesday, January 14** | 4:00-4:20 | **[Introduction to Galaxy and the Galaxy Ecosystem](https://plan.core-apps.com/pag_2020/event/a8f1e9dbae7dc0d6d1e5f05d4657f89d)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-intro-slides.pdf) | [Dave Clements](/src/people/dave-clements/index.md) | +| **Tuesday, January 14** | 4:00-4:20 | **[Introduction to Galaxy and the Galaxy Ecosystem](https://plan.core-apps.com/pag_2020/event/a8f1e9dbae7dc0d6d1e5f05d4657f89d)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-intro-slides.pdf) | [Dave Clements](/people/dave-clements/) | | | 4:20-4:50 | **[Galaxy for Excellence in Breeding](https://plan.core-apps.com/pag_2020/event/0faacece23744ad32bb082ce6b8c5e27)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-eib-slides.pdf) | [Star Yanxin Gao](https://twitter.com/stargao3) | -| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/src/people/mo-heydarian/index.md), [Dave Clements](/src/people/dave-clements/index.md), Umesh Rosyara, Jose Crossa, Mathias Lorieux | +| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/people/mo-heydarian/index.md), [Dave Clements](/src/people/dave-clements/), Umesh Rosyara, Jose Crossa, Mathias Lorieux | diff --git a/content/events/admin-training2016/index.md b/content/events/admin-training2016/index.md index a504d601f9..f2a57c52e8 100644 --- a/content/events/admin-training2016/index.md +++ b/content/events/admin-training2016/index.md @@ -70,8 +70,8 @@ See the [Advanced Session](/src/events/admin-training2016/advanced-session/index # Instructors Instructors are from the [Galaxy Project Team](/src/galaxy-team/index.md) and the Galaxy Community: -* [Nate Coraor](/src/people/nate/index.md), lead sys admin and a software engineer for the Galaxy Project -* [Martin Čech](/src/people/marten/index.md), software engineer and frequent sys admin for the Galaxy Project. +* [Nate Coraor](/people/nate/), lead sys admin and a software engineer for the Galaxy Project +* [Martin Čech](/people/marten/), software engineer and frequent sys admin for the Galaxy Project. * [Simon Gladman](https://www.vlsci.org.au/researcher/sgladman), software engineer and bioinformatician with [VLSCI](https://www.vlsci.org.au/) and has done extensive work with the [Genomics Virtual Lab](https://www.genome.edu.au/). # Registration diff --git a/content/events/archive/wayback/index.md b/content/events/archive/wayback/index.md index e33c5aa948..2186052b03 100644 --- a/content/events/archive/wayback/index.md +++ b/content/events/archive/wayback/index.md @@ -76,7 +76,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -97,7 +97,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -157,7 +157,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -178,7 +178,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -227,7 +227,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -237,7 +237,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -258,21 +258,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + - + - + @@ -314,7 +314,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -418,7 +418,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -439,14 +439,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + - + @@ -456,28 +456,28 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + - + - + - + @@ -491,7 +491,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -526,7 +526,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -564,7 +564,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -613,7 +613,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -724,7 +724,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -745,7 +745,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -759,7 +759,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -773,7 +773,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -787,7 +787,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -851,7 +851,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -872,7 +872,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -904,7 +904,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -946,7 +946,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - +
Presenter John Chilton, Minnesota Supercomputing Institute
Greg Von Kuster, Penn State University 		John Chilton, Minnesota Supercomputing Institute
Greg Von Kuster, Penn State University
Links
Presentations NBIC Galaxy at SURFsara's HPC cloud
Hailiang Leon Mei
Slides
Galaxy Project Update
Dan Blankenberg
Slides
 NBIC Galaxy at SURFsara's HPC cloud
Hailiang Leon Mei
Slides
Galaxy Project Update
Dan Blankenberg
Slides
Links
Presentations Galaxy at Pathogen Portal
Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update
Dannon Baker
 Galaxy at Pathogen Portal
Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update
Dannon Baker
Links
Presentations GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
 GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
Links
Topics GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
 GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
Links
Topics IU Galaxies - tips and tricks (Slides)
Carrie Ganote, National Center for Genome Analysis Support (NCGAS), Pervasive Technology Institute, Indiana University
Galaxy Project Update: Galaxy's new tool form support (Slides)
Aysam Guerler, Galaxy, Johns Hopkins University
 IU Galaxies - tips and tricks (Slides)
Carrie Ganote, National Center for Genome Analysis Support (NCGAS), Pervasive Technology Institute, Indiana University
Galaxy Project Update: Galaxy's new tool form support (Slides)
Aysam Guerler, Galaxy, Johns Hopkins University
Links
Topics Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
Links
Topics Genomic data management at Canada's National Microbiology Laboratory with IRIDA and Galaxy
Aaron Petkau, Slides
Adding transparency and automation into the Galaxy tool installation process
Enis Afgan, Slides, GitHub Repo
Genomic data management at Canada's National Microbiology Laboratory with IRIDA and Galaxy
Aaron Petkau, Slides
Adding transparency and automation into the Galaxy tool installation process
Enis Afgan, Slides, GitHub Repo
Links
Topics Automating Galaxy deployment @ artbio.fr: the pros and cons of Ansible (Slides)
Marius van den Beek, Institute de Biologie Paris
The Wheels on the Galaxy go round and round: Python Wheels in Galaxy (Slides)
Nate Coraor, Penn State University
 Automating Galaxy deployment @ artbio.fr: the pros and cons of Ansible (Slides)
Marius van den Beek, Institute de Biologie Paris
The Wheels on the Galaxy go round and round: Python Wheels in Galaxy (Slides)
Nate Coraor, Penn State University
Links
Topics The Galaxy Portal: Accessing Galaxy from Mobile Devices (Slides)
Ivar Grytten and Geir Kjetil Sandve, University of Oslo
Tool Development Developments (PDF)
John Chilton, Penn State University
 The Galaxy Portal: Accessing Galaxy from Mobile Devices (Slides)
Ivar Grytten and Geir Kjetil Sandve, University of Oslo
Tool Development Developments (PDF)
John Chilton, Penn State University
Links
Topics Galaxy in Production at the University of Minnesota (Slides)
Evan Bollig and JJ Johnson of the Minnesota Supercomputing Institute
Galaxy Radio Telescope (Slides)
Helena Rasche
 Galaxy in Production at the University of Minnesota (Slides)
Evan Bollig and JJ Johnson of the Minnesota Supercomputing Institute
Galaxy Radio Telescope (Slides)
Helena Rasche
Links December 15-16 Metaproteomics CodeFest Online Online Pratik Jagtap, Björn Grüning Pratik Jagtap, Björn Grüning
December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online Dannon Baker, Dave Clements Dannon Baker, Dave Clements
November 8-20 Advanced Sequencing Technologies & Applications
Application deadline is July 15
 North America Cold Spring Harbor Laboratory, New York, United States
Training offered by GTN Member
Jeremy Goecks
Training offered by GTN Member
Jeremy Goecks
November 16 Introduction to Galaxy Workshop North America University of Utah, Salt Lake City, Utah, United States
Training offered by GTN Member
Dave Clements
Training offered by GTN Member
Dave Clements
November 2-3 Bioconda Contribution Fest Around the World Online Björn Grüning Björn Grüning
October 25-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy Dannon Baker, Björn Grüning Dannon Baker, Björn Grüning
October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening Hans-Rudolf Hotz and Bjoern Gruening
October 20 Genome Program Joint Workshop Asia Kunsan National University, Gunsan, South Korea Anton Nekrutenko Anton Nekrutenko
October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening Hans-Rudolf Hotz and Bjoern Gruening
October 6-7 Galaxy Training Contribution Fest Around the World Online Björn Grüning Björn Grüning
August 18 GalaxyAdmins Web Meetup Around the World Online Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements Slides
August 9-10 Introduction to Galaxy Workflows North America Workflows Workshop, Distributed
Training offered by GTN Member
Dave Clements
Training offered by GTN Member
Dave Clements 		Slides
August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop North America ICBO 2016, Corvallis, Oregon, United States
Training offered by GTN Member
Dave Clements
Training offered by GTN Member
Dave Clements 		Tutorial, Slides
July 21 Introduction to Galaxy North America Cornell University, Ithaca, New York, United States
Training offered by GTN Member
Dave Clements
Training offered by GTN Member
Dave Clements 		Slides
July 19-20 Introduction to Galaxy North America University of Rochester, Rochester, New York, United States
Training offered by GTN Member
Dave Clements
Training offered by GTN Member
Dave Clements 		Slides
July 19 Jetstream - performance, early experience, and early results North America XSEDE16, Miami, Florida, United States James Taylor James Taylor
July 19 CloudBridge: a Simple Cross-Cloud Python Library North America XSEDE16, Miami, Florida, United States Enis Afgan Enis Afgan
July 13-17 An Introduction to Using Galaxy for Genetic Data Analysis North America The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States Dave Clements Dave Clements Slides, Tutorial
July 3-7 Poster: Detection of ultra-rare mitochondrial variants Australia SMBE 2016, Gold Coast, Queensland, Australia Anton Nekrutenko Anton Nekrutenko
June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements Slides
June 6 Introduction to cloud computing (and its application in bioinformatics) Europe Zagreb, Croatia Enis Afgan Enis Afgan
April 28 Galaxy Workshop Tokyo 2016 Asia RCAST, The University of Tokyo, Japan Tazro Ohta, James Taylor Tazro Ohta, James Taylor Video (Japanese)
April 21 The Galaxy Portal: Accessing Galaxy from Mobile Devices and Tool Development Developments Around the World GalaxyAdmins Web Meetup, Online Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz
April 20 Galaxy Update North America BUG, Oregon State University, Corvallis, Oregon, United States Dave Clements Dave Clements
April 6-7 Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies Europe Galaxy DevOps Workshop 2016, Heidelberg, Germany
Training offered by GTN Member
Björn Grüning
Training offered by GTN Member
Björn Grüning
April 4 IUC Hackathon - Conda dependencies Around the World Online Björn Grüning, Rémi Marenco, Nitesh Turaga Björn Grüning, Rémi Marenco, Nitesh Turaga
February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States
Training offered by GTN Member
Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo
Training offered by GTN Member
Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo
February 18 GalaxyAdmins Web Meetup Around the World Online Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements
January 21, 22 Introduction to Galaxy Workshop North America Icahn School of Medicine at Mt. Sinai, New York, New York, United States
Training offered by GTN Member
Dave Clements, Andrew Sharp
Training offered by GTN Member
Dave Clements, Andrew Sharp 		Slides
January 8 Introduction to Galaxy Workshop North America Arizona State University, Tempe, Arizona, United States
Training offered by GTN Member
Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko
Training offered by GTN Member
Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko
@@ -1049,7 +1049,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online - IUC, John Chilton + IUC, John Chilton @@ -1100,7 +1100,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November 12-13 Engaging Biologists with Big Data Using Interactive Genome Annotation BD2K All-Hands Grantee Meeting, Bethesda, Maryland, United States - Jeremy Goecks + Jeremy Goecks Poster @@ -1126,12 +1126,12 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States -
Training offered by GTN Member
Dan Blankenberg, John Chilton +
Training offered by GTN Member
Dan Blankenberg, John Chilton Common Workflow Language on Galaxy
Part of Portable Bioinformatics Workshop
- John Chilton + John Chilton @@ -1143,7 +1143,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 28 - November 3 Computational & Comparative Genomics Course North America Cold Spring Harbor Laboratory, New York, United States -
Training offered by GTN Member
James Taylor +
Training offered by GTN Member
James Taylor @@ -1159,17 +1159,17 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Poster 55: From the ground to the cloud in just minutes—Building a customized Galaxy analysis server using only a web browser - Dan Blankenberg + Dan Blankenberg Poster 59: Galaxy Tool World Progression—Happier developers, happier users - Martin Cech + Martin Cech Poster Poster 63: Building more expressive Galaxy workflows - John Chilton + John Chilton @@ -1189,7 +1189,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Poster 195: Galaxy Methylation Toolkit as a Galaxy flavor - Nitesh Turaga + Nitesh Turaga Poster @@ -1217,7 +1217,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 15 October Galaxy Admins Meetup Around the World Online - David Kovalic, Hans-Rudolf Hotz, Dave Clements + David Kovalic, Hans-Rudolf Hotz, Dave Clements Video, Slides @@ -1340,7 +1340,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s September 17-18 Utilizing the Galaxy Analysis Framework at Core Facilities North America Western Association of Core Directors (WACD) Annual Meeting, Portland, Oregon, United States - Dave Clements + Dave Clements Slides, Slides with notes @@ -1386,7 +1386,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s August 20 Genomic data management at Canada's National Microbiology Laboratory with IRIDA and Galaxy Around the World August 2015 GalaxyAdmins Web Meetup, Online - Hans-Rudolf Hotz, Aaron Petkau + Hans-Rudolf Hotz, Aaron Petkau Slides, Video @@ -1528,7 +1528,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 22 Massively parallel sequence data analysis workshop (introduction to Galaxy framework for variant calling) Australia Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia -
Training offered by GTN Member
Ross Lazarus, Andrew Lonie +
Training offered by GTN Member
Ross Lazarus, Andrew Lonie @@ -1556,7 +1556,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester Around the World June 2015 GalaxyAdmins Web Meetup, Online - Peter Briggs, John Chilton, Hans-Rudolf Hotz + Peter Briggs, John Chilton, Hans-Rudolf Hotz Slides @@ -1570,7 +1570,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 11-12 Introduction to Galaxy: RNA-seq and ChIP-seq data analysis Workshop Europe University of Cambridge, Cambridge, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements Slides @@ -1584,21 +1584,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 8-9 Introduction to Galaxy Workshop
Workshop is full, but there is a waiting list
Europe University of Glasgow, Glasgow, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements Slides June 6-9 WS02: NGS Variant Analysis with Galaxy Europe ESHG 2015, Glasgow, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements Slides June 4 Analysis Reproducibility North America Reproducibility of Data Collection and Analysis: Modern Technologies in Genome Technology: Potentials and Pitfalls, NIH, Bethesda, Maryland, United States - James Taylor + James Taylor Slides, Video (Chapter 8) @@ -1645,7 +1645,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Building and provisioning computational cluster environments on academic and commercial clouds - Enis Afgan + Enis Afgan Paper @@ -1666,7 +1666,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s May 27 Introduction to Galaxy for Next Generation Sequencing Analysis North America Penn State College of Medicine, Hershey, Pennsylvania, United States -
Training offered by GTN Member
Anton Nekrutenko, Jill Curry +
Training offered by GTN Member
Anton Nekrutenko, Jill Curry @@ -1680,7 +1680,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s May 15 RNA-Seq Galaxy Workshop North America Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko Slides @@ -1783,14 +1783,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s April 17-18 Building data analysis ecosystem in life sciences with Galaxy The 3rd Annual LA Conference on Computational Biology & Bioinformatics, Louisiana State University, Baton Rouge, Louisiana, United States - Anton Nekrutenko + Anton Nekrutenko Slides April 16 GalaxyAdmins April 2015 Meetup Online - Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler + Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler Slides, video @@ -1825,7 +1825,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s April 1 Workshop: NGS Analysis and Workflows using Galaxy Stanford Center for Genomics & Personalized Medicine, Stanford University, Palo Alto, CA, United States -
Training offered by GTN Member
Ramesh V Nair, Somalee Datta, Jennifer Jackson, Anushka Brownley +
Training offered by GTN Member
Ramesh V Nair, Somalee Datta, Jennifer Jackson, Anushka Brownley @@ -1841,7 +1841,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Use of Genomics Visualization Methods within Galaxy Platform - Aysam Guerler + Aysam Guerler slides @@ -1886,14 +1886,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s March 23 The Galaxy Project Global Invertebrate Genomics Alliance (GIGA) II Workshop, Münich, Germany - James Taylor + James Taylor Slides March 17 Using Galaxy Workshop Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko @@ -1914,7 +1914,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s March 2-3 Workshop on Bioinformatics Methods in Genomics RBI, Zagreb, Croatia -
Training offered by GTN Member
Enis Afgan +
Training offered by GTN Member
Enis Afgan @@ -1932,7 +1932,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 27 Introduction to Galaxy Workshop Northwestern University, Chicago, Illinois, United States -
Training offered by GTN Member
Dave Clements, Matt Schipma +
Training offered by GTN Member
Dave Clements, Matt Schipma Slides @@ -1953,14 +1953,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 23-27 Bioinformatics Galaxy Course University of Frieburg, Frieburg, Germany -
Training offered by GTN Member
Björn Grüning +
Training offered by GTN Member
Björn Grüning February 26 Democratizing the ability to analyze genomic data Medical University of Innsbruck, Innsbruck, Austria - Enis Afgan + Enis Afgan @@ -1974,7 +1974,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 16-20 Accessible and Reproducible Large-Scale Analysis with Galaxy Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States - James Taylor + James Taylor Slides @@ -1992,14 +1992,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 19 February 2015 GalaxyAdmins Web Meetup Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements Slides, Video February 18 Baltimore Area Galaxy Meetup Baltimore, Maryland, United States - Enis Afgan, Nitesh Turaga + Enis Afgan, Nitesh Turaga Slides @@ -2038,7 +2038,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s January 22 Baltimore Area Galaxy Meetup
This meetup is now full.
Baltimore, Maryland, United States - Enis Afgan, Nitesh Turaga + Enis Afgan, Nitesh Turaga Slides @@ -2052,14 +2052,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s January 15-16 Accessible and Reproducible Genomics at Scale with Galaxy Revolutionizing Next-Generation Sequencing: Tools and Technologies, Leuven, Belgium - James Taylor + James Taylor January 10-14 Galaxy for SNP and Variant Data Analysis Plant and Animal Genome XXIII (PAG2015), San Diego, California, United States - Dave Clements + Dave Clements Slides @@ -2156,7 +2156,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Introduction to Galaxy Workshop North America Virginia State University, Petersburg, Virginia, United States Slides - Glenn Harris, Dave Clements + Glenn Harris, Dave Clements December 9-11 @@ -2220,7 +2220,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Cluster to Cloud - Genomics at Scale GCE: The 9th Gateway Computing Environments Workshop, Supercomputing 2014 (SC14), New Orleans, Louisiana, United States Paper - Enis Afgan + Enis Afgan FACE-IT: A Science Gateway for Food Security Research @@ -2270,7 +2270,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Deciphering Big Data Stacks: An Overview of Big Data Tools Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-14), Supercomputing 2014 (SC14), New Orleans, Louisiana, United States - Enis Afgan + Enis Afgan November 12 @@ -2284,12 +2284,12 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Rapidly bringing software to biologists with Galaxy and Docker Biological Data Science, Cold Spring Harbor Laboratory, New York, United States Slides, PDF - John Chilton + John Chilton Adventures in scaling Galaxy Slides, PDF - James Taylor + James Taylor P22: PIPE-CLIP: A comprehensive online tool for CLIP-seq data analysis @@ -2365,7 +2365,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy: Accessible and Reproducible Data Analysis for Bench Scientists Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States Slides - Dave Clements + Dave Clements October 18-22 @@ -2389,7 +2389,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Accessible, Transparent, And Reproducible Genomics With Galaxy IDIES Annual Symposium, Johns Hopkins University, Baltimore, Maryland, United States Slides - James Taylor + James Taylor October 14 @@ -2444,7 +2444,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany Slides - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop @@ -2487,7 +2487,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workshop including "Using Galaxy: RNA-seq" Stanford University, Palo Alto, CA, US Slides - Organizers, Jennifer Hillman-Jackson + Organizers, Jennifer Hillman-Jackson September 22-23 @@ -2522,7 +2522,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy: Data intensive biology for everyone Johns Hopkins XSEDE Day, Baltimore, Maryland, United States Slides - James Taylor + James Taylor September 11 @@ -2560,7 +2560,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Creating and Using Tumor Genome Profiles with Galaxy Next Generation Dx Summit, Washington, DC, United States Slides - Jeremy Goecks + Jeremy Goecks August 15 @@ -2577,7 +2577,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform University of São Paulo (USP), São Paulo, Brazil Slides - Dave Clements + Dave Clements July 18 @@ -2730,7 +2730,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Installing Galaxy Workshop
Application deadline: April 28
GMOD Online Training - Carl Eberhard, Amelia Ireland + Carl Eberhard, Amelia Ireland May 19-21 @@ -2775,14 +2775,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Analysis Reproducibility in Data (and Software) Dependent Research NIH BD2K Workshop on Discovering, Citing, Tracking Biomedical Software, Bethesda, Maryland, United States Slides, Video (starting at 19 minutes) - James Taylor + James Taylor May 13 Galaxy Workshop Institute of Genetics and Molecular Medicine (IGMM), Edinburgh, UK Sides - Dave Clements + Dave Clements May 12 @@ -2889,7 +2889,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson March 24-25 @@ -2910,7 +2910,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workshop University of Georgia, Athens, Georgia, United States Slides - Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam + Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam @@ -2920,7 +2920,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s GMOD Malaysia 2014 Kuala Lumpur, Malaysia Slides - Amelia Ireland, Dave Clements + Amelia Ireland, Dave Clements February 27 @@ -2941,7 +2941,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States - Anton Nekrutenko, JamesTaylor + Anton Nekrutenko, JamesTaylor February 10-14 @@ -2998,18 +2998,18 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s 2014 GMOD Meeting San Diego, California, United States Links - Dave Clements + Dave Clements January 11-15 Galaxy for NGS Data Analysis: A Hands-on Computer Demo Plant and Animal Genome XXII (PAG 2014), San Diego, California, United States Links - Dave Clements, Anushka Brownley + Dave Clements, Anushka Brownley Galaxy Cloudman: A Gentle Introduction to Data Analysis on the Cloud
Part of the GMOD Workshop
- Dave Clements + Dave Clements Plus 3 more talks and 4 posters @@ -3113,7 +3113,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Using Galaxy to Understand Cancer Genomics National Cancer Institute, Rockville, Maryland, United States Slides, Video - Jeremy Goecks + Jeremy Goecks December 9 @@ -3165,7 +3165,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November GalaxyAdmins Meetup Online Slides, Screencast - Dave Clements, Srinivas Maddhi, Nate Coraor + Dave Clements, Srinivas Maddhi, Nate Coraor November 19 @@ -3193,7 +3193,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Computational and Comparative Genomics Course
Application Deadline: July 15, 2013
Cold Spring Harbor Laboratory, New York, United States - James Taylor + James Taylor November 6-8 @@ -3221,7 +3221,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy 101 NGS: Introduction to Polymorphism Detection via Variant Analysis
Guest Lecture BME110 University of California, Santa Cruz, United States Live demo & discussion
ucsc-bme110-20131106-actual - Jennifer Jackson + Jennifer Jackson November 2-6 @@ -3249,27 +3249,27 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Wrangling Galaxy’s reference data Genome Informatics, Cold Spring Harbor Laboratory, New York, United States - Dan Blankenberg + Dan Blankenberg Improving reproducibility using automated testing frameworks - Dave Bouvier + Dave Bouvier Galaxy's long-term sustainability—Deployment to the XSEDE system - Nate Coraor + Nate Coraor Understanding cancer genomes using Galaxy Poster - Jeremy Goecks + Jeremy Goecks Finding missing analysis tools with Galaxy ToolShed—A case of mitochondrial RNA modification - Anton Nekrutenko + Anton Nekrutenko Bioinformatics tutorials using Galaxy @@ -3298,7 +3298,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
Polymorphism Detection and Visualization - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders @@ -3325,7 +3325,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s NGS Data Analysis and Galaxy Workshop
University of Cape Town
2013 South Africa Galaxy Workshop Tour Slides - Dave Clements + Dave Clements October 20-25 @@ -3371,14 +3371,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States Galaxy 101 NGS: Introduction to Polymorphism Detection, Managing a Local Galaxy Instance - Anton Nekrutenko, Jennifer Jackson, Anushka Brownley + Anton Nekrutenko, Jennifer Jackson, Anushka Brownley October 14-18 NGS Data Analysis and Galaxy Workshop
University of Pretoria
2013 South Africa Galaxy Workshop Tour Slides - Dave Clements + Dave Clements October 13-16 @@ -3406,19 +3406,19 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Next-Generation Sequencing Data Interpretation: Enhancing Reproducibility and Accessibility NGS & Bioinformatics Summit Europe, Berlin, Germany - Anton Nektutenko + Anton Nektutenko Using Galaxy to Provide a NGS Analysis Platform Slides - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 4 Galaxy Ecosystem & UCSC
Guest Lecture BME110 University of California, Santa Cruz, United States Slides & Live Demo - Jennifer Jackson + Jennifer Jackson October 3 @@ -3439,7 +3439,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy as a platform for High-throughput Genomics Beyond the Genome 2013, San Francisco, California, United States Slides - Jeremy Goecks + Jeremy Goecks Development of a genomic region database and analysis tool for the Galaxy platform @@ -3451,14 +3451,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Analysis of Genomic Sequence Data With Galaxy, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States - James Taylor + James Taylor September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg September 27 @@ -3535,7 +3535,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Introduction to Galaxy Workshop
National Institute of Environmental Health Sciences (NIEHS)
2013 Research Triangle Workshop Tour, North Carolina, United States Slides - Dave Clements + Dave Clements Introduction to Galaxy Workshop
University of North Carolina, Chapel Hill
@@ -3580,14 +3580,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy in a Clinical Setting: Architecture and Storage Implications The Clinical Genome Conference, San Francisco, California, United States - Sanjay Joshi + Sanjay Joshi June 20-22 W1: Next-generation sequencing data analysis with GenomeSpace and Galaxy FGED Conference, Seattle, Washington Slides - Dave Clements + Dave Clements June 21 @@ -3620,21 +3620,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Genomics and Epigenomics with Deep Sequencing, the 24th CDB Meeting RIKEN, CDB, Kobe, Japan - Anton Nekrutenko + Anton Nekrutenko June 9-13 61st ASMS Conference on Mass Spectrometry and Allied Topics
Includes at least 1 workshop and 9 posters either about or utilizing Galaxy
Minneapolis, Minnesota, United States ASMS2013 - John Chilton + John Chilton June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 6-7 @@ -3713,28 +3713,28 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workflows for Bioinformatics Analysis, and
Workshop 1A – Galaxy Workflows for Bioinformatics Analysis Workshop in Next-Generation Sequence Analysis and Metabolomics (WiNGS), UNC-Charlotte, North Carolina, United States - James Taylor + James Taylor May 15 GalaxyAdmins May 2013 Meetup GalaxyAdmins web meetup Slides, screencast - Andrew Warren, Srinivas Maddhi, Dave Clements + Andrew Warren, Srinivas Maddhi, Dave Clements May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States - Anton Nekrutenko + Anton Nekrutenko April 29 - May 2 Introduction to Galaxy Workshops
2013 Galaxy Workshop Tour
Washington University in St. Louis Slides - Dave Clements + Dave Clements Saint Louis University @@ -3756,14 +3756,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Next generation sequencing data interpretation: enhancing reproducibility and accessibility Reed College, Portland, Oregon, United States - Anton Nekrutenko + Anton Nekrutenko April 12 Transparent, accessible, reproducible analysis with Galaxy The Genome Analysis Centre (TGAC), Norwich, United Kingdom Slides - Dave Clements + Dave Clements April 11 @@ -3800,7 +3800,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom Galaxy Intro slides, GO Galaxy Slides - Dave Clements, Chris Mungall + Dave Clements, Chris Mungall April 7-8 @@ -3814,7 +3814,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Project Update 2013 GMOD Meeting, Cambridge, United Kingdom, immediately prior to Biocuration 2013 Slides - Dave Clements + Dave Clements Community Building and Support @@ -3869,7 +3869,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Feature Update
UCSC Genome Browser Staff University of California, Santa Cruz, United States Slides & Live Demo - Jennifer Jackson + Jennifer Jackson March 8 @@ -3883,21 +3883,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy for Biologists Caltech, Pasadena, California, United States Slides - Dave Clements + Dave Clements March 2-5 Accessible, Transparent and Reproducible Analysis With Galaxy, part of
SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis
Galaxy for Core Facilities, part of
"W6: Community Resource Solutions to Analyzing Large Genomic Data Sets"
ABRF 2013
Palm Springs, California, United States SW1 Workshop slides, W6 Workshop slides - Dave Clements + Dave Clements February 4 & 5 Introduction to Galaxy Workshop Johns Hopkins University, Baltimore, Maryland, United States Slides - Dave Clements, Mo Heydarian + Dave Clements, Mo Heydarian February 4 @@ -3911,7 +3911,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Enabling Compute Clusters atop OpenStack OpenStack MiniConf, Linux Conf AU, Canberra, Australia - Enis Afgan + Enis Afgan January 14-18 @@ -3925,14 +3925,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan January GalaxyAdmins Web Meetup Slides
Related Documentation
Video - John Chilton, Srinivas Maddhi, Dave Clements + John Chilton, Srinivas Maddhi, Dave Clements January 12-16 Galaxy Update 2013 Part of the GMOD Workshop at Plant and Animal Genome (PAG 2013), San Diego, California, United States Slides & Live Demo - Jennifer Jackson + Jennifer Jackson @@ -3973,7 +3973,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Computaional & Comparative Genomics Course
This was rescheduled due to hurricane Sandy
Cold Spring Harbor Laboratory, New York, United States - William Pearson, James Taylor + William Pearson, James Taylor November 28 @@ -3994,7 +3994,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Analyzing NGS data in a Bioinformatics Core Facility Next Generation Sequencing Congress 2012, London Heathrow, United Kingdom - Hans-Rudolf Hotz + Hans-Rudolf Hotz November 14 @@ -4008,7 +4008,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Slides
Tutorial - Jeremy Goecks, Jennifer Jackson + Jeremy Goecks, Jennifer Jackson Working with High-Throughput Data and Data Visualization @@ -4040,14 +4040,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy 101 and RNA-seq Analysis and Visualization QB3 - Computational Genomics Resource Laboratory, Univ of California Berkeley Slides
Tutorials: Galaxy101, RNA-seq - Jeremy Goecks, Jennifer Jackson + Jeremy Goecks, Jennifer Jackson October 28 - November 2 Genomic Virtual Laboratory Workshop eResearch Australasia, Sydney, Australia - Enis Afgan + Enis Afgan October 21-24 @@ -4061,28 +4061,28 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Advanced Sequencing Technologies and Applications Course Cold Spring Harbor Laboratory, New York, United States - Anton Nekrutenko + Anton Nekrutenko October 22 Introduction to Galaxy Workshop Purdue University Slides - Dave Clements + Dave Clements October 19 Transparent, Accessible, Reproducible Biological Analysis with Galaxy Indiana University Slides - Dave Clements + Dave Clements October 16-17 Introduction to Galaxy Workshop University of Illinois at Urbana-Champaign Slides - Dave Clements + Dave Clements October 15-17 @@ -4110,21 +4110,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Lessons from Galaxy, a Web-based Platform for High-throughput Genomic Analyses Extending High-Performance Computing Beyond its Traditional User Communities Workshop, part of 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States Slides - Jeremy Goecks + Jeremy Goecks October 3 (first Swiss) Galaxy Workshop SyBIT Tech Day, Bern, Switzerland Links - Hans-Rudolf Hotz + Hans-Rudolf Hotz September 27-29 Informatics Workshop Beyond the Genome 2012, Harvard Medical School, Boston, Massachusetts - James Taylor + James Taylor September 18-20 @@ -4152,7 +4152,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Transparent, accessible, reproducible analysis with Galaxy South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa Slides - Dave Clements + Dave Clements Assembling a cassava transcriptome using Galaxy on a high performance computing cluster @@ -4164,14 +4164,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Systems Bioinformatics Workshop Institute for Systems Biology
Seattle, Washington, United States - James Taylor + James Taylor September 3-4 Galaxy Workshop University of Pretoria, Pretoria, South Africa Slides - Dave Clements + Dave Clements September 6-7 @@ -4182,7 +4182,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s http://gmod.org/wiki/2012 GMOD Summer School US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Tutorial - Dave Clements + Dave Clements August 1-3 @@ -4196,7 +4196,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s 2012 Galaxy Community Conference University of Illinois Chicago, United States Program - Dave Clements + Dave Clements July 24-27 @@ -4224,7 +4224,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Atelier Galaxy Le Centre de Génomique Fonctionnelle Bordeaux - Anton Nekrutenko + Anton Nekrutenko June 26 @@ -4245,7 +4245,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore - James Taylor + James Taylor May 30 - June 2 @@ -4259,7 +4259,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Tour de France 2012 Perpignan, Montpellier, Lyon, Paris - Nate Coraor, Anton Nekrutenko, JamesTaylor + Nate Coraor, Anton Nekrutenko, JamesTaylor May 23-25 @@ -4273,7 +4273,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Expression Dynamics of Human XBP1 Revealed using an Integrative Approach (and Galaxy), talk, WiNGS, The Workshop in Next-Generation Sequence Analysis!, UNC Charlotte, North Carolina, United States Slides - Jeremy Goecks + Jeremy Goecks Workflows and Galaxy, workshop @@ -4291,7 +4291,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Staying on top of evolving best practices with Galaxy, Poster The Biology of Genomes, Cold Spring Harbor Laboratory, New York, United States - Dan Blankenberg + Dan Blankenberg http://gmod.org/wiki/|GMOD in the Cloud @@ -4301,7 +4301,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Integrative venomics reveals different infection strategies for parasitic wasps, poster - Jeremy Goecks + Jeremy Goecks April 29- May 1 @@ -4334,35 +4334,35 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Introduction to Galaxy Iowa State University Slides - DaveClements + DaveClements April 19 Introduction to Galaxy University of Iowa Slides - DaveClements, Ann Black-Ziegelbein + DaveClements, Ann Black-Ziegelbein April 12-13 Introduction to Galaxy Johns Hopkins University Slides - DaveClements + DaveClements April 11 Introduction to Galaxy University of Maryland Slides - DaveClements + DaveClements April 5-6 http://gmod.org/wiki/April 2012 GMOD Meeting
Including a Galaxy Workshop on evening of April 5 Washington DC, immediately following Biocuration 2012 Project Update, CloudMan Workshop, Community Building lightning talk - Dave Clements + Dave Clements April 4-5 @@ -4390,14 +4390,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s 2012 Workshop on Genomics
Features Galaxy and much more.
Český Krumlov, Czech Republic - James Taylor + James Taylor January 14-18 Galaxy Session @ GMOD Workshop,
The Galaxy Platform: Running Analyses in the Cloud @ Cloud Computing Session
... Plus at least 4 more talks and posters PAG 2012, San Diego, California, United States All talks - Dave Clements
Dannon Baker + Dave Clements
Dannon Baker January 17 @@ -4431,28 +4431,28 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Using Galaxy to provide an NGS Analysis Platform
as part of the Data Analysis, Management and Storage Strategies Session Next Generation Sequencing Congress 2011, London, United Kingdom Slides - Hans-Rudolf Hotz + Hans-Rudolf Hotz November 9-15 Compuational & Comparative Genomics Course
Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States - James Taylor + James Taylor November 8-21 Advanced Sequencing Technologies & Applications Course
Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States - James Taylor + James Taylor November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes Genome Informatics 2011, Cold Spring Harbor, New York, United States - Dan Blankenberg + Dan Blankenberg October 27 @@ -4466,35 +4466,35 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Exploit your Data: Galaxy and the GMOD Tool Suite
This workshop will both cover Galaxy and provide an overview of the GMOD tool suite. University of Tasmania, Hobart, Australia Slides - Dave Clements + Dave Clements October 23-24 The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool BioVis 2011, Providence, Rhode Island, United States Slides - Jeremy Goecks + Jeremy Goecks October 12-14 Galaxy Update and Galaxy Workshop
The workshop will cover an introduction to Galaxy, including analyzing data with tools and visualizations, using Galaxy in the cloud, and running your own instance and adding new tools. October 2011 GMOD Meeting, Ontario Institute for Cancer Research (OICR), Toronto, Canada Talk slides, Workshop slides - Dan Blankenberg + Dan Blankenberg October 9-12 Exploit your Data: Galaxy and the GMOD Tool Suite
This workshop will both cover Galaxy and provide an overview of the GMOD tool suite. This workshop is sponsored by CSIRO and AMATA. AMATA 2011, Canberra, Australia Slides - Dave Clements + Dave Clements October 3-7 Workshop on Genomics
Includes the half-day Galaxy: Introduction and Introductory Laboratory session Smithsonian Institution, Washington, DC, United States - Anton Nekrutenko + Anton Nekrutenko September 22 @@ -4515,14 +4515,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Transparent, accessible, reproducible analysis with Galaxy Genome Informatics Workshop @ Beyond the Genome 2011, Washington DC, United States - James Taylor + James Taylor September 19 Galaxy for high-throughput NGS analysis MipTec, Next Generation Sequencing for Research and Clinical Genomics User Group, Basel, Switzerland - Dan Blankenberg + Dan Blankenberg September 12-20 @@ -4536,21 +4536,21 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy: A Web-based Platform for Accessible, Reproducible, and Transparent High-throughput Biology and Galaxy Workshop UAB Research Computing Day, Birmingham, Alabama, United States Talk slides - Jeremy Goecks + Jeremy Goecks July 10-23 Workshop on Comparative Genomics North America
Includes a day long Galaxy session Fort Collins, Colorado, United States - Dan Blankenberg + Dan Blankenberg July 17-22 Accessible, Transparent, Reproducible Data Analysis with Galaxy
TeraGrid'11 Salt Lake City, Utah, United States Slides - James Taylor + James Taylor July 15-19 @@ -4564,7 +4564,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workshops @ USC Los Angeles, California, United States Intro talk slides, NGS analyses slides, ISI seminar slides - Jeremy Goecks + Jeremy Goecks June 22 @@ -4578,14 +4578,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Arthropod Genomics Symposium
Genome Project 101 Workshop Kansas City, Missouri, United States Workshop page - Dave Clements + Dave Clements May 28-31 European Human Genetics Conference 2011 (ESHG)
Galaxy Workshop Amsterdam, the Netherlands Slides - Dave Clements + Dave Clements May 25-26 @@ -4599,7 +4599,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Using Galaxy Workshop University of Manchester, United Kingdom - Dan Blankenberg + Dan Blankenberg April 13-14 @@ -4613,42 +4613,42 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Dynamically Scalable, Accessible Analysis for High-Throughput Sequence Data
BioIT World Boston, Massachusetts, United States - Enis Afgan + Enis Afgan March 5-12 GMOD Americas 2011
Talk and course session Durham, North Carolina, United States Slides - Dave Clements + Dave Clements February 19-22 Galaxy Next Generation Sequencing Functionality from Sample Tracking to SNP Calling
ABRF 2011 San Antonio, Texas, United States - Greg von Kuster + Greg von Kuster February 2-5 Management and Analysis of Second and Third Generation Sequencing Data with Galaxy
AGBT 2011 Marco Island, Florida, United States Slides - Anton Nekrutenko, James Taylor + Anton Nekrutenko, James Taylor January 15-19 Galaxy: Analyze, Visualize, Communicate
Plant and Animal Genome XIX (PAG 2011) San Diego, California, United States Slides - Dan Blankenberg + Dan Blankenberg January 9-21 Workshop on Comparative Genomics, Europe
Includes sessions on Galaxy Český Krumlov, Czech Republic - Anton Nekrutenko + Anton Nekrutenko @@ -4689,7 +4689,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s The elastic analysis with galaxy on the cloud Beyond the Genome, Boston, Massachusetts - Enis Afgan + Enis Afgan July 9-13 @@ -4703,7 +4703,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Deploying Galaxy on the Cloud BOSC 2010 Boston, Massachusetts, United States Slides - Enis Afgan + Enis Afgan May 15-16 @@ -4717,6 +4717,6 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Animal Genomics with Galaxy: Analyze, Publish, and Visualize
Plant and Animal Genome XVIII (PAG 2010) San Diego, California, United States Slides - Dan Blankenberg + Dan Blankenberg diff --git a/content/events/asu2016/index.md b/content/events/asu2016/index.md index fcdb7bac0e..8eec25dec4 100644 --- a/content/events/asu2016/index.md +++ b/content/events/asu2016/index.md @@ -11,7 +11,7 @@ title: Introduction to Galaxy Workshop **January 8, 2016** **Instructor**
-[Anton Nekrutenko](/src/people/anton/index.md), Galaxy Project, [Penn State University](http://www.psu.edu)
+[Anton Nekrutenko](/people/anton/), Galaxy Project, [Penn State University](http://www.psu.edu)
**Location: [Life Sciences E (LSE)](https://maps.asu.edu/?id=120&mrkIid=62941) 244, Tempe Main Campus**
@@ -108,4 +108,4 @@ This workshop is supported by [Biodiversity Knowledge Integration Center (BioKIC ## Questions? -Contact [Nico Franz](https://sols.asu.edu/people/nico-franz) or [Melissa A. Wilson Sayres](https://sols.asu.edu/people/melissa-wilson-sayres) at ASU, or [Anton Nekrutenko](/src/people/anton/index.md) of the Galaxy Project. +Contact [Nico Franz](https://sols.asu.edu/people/nico-franz) or [Melissa A. Wilson Sayres](https://sols.asu.edu/people/melissa-wilson-sayres) at ASU, or [Anton Nekrutenko](/people/anton/) of the Galaxy Project. diff --git a/content/events/bio-it-world2014/w14/index.md b/content/events/bio-it-world2014/w14/index.md index a4f666760d..c1814db20b 100644 --- a/content/events/bio-it-world2014/w14/index.md +++ b/content/events/bio-it-world2014/w14/index.md @@ -1,7 +1,7 @@ --- title: "Workshop 14: Running a Local Galaxy Instance" --- -[Adam Kraut](http://bioteam.net/company-leadership/), [Nate Coraor](/src/people/nate/index.md), [Anushka Brownley](http://bioteam.net/company-leadership/), Tristan Lubinski, [James Reaney](http://www.sgi.com/solutions/genomics) +[Adam Kraut](http://bioteam.net/company-leadership/), [Nate Coraor](/people/nate/), [Anushka Brownley](http://bioteam.net/company-leadership/), Tristan Lubinski, [James Reaney](http://www.sgi.com/solutions/genomics)
![](https://dev.twitter.com/sites/default/files/images_documentation/bird_blue_16.png) #usegalaxy #BioIT2014 diff --git a/content/events/bioitworld2014/index.md b/content/events/bioitworld2014/index.md index d8dacfe5bf..cf1318ba8a 100644 --- a/content/events/bioitworld2014/index.md +++ b/content/events/bioitworld2014/index.md @@ -19,7 +19,7 @@ Galaxy will have a significant presence at the [Bio-IT World Conference](http:// Tuesday
April 29 8:00-11:30 W4: Analyzing NGS Data in Galaxy - Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski + Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski @@ -30,7 +30,7 @@ Galaxy will have a significant presence at the [Bio-IT World Conference](http:// W14: Running a Local Galaxy Instance - Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney + Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney Tutorial script @@ -62,7 +62,7 @@ Galaxy will have a significant presence at the [Bio-IT World Conference](http:// 2:30-3:00 Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy - Jeremy Goecks + Jeremy Goecks Slides diff --git a/content/events/caltech2013/index.md b/content/events/caltech2013/index.md index 606767ba64..357e619d19 100644 --- a/content/events/caltech2013/index.md +++ b/content/events/caltech2013/index.md @@ -26,7 +26,7 @@ There will be two Galaxy-related events on the Caltech Campus on March 5, 2013:
**11am-2pm, March 5, 2013, 151 Braun** (lunch provided for participants)
**[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2013CaltechGalaxyForBiologists.pdf)**
-**[Dave Clements](/src/people/dave-clements/index.md)**
+**[Dave Clements](/people/dave-clements/)**
**Emory University**

@@ -86,10 +86,10 @@ This workshop is generously supported by an [AWS in Education](http://aws.amazon
**2:30-4:30pm, March 5, BBB 024** (note revised time, new location)
-**[Dave Clements](/src/people/dave-clements/index.md)**
+**[Dave Clements](/people/dave-clements/)**
**Emory University**

-This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/src/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/src/people/dannon-baker/index.md) and [Nate Coraor](/src/people/nate/index.md), two members of the [core Galaxy development team](/src/galaxy-team/index.md). +This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/people/dannon-baker/index.md) and [Nate Coraor](/src/people/nate/), two members of the [core Galaxy development team](/src/galaxy-team/). *This discussion is open to any member of the Caltech community. It is free, but space is limited and advanced registration is strongly encouraged.*
diff --git a/content/events/cornell2016/index.md b/content/events/cornell2016/index.md index 53fcfde2c4..2e8360f54e 100644 --- a/content/events/cornell2016/index.md +++ b/content/events/cornell2016/index.md @@ -16,7 +16,7 @@ image: Cornell University
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md)** +**Instructor: [Dave Clements](/people/dave-clements/)** **9:00-5:00
Location: [Room B30A](https://mannlib.cornell.edu/rooms-labs/classrooms-labs/b30a-computer-lab), Mann library
diff --git a/content/events/eccb2014/index.md b/content/events/eccb2014/index.md index 237c6ae3bf..2bb562ea35 100644 --- a/content/events/eccb2014/index.md +++ b/content/events/eccb2014/index.md @@ -68,6 +68,6 @@ There were several sessions and posters featuring Galaxy at the [13th European C 14:00-14:30 ID02: A panel of European Public Galaxy Instances
1. Galaxy Project Introduction
2. deepTools: user-friendly tools for data visualization
3. The Nebula ChIP-Seq web service
4. The French Institute of Bioinformatics (IFB) academic cloud infrastructure for life sciences
1. Slides
2. Slides - Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet + Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet diff --git a/content/events/galaxy-tour-de-france2012/index.md b/content/events/galaxy-tour-de-france2012/index.md index bc2e0a3f6a..6273af66aa 100644 --- a/content/events/galaxy-tour-de-france2012/index.md +++ b/content/events/galaxy-tour-de-france2012/index.md @@ -110,11 +110,11 @@ If you attend both workshops and plan to eat in the area, there are many choices ## Meet the Team! -
Nate Coraor!   Anton Nekrutenko!   James Taylor!
+
Nate Coraor!   Anton Nekrutenko!   James Taylor!
-* [Nate Coraor](/src/people/nate/index.md) -* [Anton Nekrutenko](/src/people/anton/index.md) -* [James Taylor](/src/people/james-taylor/index.md) +* [Nate Coraor](/people/nate/) +* [Anton Nekrutenko](/people/anton/) +* [James Taylor](/people/james-taylor/) ## Sponsors diff --git a/content/events/gaw2014/index.md b/content/events/gaw2014/index.md index c39b8847c3..adc7f59616 100644 --- a/content/events/gaw2014/index.md +++ b/content/events/gaw2014/index.md @@ -47,7 +47,7 @@ GAW 2014 also included poster session and keynote speakers. 10:10-10:35 - Keynote: Reproducible complex analyses as a scientific commodity: Why Galaxy matters
Ross Lazarus (download pdf slides) + Keynote: Reproducible complex analyses as a scientific commodity: Why Galaxy matters
Ross Lazarus (download pdf slides) 10:35-11:00 @@ -71,11 +71,11 @@ GAW 2014 also included poster session and keynote speakers. 14:05-14:40 - Galaxy in the wild: Galaxy Architecture and Supporting Production Level Genomics
Nate Coraor (download PDF slides) + Galaxy in the wild: Galaxy Architecture and Supporting Production Level Genomics
Nate Coraor (download PDF slides) 14:40-15:20 - Introduction to the Tool Shed: Tight dependency control for reproducible analysis
Ross Lazarus (download pdf slides) + Introduction to the Tool Shed: Tight dependency control for reproducible analysis
Ross Lazarus (download pdf slides) 15:20-15:50 @@ -83,11 +83,11 @@ GAW 2014 also included poster session and keynote speakers. 15:50-16:20 - CloudMan Project
Enis Afgan (download pdf slides) + CloudMan Project
Enis Afgan (download pdf slides) 16:20-17:00 - Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan + Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan @@ -126,7 +126,7 @@ Posters to be displayed throughout the day: 09:10-09:50 - Keynote: Galaxy - past, present and future
Nate Coraor (download PDF slides) + Keynote: Galaxy - past, present and future
Nate Coraor (download PDF slides) 9:50-10:30 @@ -272,7 +272,7 @@ The first Galaxy Australasia Workshop was held on Monday 24th and Tuesday 25th M **Day 1** was held at the [Monash Biomedical Imaging](http://www.mbi.monash.edu.au/) Auditorium at [Monash University](http://www.monash.edu.au/). The large auditorium did make the audience seem small, and perhaps the distance of the venue from the Melbourne CBD discouraged those few who had registered but did not attend. -*[Ross Lazarus](/src/people/fubar/index.md)* ([Baker IDI/Galaxy](https://www.bakeridi.edu.au/)) opened in his usual entertaining manner and told us [Why Galaxy matters: Reproducible complex analyses as a scientific commodity](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gaw2014/ross_repro_research.pdf). +*[Ross Lazarus](/people/fubar/)* ([Baker IDI/Galaxy](https://www.bakeridi.edu.au/)) opened in his usual entertaining manner and told us [Why Galaxy matters: Reproducible complex analyses as a scientific commodity](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gaw2014/ross_repro_research.pdf).
GVL
@@ -294,7 +294,7 @@ The day closed amidst the usual scrum of organising taxis and public transport **Day 2** was held in the [Melbourne Convention Centre](http://mcec.com.au/), alongside CSIRO’s [Computational and Simulation Sciences and eResearch conference.](http://wp.csiro.au/css/ ) -*[Nate Coraor](/src/people/nate/index.md)*, our special guest from the Galaxy Project, entertained us with a look at [working versions of Galaxy from the past, and updated us on Galaxy in the present and coming in the future](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gaw2014/coraor_past_present_future.pdf). +*[Nate Coraor](/people/nate/)*, our special guest from the Galaxy Project, entertained us with a look at [working versions of Galaxy from the past, and updated us on Galaxy in the present and coming in the future](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gaw2014/coraor_past_present_future.pdf).
Latrobe University WEHI
diff --git a/content/events/gcc2011/index.md b/content/events/gcc2011/index.md index c36f1f0f9d..bb12e15079 100644 --- a/content/events/gcc2011/index.md +++ b/content/events/gcc2011/index.md @@ -38,7 +38,7 @@ Listed in the order they were given: | *Galaxy Deployment and API* | Nate Coraor, Penn State University, and Dannon Baker, Emory University | [PowerPoint](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/GalaxyDeploymentandAPI.ppt), [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/GalaxyDeploymentandAPI.pdf) | [Watch](http://vimeo.com/24869193) | | *Pathogenomics Analysis and Visualization* | Freddy de Bree, Central Veterinary Institute at Wageningen UR | | [Watch](http://vimeo.com/24869089) | | *National Collaborative Platform for Genomics and Proteomics Data Analysis* | Hailiang Mei, NBIC | [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/NationalCollaborativePlatformForGenomicsAndProteomicsDataAnalysis.pdf) | [Watch](http://vimeo.com/24869172) | -| *Using Galaxy to Provide Tools for the Analysis of Diverse Local Datasets* | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), Friedrich Miescher Institute for Biomedical Research | [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/SixKeyInsights.pdf) | [Watch](http://vimeo.com/24869041) | +| *Using Galaxy to Provide Tools for the Analysis of Diverse Local Datasets* | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Friedrich Miescher Institute for Biomedical Research | [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/SixKeyInsights.pdf) | [Watch](http://vimeo.com/24869041) | | *Deploying Galaxy for Use with High-Throughput Screening Experiments* | Grainne Kerr, German Cancer Research Center and Heidelberg University | [PowerPoint](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/DeployingGalaxyForUseWithHigh-ThroughputScreeningExperiments.pptx), [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/DeployingGalaxyForUseWithHigh-ThroughputScreeningExperiments.pdf) | [Watch](http://vimeo.com/24868750) | | *A Galactic Experience and Extending Galaxy Sample Tracking* | Jelle Scholtalbers, TRON gGmbH | [OpenOffice](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/AGalacticExperienceAndExtendingGalaxySampleTracking.odp), [PDF](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/AGalacticExperienceAndExtendingGalaxySampleTracking.pdf) | [Watch](http://vimeo.com/24868944) | | *Movement of Large Datasets via Integration of GridFTP and GlobusOnline with a Production Galaxy Setup at the University of Chicago* | Neil Bahroos and Alex Rodriquez, University of Chicago | | [Watch](http://vimeo.com/24868993) | @@ -79,7 +79,7 @@ Relocate the links from the current pages in Bitbucket to here. Each breakout has its own wiki page for notes. Someone in each group was selected to take notes, either directly on the wiki page, or just in a text editor (in which case, they will show up in June). -* [Visualization and Visual Analytics](/src/events/gcc2011/visualization-and-visual-analytics/index.md) ([Jeremy Goecks](/src/people/jeremy-goecks/index.md)) +* [Visualization and Visual Analytics](/src/events/gcc2011/visualization-and-visual-analytics/index.md) ([Jeremy Goecks](/people/jeremy-goecks/)) * [Sample Tracking and Instrument Integration](/src/events/gcc2011/sample-tracking-and-instrument-integration/index.md) (Greg Von Kuster) * [Thinking Big: CloudMan, Grid, and Scalability](/src/events/gcc2011/thinking-big-cloudman-grid-and-scalability/index.md) (Enis Afgan) * [Workflows and API](/src/events/gcc2011/workflows-and-api/index.md) (Kanwei Li) diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index a8bb14200b..21aa6a5181 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -18,7 +18,7 @@ Abstracts for talks that were presented at the [GCC2012 main sessions](/src/even
 
-**[Anton Nekrutenko](/src/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/index.md)2** +**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -156,7 +156,7 @@ Our web service, [Nebula](http://nebula.curie.fr/), was designed for biologists. ## Implications of a Galaxy Community Cloud in Clinical Genomics -**[Sanjay Joshi](/src/people/sanjay-joshi/index.md)1** +**[Sanjay Joshi](/people/sanjay-joshi/)1** 1 Chief Technical Officer (CTO), [Life Sciences](http://www.isilon.com/industry/lifesciences), [EMC Isilon](http://emc.com/) @@ -170,7 +170,7 @@ The intersection of the established Galaxy Research community with the requireme
-**[Enis Afgan](/src/people/enis-afgan/index.md)1,2** +**[Enis Afgan](/people/enis-afgan/)1,2** 1 [Ruđer Bošković Institute (RBI)](http://www.irb.hr/eng/)
2 [Victoria Life Sciences Computation Initiative (VLSCI)](http://www.vlsci.org.au/), [University of Melbourne](http://www.unimelb.edu.au/) @@ -229,7 +229,7 @@ Contact: support@oqtans.org; ratschg@mskcc.org
-**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/src/people/dan/index.md)2, [Anton Nekrutenko](/src/people/anton/index.md)2 and Oliver Hobert1
+**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/people/dan/index.md)2, [Anton Nekrutenko](/src/people/anton/)2 and Oliver Hobert1
1 Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
2 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA, USA
@@ -294,7 +294,7 @@ As the cost of next generation sequencing decreases and the accessibility increa
-**[Jeremy Goecks](/src/people/jeremy-goecks/index.md)1** +**[Jeremy Goecks](/people/jeremy-goecks/)1** 1 [Emory University](http://emory.edu/) @@ -310,7 +310,7 @@ The Galaxy team is building a framework for Web-based visualization of next-gene
-**[Mike Lelivelt](/src/people/mike-lelivelt/index.md)1** +**[Mike Lelivelt](/people/mike-lelivelt/)1** 1 Director of Bioinformatics and Software Products, [Ion Torrent](http://lifetech.com) @@ -324,7 +324,7 @@ Ion Torrent has pioneered an entirely new approach to sequencing that enables a ## High level distributed processing pipelines with Galaxy -**Brad Chapman1** ([bchapman@hsph.harvard.edu](mailto:bchapman@hsph.harvard.edu)), Shannan Ho Sui1, [Enis Afgan](/src/people/enis-afgan/index.md)3, Ilya Sytchev2, Jason Evans1, Oliver Hofmann1, Winston Hide1 +**Brad Chapman1** ([bchapman@hsph.harvard.edu](mailto:bchapman@hsph.harvard.edu)), Shannan Ho Sui1, [Enis Afgan](/people/enis-afgan/)3, Ilya Sytchev2, Jason Evans1, Oliver Hofmann1, Winston Hide1 1 [Harvard School of Public Health](http://compbio.sph.harvard.edu/chb/)
2 Center for Stem Cell Bioinformatics, Harvard Stem Cell Institute
@@ -452,7 +452,7 @@ GenomeSpace is a software environment that provides a connection layer between b
-**[Greg von Kuster](/src/people/greg_vonkuster/index.md)1** +**[Greg von Kuster](/people/greg_vonkuster/)1** 1 [Penn State University](http://psu.edu/) diff --git a/content/events/gcc2012/organizing-committee/index.md b/content/events/gcc2012/organizing-committee/index.md index 7d0c5ed9b1..fa889671e3 100644 --- a/content/events/gcc2012/organizing-committee/index.md +++ b/content/events/gcc2012/organizing-committee/index.md @@ -9,7 +9,7 @@ title: GCC2012 Organizing Committee **Neil Bahroos** [University of Illinois at Chicago (UIC)](http://www/uic.edu/)

- **[Dave Clements](/src/people/dave-clements/index.md)** + **[Dave Clements](/people/dave-clements/)** [Emory University](/src/community/Emory University/index.md)

**[Christopher Fields](http://www.bioperl.org/wiki/User:Cjfields)** [University of Illinois at Urbana-Champaign](http://www.illinois.edu/)

diff --git a/content/events/gcc2012/program/breakouts/automation-strategies/index.md b/content/events/gcc2012/program/breakouts/automation-strategies/index.md index eb8307ef54..323f42553c 100644 --- a/content/events/gcc2012/program/breakouts/automation-strategies/index.md +++ b/content/events/gcc2012/program/breakouts/automation-strategies/index.md @@ -7,7 +7,7 @@ title: Automation strategies for Data, Tools, & Config -A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/src/people/john-chilton/index.md), [Enis Afgan](/src/people/enis-afgan/index.md), [Dave Bouvier](/src/people/dave-bouvier/index.md) and [Jen Jackson](/src/people/jennifer-jackson/index.md) +A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/people/john-chilton/index.md), [Enis Afgan](/people/enis-afgan/index.md), [Dave Bouvier](/src/people/dave-bouvier/) and [Jen Jackson](/src/people/jennifer-jackson/) This involves turning the base Galaxy into a production machine: * download of associated genomes and data files, diff --git a/content/events/gcc2012/program/breakouts/bioinformatics-training/index.md b/content/events/gcc2012/program/breakouts/bioinformatics-training/index.md index 0f688fc80c..65a1f60173 100644 --- a/content/events/gcc2012/program/breakouts/bioinformatics-training/index.md +++ b/content/events/gcc2012/program/breakouts/bioinformatics-training/index.md @@ -29,7 +29,7 @@ title: Bioinformatics Training and Teaching with Galaxy # Notes -These notes are a rough first grouping of [Dave Clements'](/src/people/dave-clements/index.md) notes from the breakout. Please feel free to update them. +These notes are a rough first grouping of [Dave Clements'](/people/dave-clements/) notes from the breakout. Please feel free to update them. ## Platforms diff --git a/content/events/gcc2012/program/breakouts/end-users/index.md b/content/events/gcc2012/program/breakouts/end-users/index.md index cb9733b710..ef407f775f 100644 --- a/content/events/gcc2012/program/breakouts/end-users/index.md +++ b/content/events/gcc2012/program/breakouts/end-users/index.md @@ -15,11 +15,11 @@ title: Galaxy End Users * Karen Reddy * -* [Anton](/src/people/anton/index.md), [Dan](/src/people/dan/index.md), Rémi, and [Jen](/src/people/jennifer-jackson/index.md) from [Galaxy Team](/src/galaxy-team/index.md) +* [Anton](/people/anton/index.md), [Dan](/people/dan/index.md), Rémi, and [Jen](/src/people/jennifer-jackson/) from [Galaxy Team](/src/galaxy-team/) # Notes -These are a merged grouping of [Anton's](/src/people/anton/index.md), [Dan's](/src/people/dan/index.md), and [Jen's](/src/people/jennifer-jackson/index.md) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. +These are a merged grouping of [Anton's](/people/anton/index.md), [Dan's](/people/dan/), and [Jen's](/src/people/jennifer-jackson/) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. ## Platforms diff --git a/content/events/gcc2012/program/breakouts/index.md b/content/events/gcc2012/program/breakouts/index.md index 9cf48470c4..71f490c621 100644 --- a/content/events/gcc2012/program/breakouts/index.md +++ b/content/events/gcc2012/program/breakouts/index.md @@ -5,10 +5,10 @@ Breakouts are informal, open discussion sessions where participants interested i GalaxyCzars
Ann Black-Ziegelbein - Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson + Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson - Bioinformatics Training and Teaching with Galaxy
Dave Clements + Bioinformatics Training and Teaching with Galaxy
Dave Clements Galaxy API and Extending it; Workflow Enhancements
Clare Sloggett, Scott McManus diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index eacab892d7..4d0b0878d5 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -10,7 +10,7 @@ The [2012 Galaxy Community Conference](/src/events/gcc2012/program//index.md) in ### Summaries -* Peter Li, [Jeremy Goecks](/src/people/jeremy-goecks/index.md) and Tin Lap Lee's [Meeting report](http://genomebiology.com/2012/13/8/318) in [Genome Biology](http://genomebiology.com/). +* Peter Li, [Jeremy Goecks](/people/jeremy-goecks/) and Tin Lap Lee's [Meeting report](http://genomebiology.com/2012/13/8/318) in [Genome Biology](http://genomebiology.com/). * Peter Li's [GigaBlog post](http://blogs.biomedcentral.com/gigablog/2012/08/06/enabling-bioinformatics-tools-to-smoke-the-peace-pipe-together/) * Brad Chapman's [day 1](http://chapmanb.posterous.com/galaxy-developer-conference-day-1) and [day 2](http://chapmanb.posterous.com/galaxy-community-conference-2012-notes-from-d-90717) summaries. @@ -35,9 +35,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -45,9 +45,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 11:00 - WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
- WS6: Galaxy API
Dannon Baker
+ WS4: Galaxy Code Architecture
James Taylor
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS6: Galaxy API
Dannon Baker
12:30 @@ -55,9 +55,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 @@ -65,9 +65,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 4:00 - WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
- WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
- WS6: Galaxy API
Dannon Baker
+ WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
+ WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
+ WS6: Galaxy API
Dannon Baker
5:30 @@ -84,7 +84,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | **8:00-9:00** | Continental Breakfast, Registration Open | | **9:00-9:10** | **Welcome:** [William Hendrickson](http://www.uic.edu/depts/mcmi/faculty/hendrickson/), [University of Illinois at Chicago (UIC)](http://www/uic.edu/) | | **9:10-10:40** | **Session 1:** Moderator: [Tin Lap Lee](http://www.sbs.cuhk.edu.hk/TeachingStaffDetails.asp?TE_NAME=LEE%20Tin%20Lap), [Chinese University of Hong Kong](http://www.cuhk.edu.hk/) | -| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/src/people/anton/index.md) and [James Taylor](/src/people/james-taylor/index.md), Galaxy Project
| +| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/people/anton/index.md) and [James Taylor](/src/people/james-taylor/), Galaxy Project
| | 9:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Luo.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 31:55)*
*[Integration of S-MART, a toolbox to aid RNA-seq data analysis in Galaxy](/src/events/gcc2012/abstracts/index.md#integration-of-s-mart-a-toolbox-to-aid-rna-seq-data-analysis-in-galaxy)*
Yufei Luo, Unité de recherche en Génomique-Info, INRA
| | 10:00 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Park.pdf), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ xx:yy), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5)*
*[Connecting Galaxy to a Data Repository](/src/events/gcc2012/abstracts/index.md#connecting-galaxy-to-a-data-repository)*
Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School
| | 10:20 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/MaillolDufayard.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5) (starts @ 11:45)*
*[Role of Galaxy in a bioinformatic plant breeding platform](/src/events/gcc2012/abstracts/index.md#role-of-galaxy-in-a-bioinformatic-plant-breeding-platform)*
Vincent Maillol and Jean-Francois Dufayard, INRA and CIRAD
| @@ -96,8 +96,8 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | 12:10 |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lermine.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lermine.ppt), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=26bcce7b2387420) (starts @ 58:45), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=e63450b12c16451)*
*[Nebula - A Web-Server for Advanced ChIP-Seq Data Analysis](/src/events/gcc2012/abstracts/index.md#nebula---a-web-server-for-advanced-chip-seq-data-analysis)*
Alban Lermine, Institut Curie
| | **12:30-1:50** | **Lunch: ** Sponsored by [EMC Isilon](http://www.emc.com/isilon) | | | **[Implications of a Galaxy Community Cloud in Clinical Genomics](Events/GCC2012/Abstracts#Implications of a Galaxy Community Cloud in Clinical Genomics)**
Sanjay Joshi, Chief Technical Officer (CTO), [Life Sciences](http://www.isilon.com/industry/lifesciences), [EMC Isilon](http://www.emc.com/isilon)
[EMC Isilon](http://www.emc.com/isilon) Sponsor Presentation
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=b061c1974ff0407)* | -| **1:50-3:10** | **Session 3:**
Moderator: [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), [Friedrich Miescher Institute for Biomedical Research](http://www.fmi.ch/) | -| 1:50 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Afgan.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=7c7f3063681d4af)*
*[Establishing a National Genomics Virtual Laboratory with Galaxy CloudMan](/src/events/gcc2012/abstracts/index.md#establishing-a-national-genomics-virtual-laboratory-with-galaxy-cloudman)*
[Enis Afgan](/src/people/enis-afgan/index.md), [Ruđer Bošković Institute (RBI)](http://www.irb.hr/eng/), [Victoria Life Sciences Computation Initiative (VLSCI)](http://www.vlsci.org.au/)
| +| **1:50-3:10** | **Session 3:**
Moderator: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Friedrich Miescher Institute for Biomedical Research](http://www.fmi.ch/) | +| 1:50 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Afgan.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=7c7f3063681d4af)*
*[Establishing a National Genomics Virtual Laboratory with Galaxy CloudMan](/src/events/gcc2012/abstracts/index.md#establishing-a-national-genomics-virtual-laboratory-with-galaxy-cloudman)*
[Enis Afgan](/people/enis-afgan/), [Ruđer Bošković Institute (RBI)](http://www.irb.hr/eng/), [Victoria Life Sciences Computation Initiative (VLSCI)](http://www.vlsci.org.au/)
| | 2:10 |
*[Slides](http://bjoern.gruenings.eu/GCC-2012), [Source](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/GruningSource.zip), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=7c7f3063681d4af) (starts at 22:00), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=5d4fa321f2e848f)*
*[Keeping Track of Life Science Data](/src/events/gcc2012/abstracts/index.md#keeping-track-of-life-science-data)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| | 2:30 |
*[PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Sreedharan.ppt), [PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Sreedharan.PDF), [Video](https://uic.sharestream.net/ssdcms/i.do?u=5d4fa321f2e848f) (starts at 3:00)*
*[Easier Workflows & Tool Comparison with Oqtans+](/src/events/gcc2012/abstracts/index.md#easier-workflows--tool-comparison-with-oqtans)*
[Vipin T Sreedharan](http://raetschlab.org///members/vipin.1.html), [Friedrich Miescher Laboratory](http://www.fml.tuebingen.mpg.de/) and [Memorial Sloan-Kettering Cancer Center](http://www.mskcc.org/)
| | 2:50 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Minevich.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=5d4fa321f2e848f) (starts @ 19:25)*
*[CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences](/src/events/gcc2012/abstracts/index.md#cloudmap-a-cloud-based-pipeline-for-analysis-of-mutant-genome-sequences)*
Gregory Minevich, Columbia University
| @@ -106,7 +106,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | 3:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Sun.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=a6208a4628164b7)*
*[GPS: a real-time recommendation system for ChIP-Seq analysis](/src/events/gcc2012/abstracts/index.md#gps-a-real-time-recommendation-system-for-chip-seq-analysis)*
Hanfei Sun, Dana-Farber Cancer Institute
| | 4:00 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lee.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=a6208a4628164b7) (starts @ 16:45)*
*[Integration of Taverna workflows on a Galaxy-based platform for large-scale genomics analysis](/src/events/gcc2012/abstracts/index.md#integration-of-taverna-workflows-on-a-galaxy-based-platform-for-large-scale-genomics-analysis)*
Tin-Lap Lee, The Chinese University of Hong Kong
| | 4:20 |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Reddy.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Reddy.pptx), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=a6208a4628164b7) (starts @ 35:30), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=6b93204632704bd)*
*[NGS analysis for Biologists: experiences from the cloud](/src/events/gcc2012/abstracts/index.md#ngs-analysis-for-biologists-experiences-from-the-cloud)*
Karen Reddy, Johns Hopkins University
| -| 4:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Goecks.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=6b93204632704bd) (starts @ 8:40)*
*[The Galaxy Visualization Framework](/src/events/gcc2012/abstracts/index.md#the-galaxy-visualization-framework)*
[Jeremy Goecks](/src/people/jeremy-goecks/index.md), Emory University
| +| 4:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Goecks.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=6b93204632704bd) (starts @ 8:40)*
*[The Galaxy Visualization Framework](/src/events/gcc2012/abstracts/index.md#the-galaxy-visualization-framework)*
[Jeremy Goecks](/people/jeremy-goecks/), Emory University
| | **5:00-5:15** | **Break** | | **5:15-6:15** | ***[Ion Torrent](http://www.lifetechnologies.com/): [Open, Accessible, Enabling](Events/GCC2012/Abstracts#Ion Torrent: Open, Accessible, Enabling)***
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
[Ion Torrent](http://www.lifetechnologies.com/) Sponsor Presentation
*[PDF](/attachment:Documents/Presentations/GCC2012/Lelivelt.pdf), [PPT](/attachment:Documents/Presentations/GCC2012/Lelivelt.ppt), [Video](https://uic.sharestream.net/ssdcms/i.do?u=66878bd05a11401)*
| | **7pm** | ***Conference Dinner @ [Haymarket Pub & Brwery](http://www.haymarketbrewing.com/)
Sponsored by [Ion Torrent](http://www.lifetechnologies.com/)*** | @@ -130,7 +130,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | 11:55 |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Liefeld.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Liefeld.pptx), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=cc90a8540a7f4ec) (starts @ 54:10), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=afa05c3a39584a7)*
*[GenomeSpace](/src/events/gcc2012/abstracts/index.md#genomespace)*
Ted Liefeld, Broad Institute
| | **12:15-1:10** | **Lunch** | | **1:10-2:50** | **Session 7**
Moderator: Ross Lazarus, [BakerIDI](http://www.bakeridi.edu.au/) | -| **1:10** |
*[PDF](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.pdf), [PPT](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.ppt),[Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad)*
*[Tool Shed and Changes to Galaxy Distributions](/src/events/gcc2012/abstracts#tool_shed_and_hanges_to_galaxy_distributions)*
[Greg von Kuster](/src/people/greg_vonkuster/index.md), Penn State University
| +| **1:10** |
*[PDF](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.pdf), [PPT](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.ppt),[Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad)*
*[Tool Shed and Changes to Galaxy Distributions](/src/events/gcc2012/abstracts#tool_shed_and_hanges_to_galaxy_distributions)*
[Greg von Kuster](/people/greg_vonkuster/), Penn State University
| | **1:30** | **Lightning Talks** | | |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Helseth.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Helseth.pptx), [Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad) (starts @ 24:40)*
*Customizing Galaxy for a Hospital Environment*
Larry Helseth, NorthShore University HealthSystem
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Coraor.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad) (starts @ 30:30)*
*ObjectStore*
Nate Coraor, Penn State University
| @@ -142,7 +142,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.ppt), Video*
*Galaxy-P*
Pratik Jagtap, University of Minnesota
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Sandve.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421)*
*The Genomic Hyperbrowser: Prove Your Point*
Geir Kjetil Sandve, University of Oslo
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Gruning.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 6:10)*
*[ChemicalToolBox](/src/chemical-tool-box/index.md)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| -| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/src/people/anton/index.md), Penn State University, [James Taylor](/src/people/james-taylor/index.md), Emory University
| +| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/index.md), Penn State University, [James Taylor](/src/people/james-taylor/), Emory University
| | **2:55-3:15** | **Break** | | **3:15-5:00** | **Session 8: Breakouts**
Moderator: Dave Clements, [Emory University](http://www.emory.edu/)
[Breakouts](/src/eents/gcc2012/program/breakouts/index.md) | | **5:00** | **[2012 Galaxy Community Conference](/src/events/gcc2012/index.md) ends** | diff --git a/content/events/gcc2012/sponsorships/index.md b/content/events/gcc2012/sponsorships/index.md index f979cbe9ee..688096e915 100644 --- a/content/events/gcc2012/sponsorships/index.md +++ b/content/events/gcc2012/sponsorships/index.md @@ -16,7 +16,7 @@ Sponsorships are available at four different levels. Ion Torrent - Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss + Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss @@ -29,7 +29,7 @@ Sponsorships are available at four different levels. EMC Isilon - EMC Isilon

GCC Representatives:
Sanjay Joshi • Alpesh Shah
Scott Wilson • Kristine Swander + EMC Isilon

GCC Representatives:
Sanjay Joshi • Alpesh Shah
Scott Wilson • Kristine Swander @@ -49,7 +49,7 @@ Sponsorships are available at four different levels. The Institute for Genomic Biology - Radhika Khetani + Radhika Khetani Roy J. Carver Biotechnology Center diff --git a/content/events/gcc2012/training-day/index.md b/content/events/gcc2012/training-day/index.md index 25524793a6..55bf71c920 100644 --- a/content/events/gcc2012/training-day/index.md +++ b/content/events/gcc2012/training-day/index.md @@ -29,9 +29,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -39,9 +39,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 11:00 - WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
- WS6: Galaxy API
Dannon Baker
+ WS4: Galaxy Code Architecture
James Taylor
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS6: Galaxy API
Dannon Baker
12:30 @@ -49,9 +49,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 @@ -59,9 +59,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 4:00 - WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
- WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
- WS6: Galaxy API
Dannon Baker
+ WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
+ WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
+ WS6: Galaxy API
Dannon Baker
5:30 diff --git a/content/events/gcc2013/abstracts/posters/index.md b/content/events/gcc2013/abstracts/posters/index.md index 705c9a72d7..1042961199 100644 --- a/content/events/gcc2013/abstracts/posters/index.md +++ b/content/events/gcc2013/abstracts/posters/index.md @@ -45,7 +45,7 @@ Links: ### P3: BioBlend - automating bioinformatics with Galaxy and CloudMan -**Clare Sloggett**1, [Nuwan Goonasekera](http://versi.edu.au/about-us/versi-team#Nuwan)1,2,4, [Enis Afgan](/src/people/enis-afgan/index.md)1,3,4 +**Clare Sloggett**1, [Nuwan Goonasekera](http://versi.edu.au/about-us/versi-team#Nuwan)1,2,4, [Enis Afgan](/people/enis-afgan/)1,3,4 1 Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne
2 Victorian eResearch Strategic Initiative (VeRSI), University of Melbourne, Melbourne, Australia
diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index f93cb18858..1ce639dfb9 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -37,9 +37,9 @@ Victoria is an assistant professor of [Statistics](http://www.stat.columbia.edu/ ### Reproducible research and the 90/10 rule: Improving the ratio of light script to dark script matter in your Galaxy -
+
-**[Ross Lazarus](/src/people/fubar/index.md)1**, Antony Kaspi1, Mark Ziemann1 and The [Galaxy Team](/src/galaxy-team/index.md) 2. +**[Ross Lazarus](/people/fubar/index.md)1**, Antony Kaspi1, Mark Ziemann1 and The [Galaxy Team](/src/galaxy-team/) 2. 1 BakerIDI Heart and Diabetes Research Institute, 75 Commercial Rd, Melbourne, VIC 3004, Australia
2 http://wiki.galaxyproject.org[/GalaxyTeam](/src/events/gcc2013/abstracts/talks/GalaxyTeam/index.md) @@ -257,7 +257,7 @@ We show examples of spatial co-localization of chromatin states and fusion trans
-**[Mike Lelivelt](/src/people/mike-lelivelt/index.md)1** +**[Mike Lelivelt](/people/mike-lelivelt/)1** 1 Director of Bioinformatics and Software Products, [Ion Torrent, part of Life Technologies](http://lifetech.com) @@ -271,7 +271,7 @@ Ion Torrent has invented the first device—a new semiconductor chip—capable o
 
-**[Anton Nekrutenko](/src/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/index.md)2** +**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -284,7 +284,7 @@ An overview of where the Galaxy Project is and where it is going. ### BioBlend - automating bioinformatics with Galaxy and CloudMan -**Clare Sloggett**1, [Nuwan Goonasekera](http://versi.edu.au/about-us/versi-team#Nuwan)1,2,4, [Enis Afgan](/src/people/enis-afgan/index.md)1,3,4 +**Clare Sloggett**1, [Nuwan Goonasekera](http://versi.edu.au/about-us/versi-team#Nuwan)1,2,4, [Enis Afgan](/people/enis-afgan/)1,3,4 1 Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne
2 Victorian eResearch Strategic Initiative (VeRSI), University of Melbourne, Melbourne, Australia
@@ -365,9 +365,9 @@ In this talk, we will present Globus Genomics which is a robust, scalable, and f ### Galaxy-P: Beyond Proteomics -
+
-**[John Chilton](/src/people/john-chilton/index.md)**1, James Johnson1, Getiria Onsongo1, Ebbing de Jong1, Pratik Jagtap1, Timothy Griffin2 +**[John Chilton](/people/john-chilton/)**1, James Johnson1, Getiria Onsongo1, Ebbing de Jong1, Pratik Jagtap1, Timothy Griffin2 1 University of Minnesota Supercomputing Institute, Minneapolis, Minnesota, USA
2 University of Minnesota, Minneapolis, Minnesota, USA @@ -410,7 +410,7 @@ The experience gave us new perspectives to improve our development and productio
SanjayJoshi
-**[Sanjay Joshi](/src/people/sanjay-joshi/index.md)** +**[Sanjay Joshi](/people/sanjay-joshi/)** Chief Technical Officer (CTO), [Life Sciences](http://www.isilon.com/industry/lifesciences). [EMC Isilon Storage Division](http://www.emc.com/isilon) @@ -428,9 +428,9 @@ We will present an overview of the requirements to move Galaxy into the Clinical ### Enhancing the Galaxy Tool Shed -
Greg Von Kuster
+
Greg Von Kuster
-**[Greg von Kuster](/src/people/greg_vonkuster/index.md)**, [Daniel Blankenberg](/src/people/dan/index.md) +**[Greg von Kuster](/people/greg_vonkuster/index.md)**, [Daniel Blankenberg](/src/people/dan/) Penn State / Galaxy Team *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/VonKusterToolShed.pdf), [Vimeo](https://vimeo.com/74347850)* @@ -449,9 +449,9 @@ To ensure the quality of the Tool Shed and the available contributed Utilities, ### How to Create Your Own Web-based, Interactive Visualizations for Galaxy -
+
-**[Carl Eberhard](/src/people/carl-eberhard/index.md)**1, [Jeremy Goecks](/src/people/jeremy-goecks/index.md)1, [The Galaxy Team](/src/galaxy-team/index.md)1,2, [Anton Nekrutenko](/src/people/anton/index.md)2, and [James Taylor](/src/people/james-taylor/index.md)1 +**[Carl Eberhard](/people/carl-eberhard/index.md)**1, [Jeremy Goecks](/people/jeremy-goecks/index.md)1, [The Galaxy Team](/src/galaxy-team/index.md)1,2, [Anton Nekrutenko](/src/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 1 Emory University
2 Penn State University @@ -466,9 +466,9 @@ In this talk, we describe how to create your own visualization for Galaxy. We pr ### Managing Galaxy's Built-in Data -
+
-**[Daniel Blankenberg](/src/people/dan/index.md)** +**[Daniel Blankenberg](/people/dan/)** [Galaxy Team](/src/galaxy-team/index.md) and Penn State University @@ -484,9 +484,9 @@ Data Managers can be defined locally or installed automatically from a Tool Shed ### Contributing to Galaxy -
+
-**[Dannon Baker](/src/people/dannon-baker/index.md)**1, [Nate Coraor](/src/people/nate/index.md)2, [John Chilton](/src/people/john-chilton/index.md)3 +**[Dannon Baker](/people/dannon-baker/index.md)**1, [Nate Coraor](/people/nate/)2, [John Chilton](/src/people/john-chilton/)3 1 Emory University
2 Penn State
diff --git a/content/events/gcc2013/bof/galaxy-admins/index.md b/content/events/gcc2013/bof/galaxy-admins/index.md index 4615f32836..25fde6f24f 100644 --- a/content/events/gcc2013/bof/galaxy-admins/index.md +++ b/content/events/gcc2013/bof/galaxy-admins/index.md @@ -36,9 +36,9 @@ The [tentative time and location](/src/events/gcc2013/bof/index.md#bof-schedule) If you are interested, please add your name below and/or send an email to [Dave Clements](mailto:clements AT galaxyproject DOT org). There were about 21 people present, including: -* [Dave Clements](/src/people/dave-clements/index.md) +* [Dave Clements](/people/dave-clements/) * Shaun Webb -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * Peter Li * [Christian Andreetta](http://www.computing.uni.no/staff?nickname=christiana) * Srinivas Maddhi diff --git a/content/events/gcc2013/bof/galaxy-professionals/index.md b/content/events/gcc2013/bof/galaxy-professionals/index.md index 6c8c5799e7..46c46842b3 100644 --- a/content/events/gcc2013/bof/galaxy-professionals/index.md +++ b/content/events/gcc2013/bof/galaxy-professionals/index.md @@ -49,10 +49,10 @@ The [time and location](/src/events/gcc2013/bof/index.md#bof-schedule) for this If you are interested, please add your name below and/or send an email to [Ross Lazarus](mailto:ross DOT lazarus AT gmail DOT com). -* [Ross Lazarus](/src/people/fubar/index.md) +* [Ross Lazarus](/people/fubar/) * Mo Heydarian * Srinivas Maddhi -* [Daniel Blankenberg](/src/people/dan/index.md) +* [Daniel Blankenberg](/people/dan/) * Your name here.. ## Questions? diff --git a/content/events/gcc2013/bof/public-galaxy-servers/index.md b/content/events/gcc2013/bof/public-galaxy-servers/index.md index 2943bc6285..9c6baa518b 100644 --- a/content/events/gcc2013/bof/public-galaxy-servers/index.md +++ b/content/events/gcc2013/bof/public-galaxy-servers/index.md @@ -31,7 +31,7 @@ The [tentative time and location](/src/events/gcc2013/bof/index.md#bof-schedule) If you are interested, please add your name below and/or send an email to [Dave Clements](mailto:clements AT galaxyproject DOT org). -* [Dave Clements](/src/people/dave-clements/index.md), Galaxy Project +* [Dave Clements](/people/dave-clements/), Galaxy Project * [Dorine Francheteau](/src/galaxy-team/index.md), Galaxy Project * Eric Kuyt, Central Veterinary Institute of Wageningen UR (CVI) * Jacqueline Lee, University of Calgary diff --git a/content/events/gcc2013/bof/tool-developers/index.md b/content/events/gcc2013/bof/tool-developers/index.md index 97018c4ace..f88a06ca86 100644 --- a/content/events/gcc2013/bof/tool-developers/index.md +++ b/content/events/gcc2013/bof/tool-developers/index.md @@ -33,9 +33,9 @@ If you are interested, please add your name below and/or send an email to the [I * [Björn Grüning](mailto:bjoern.gruening AT pharmazie DOT uni-freiburg DOT de) * [JJ Johnson](mailto:jj AT umn DOT edu) * Peter Cock -* [Greg Von Kuster](/src/people/greg_vonkuster/index.md) -* [Dave Bouvier](/src/people/dave-bouvier/index.md) -* [Dan Blankenberg](/src/people/dan/index.md) +* [Greg Von Kuster](/people/greg_vonkuster/) +* [Dave Bouvier](/people/dave-bouvier/) +* [Dan Blankenberg](/people/dan/) * [Christian Andreetta](http://www.computing.uni.no/staff?nickname=christiana) * Lionel Guy, Uppsala University * Christos Kannas, University of Cyprus diff --git a/content/events/gcc2013/lightning/index.md b/content/events/gcc2013/lightning/index.md index 73f74028a4..ae4146581f 100644 --- a/content/events/gcc2013/lightning/index.md +++ b/content/events/gcc2013/lightning/index.md @@ -7,7 +7,7 @@ title: Lightning Talks -Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/src/people/fubar/index.md)) and [Session 8 on Tuesday](/src/events/gcc2013/program/index.md#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md)). **No more than half the lightning talk slots will be allocated before the meeting.** +Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/people/fubar/index.md)) and [Session 8 on Tuesday](/src/events/gcc2013/program/index.md#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/)). **No more than half the lightning talk slots will be allocated before the meeting.** If you wish to give a lightning talk, please send an abstract to [GCC2013 Scientific Committee](mailto:gcc2013-sci AT galaxyproject DOT org), either * any time before the start of [Session 2](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (to be considered for Monday or Tuesday slots), or @@ -23,7 +23,7 @@ There are two lightning talk sessions, one on each day of the [main meeting](/sr ### Day 1: Monday 1 July -During [Session 4](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july), moderated by [Ross Lazarus](/src/people/fubar/index.md). +During [Session 4](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july), moderated by [Ross Lazarus](/people/fubar/). #### Medilaxy: A Galaxy Platform For Medical Image Analysis @@ -164,7 +164,7 @@ A quick overview of the Galaxy source code organization. This can be useful for ### Day 2: Tuesday 2 July -During [Session 8](/src/events/gcc2013/program/index.md#day-2-main-meeting-2-july), moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md). +During [Session 8](/src/events/gcc2013/program/index.md#day-2-main-meeting-2-july), moderated by [Hans-Rudolf Hotz](/people/hansrudolf-hotz/). #### How to set up a Galaxy service you can count upon @@ -248,7 +248,7 @@ Our team, in collaboration with spectrometry plateforms, implements several tool
[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/GLM_GSEALightning.pdf)
-**[Ross Lazarus](/src/people/fubar/index.md)**, Mark Ziemann and Antony Kaspi. +**[Ross Lazarus](/people/fubar/)**, Mark Ziemann and Antony Kaspi. Baker IDI Heart and Diabetes Institute @@ -361,14 +361,14 @@ This is your opportunity to give an impassioned and enthralling talk about somet ## Slides -* Your slides (as PDF or PowerPoint) should be on the presentation computer before the session starts (talk to [Dave Clements](/src/people/dave-clements/index.md)) to minimize the risk of BYOD. +* Your slides (as PDF or PowerPoint) should be on the presentation computer before the session starts (talk to [Dave Clements](/people/dave-clements/)) to minimize the risk of BYOD. * You can BYOD (your own computer or whatever) but you are advised not to. * **If you do BYOD, we will start swapping out your device at 2 minutes left, rather than 1.** * Connection and fiddling time beyond the first minute comes out of your 5 minutes and ***is painful, for everyone.*** ## Gratuitous Advice -From [Ross Lazarus](/src/people/fubar/index.md), *Benevolent Lightning Session Moderator for Life* +From [Ross Lazarus](/people/fubar/), *Benevolent Lightning Session Moderator for Life* * Good lightning talks are well rehearsed and very, very focussed. * Plan on talking to 5 or 6 slides diff --git a/content/events/gcc2013/organizers/index.md b/content/events/gcc2013/organizers/index.md index ee5d677f8f..c6bacdee66 100644 --- a/content/events/gcc2013/organizers/index.md +++ b/content/events/gcc2013/organizers/index.md @@ -15,7 +15,7 @@ The GCC2013 Organizing Committee is responsible for event planning. The Organiz * **[Nils Damm Christophersen](http://www.mn.uio.no/ifi/english/people/aca/nilsch/index.html)** * [University of Oslo](http://www.uio.no/)

-* **[Dave Clements](/src/people/dave-clements/index.md)** +* **[Dave Clements](/people/dave-clements/)** * [Emory University](http://emory.edu/)

* **[Ingeborg Bjorvand Engh](http://www.mn.uio.no/ifi/english/people/aca/ingebbj/)** * [University of Oslo](http://www.uio.no/)

@@ -32,13 +32,13 @@ The Scientific Committee can be reached at [gcc2013 DASH sci AT galaxyproject DO * **[Nils Damm Christophersen](http://www.mn.uio.no/ifi/english/people/aca/nilsch/index.html)** * [University of Oslo](http://www.uio.no/)

-* **[Anton Nekrutenko](/src/people/anton/index.md)** +* **[Anton Nekrutenko](/people/anton/)** * [Penn State University](http://www.psu.edu)

* **[Karen Reddy](http://biolchem.bs.jhmi.edu/pages/facultydetail.aspx?FID=343)** * [Johns Hopkins University](http://jhu.edu/)

* **[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/index.html)** * [University of Oslo](http://www.uio.no/)

-* **[James Taylor](/src/people/james-taylor/index.md)**, Committee Chair +* **[James Taylor](/people/james-taylor/)**, Committee Chair * [Emory University](http://emory.edu) diff --git a/content/events/gcc2013/program/index.md b/content/events/gcc2013/program/index.md index e53378e448..6a182a3b07 100644 --- a/content/events/gcc2013/program/index.md +++ b/content/events/gcc2013/program/index.md @@ -33,11 +33,11 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 9:00 - Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
+ Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
- Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00 @@ -45,11 +45,11 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 12:30 - The Galaxy API
Nate Coraor, Carl Eberhard
- Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
+ The Galaxy API
Nate Coraor, Carl Eberhard
+ Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30 @@ -57,9 +57,9 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 15:00 - Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
- Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
- Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
+ Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
+ Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
+ Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
@@ -126,7 +126,7 @@ The first day of the conference will feature [accepted talks](/src/events/gcc201 10:10 -
Slides, Vimeo
Reproducible research and the 90/10 rule: Improving the ratio of light script to dark script matter in your Galaxy
Ross Lazarus, BakerIDI
+
Slides, Vimeo
Reproducible research and the 90/10 rule: Improving the ratio of light script to dark script matter in your Galaxy
Ross Lazarus, BakerIDI
10:30 @@ -212,12 +212,12 @@ The first day of the conference will feature [accepted talks](/src/events/gcc201 16:10-17:30 - Session 4
Moderator: Ross Lazarus, BakerIDI + Session 4
Moderator: Ross Lazarus, BakerIDI - + @@ -228,7 +228,7 @@ The first day of the conference will feature [accepted talks](/src/events/gcc201 - + @@ -297,7 +297,7 @@ The second and final day of the conference will feature [accepted talks](/src/e
15:50 Ion Torrent Semiconductor Sequencing Update
Mike Lelivelt, Ph.D.
Director of Bioinformatics and Software Products, Ion Torrent, part of Life Technologies
Platinum Sponsor Presentation 		Ion Torrent Semiconductor Sequencing Update
Mike Lelivelt, Ph.D.
Director of Bioinformatics and Software Products, Ion Torrent, part of Life Technologies
Platinum Sponsor Presentation 		 Ion Torrent
Slides
Medilaxy: A Galaxy Platform For Medical Image Analysis
Marco Carnini, Johannes Gutenberg University
PDF, PPTX
Establishing a genomics analysis workbench
Enis Afgan, Victorian Life Sciences Computation Initiative, University of Melbourne
PDF, PPTX
Establishing a genomics analysis workbench
Enis Afgan, Victorian Life Sciences Computation Initiative, University of Melbourne
PDF, PPTX
LiSIs: a Galaxy-based platform for Life Science Informatics Research
Christos Kannas, University of Cyprus
- + @@ -325,7 +325,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - +
9:10
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
9:40
11:10-12:30 Session 6: Extending Galaxy
Moderator: Jennifer Hillman-Jackson, Penn State University		 Session 6: Extending Galaxy
Moderator: Jennifer Hillman-Jackson, Penn State University
@@ -338,7 +338,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - + @@ -346,7 +346,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - +
11:30
Slides, Prezi, Vimeo
Galaxy-P: Beyond Proteomics
John Chilton, University of Minnesota Supercomputing Institute
Slides, Prezi, Vimeo
Galaxy-P: Beyond Proteomics
John Chilton, University of Minnesota Supercomputing Institute
11:50
12:10
Slides, Vimeo
EMC Isilon
The Clinical Galaxy: A validated platform initiative
Sanjay Joshi
Chief Technical Officer (CTO), Life Sciences, EMC Isilon
Gold Sponsor Presentation
Slides, Vimeo
EMC Isilon
The Clinical Galaxy: A validated platform initiative
Sanjay Joshi
Chief Technical Officer (CTO), Life Sciences, EMC Isilon
Gold Sponsor Presentation
@@ -367,19 +367,19 @@ The second and final day of the conference will feature [accepted talks](/src/e 13:30 -
Slides, Vimeo
Enhancing the Galaxy Tool Shed
Greg Von Kuster, Penn State University
+
Slides, Vimeo
Enhancing the Galaxy Tool Shed
Greg Von Kuster, Penn State University
13:50 -
Slides, Vimeo
How to Create Your Own Web-based, Interactive Visualizations for Galaxy
Carl Eberhard, Emory University
+
Slides, Vimeo
How to Create Your Own Web-based, Interactive Visualizations for Galaxy
Carl Eberhard, Emory University
14:05 -
Slides, Vimeo
Managing Galaxy's Built-in Data
Daniel Blankenberg, Penn State University
+
Slides, Vimeo
Managing Galaxy's Built-in Data
Daniel Blankenberg, Penn State University
14:20 -
Slides, Vimeo
Contributing to Galaxy
Dannon Baker, Emory University
+
Slides, Vimeo
Contributing to Galaxy
Dannon Baker, Emory University
@@ -390,7 +390,7 @@ The second and final day of the conference will feature [accepted talks](/src/e 15:50-17:30 - Session 8
Moderator: Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research
+ Session 8
Moderator: Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research
@@ -410,7 +410,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - + diff --git a/content/events/gcc2013/training-day/index.md b/content/events/gcc2013/training-day/index.md index 8a1ca31a8f..2f66e311b9 100644 --- a/content/events/gcc2013/training-day/index.md +++ b/content/events/gcc2013/training-day/index.md @@ -39,11 +39,11 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - + - - + + @@ -51,11 +51,11 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - - + + - + @@ -63,9 +63,9 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - - - + + + @@ -114,7 +114,7 @@ See each individual workshop's list of prerequisite for specifics.
Slides
Workflow4Metabo
Gildas Le Corguille, UPMC-CNRS
Slides
GLM for testing differential expression and GSEA in Galaxy
Ross Lazarus, Baker IDI Heart and Diabetes Institute
Slides
GLM for testing differential expression and GSEA in Galaxy
Ross Lazarus, Baker IDI Heart and Diabetes Institute
Slides
Analysis of DNA methylation data using galaxy
Pavan Videm, University of Freiburg
9:00 Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
 Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
 Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
 Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00
12:30 The Galaxy API
Nate Coraor, Carl Eberhard
 Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
 The Galaxy API
Nate Coraor, Carl Eberhard
 Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
 RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30
15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
- + @@ -144,7 +144,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University 		Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University
Content
- + @@ -269,7 +269,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University 		Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University
Content
- + @@ -336,7 +336,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Erik Garrison, Boston College
Anton Nekrutenko, Penn State University 		Erik Garrison, Boston College
Anton Nekrutenko, Penn State University
Content
- + @@ -371,7 +371,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI 		Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI
Content
- + @@ -405,7 +405,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University 		Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University
Content
- + @@ -446,7 +446,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University 		Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University
Content
- + @@ -480,7 +480,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Nate Coraor, Penn State University
Carl Eberhard, Emory University 		Nate Coraor, Penn State University
Carl Eberhard, Emory University
Content
- + diff --git a/content/events/gcc2014/abstracts/posters/index.md b/content/events/gcc2014/abstracts/posters/index.md index 4b177282fe..72bcd031b0 100644 --- a/content/events/gcc2014/abstracts/posters/index.md +++ b/content/events/gcc2014/abstracts/posters/index.md @@ -246,7 +246,7 @@ Using this approach, research group members are fully responsible for deploying ## P13: Argument Parsing Libraries for Automatic Galaxy XML Generation -**[Helena Rasche](/src/people/helena-rasche/index.md)1** and Dr. Ryland F. Young1 +**[Helena Rasche](/people/helena-rasche/)1** and Dr. Ryland F. Young11 [Center for Phage Technology](https://cpt.tamu.edu), Texas A&M University, College Station, TX @@ -461,7 +461,7 @@ On March 5th, 2014 a team of system administrators and bioinformaticians conduct ## P26: Galaxy Training Network -**[Dave Clements](/src/people/dave-clements/index.md)1,2**, [Vicky Schneider](http://www.tgac.ac.uk/training-outreach/vicky-schneider/)3, [Nikhil Joshi](http://bioinformatics.ucdavis.edu/contact-us/)4, [Joseph Fass](http://bioinformatics.ucdavis.edu/contact-us/)4, [Monica Britton](http://bioinformatics.ucdavis.edu/contact-us/)4, [Andrew Lonie](http://www.msi.unimelb.edu.au/people/andrew-lonie/)5,6, [Simon Gladman](http://www.vlsci.org.au/researcher/sgladman)5,7, [Mark Crowe](http://www.qfab.org/mark-crowe/)8 +**[Dave Clements](/people/dave-clements/)1,2**, [Vicky Schneider](http://www.tgac.ac.uk/training-outreach/vicky-schneider/)3, [Nikhil Joshi](http://bioinformatics.ucdavis.edu/contact-us/)4, [Joseph Fass](http://bioinformatics.ucdavis.edu/contact-us/)4, [Monica Britton](http://bioinformatics.ucdavis.edu/contact-us/)4, [Andrew Lonie](http://www.msi.unimelb.edu.au/people/andrew-lonie/)5,6, [Simon Gladman](http://www.vlsci.org.au/researcher/sgladman)5,7, [Mark Crowe](http://www.qfab.org/mark-crowe/)81 [Galaxy Project](http://galaxyproject.org)
2 [Johns Hopkins University](http://www.jhu.edu), Baltimore, Maryland, United States
diff --git a/content/events/gcc2014/abstracts/talks/index.md b/content/events/gcc2014/abstracts/talks/index.md index 37156f8d58..eeba71c826 100644 --- a/content/events/gcc2014/abstracts/talks/index.md +++ b/content/events/gcc2014/abstracts/talks/index.md @@ -136,7 +136,7 @@ As a trusted industry leader in designing and implementing effective scientific
 
-**[Anton Nekrutenko](/src/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/index.md)2** +**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -151,7 +151,7 @@ An overview of where the Galaxy Project is and where it is going.
-**[Mike Lelivelt](/src/people/mike-lelivelt/index.md)**1 +**[Mike Lelivelt](/people/mike-lelivelt/)**11 Director of Bioinformatics and Software Products, [Ion Torrent, part of Life Technologies](http://www.lifetechnologies.com/us/en/home/brands/ion-torrent.html) @@ -167,7 +167,7 @@ An overview of where the Galaxy Project is and where it is going.
Greg Von Kuster
-**[Greg von Kuster](/src/people/greg_vonkuster/index.md)1** and the [Galaxy Team](/src/galaxy-team/index.md) +**[Greg von Kuster](/people/greg_vonkuster/index.md)1** and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu/), State College, Pennsylvania, United States
@@ -185,7 +185,7 @@ Here we'll examine the various components and steps that comprise this process.
Peter Cock
-**[Peter Cock](http://www.hutton.ac.uk/staff/peter-cock)1,** [John Chilton](/src/people/john-chilton/index.md)2, [Björn Grüning](https://github.com/bgruening)3, [Jim Johnson](https://github.com/jj-umn)4, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo)5 +**[Peter Cock](http://www.hutton.ac.uk/staff/peter-cock)1,** [John Chilton](/people/john-chilton/)2, [Björn Grüning](https://github.com/bgruening)3, [Jim Johnson](https://github.com/jj-umn)4, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo)51 [The James Hutton Institute](http://www.hutton.ac.uk/), Scotland, United Kingdom
2 Department of Biochemistry and Molecular Biology, Penn State University, United States
@@ -230,7 +230,7 @@ We present a Galaxy based web server for processing and visualizing deeply seque
GCC2014 Hackathon Participants
-**[Dannon Baker](/src/people/dannon-baker/index.md)1, [Brad Chapman](http://bcbio.wordpress.com/)2, [John Chilton](/src/people/john-chilton/index.md)3, [Kyle Ellrott](http://www.soe.ucsc.edu/people/kellrott)4, and [GCC2014 Hackathon Participants](/src/events/gcc2014/hackathon/index.md)** +**[Dannon Baker](/people/dannon-baker/index.md)1, [Brad Chapman](http://bcbio.wordpress.com/)2, [John Chilton](/people/john-chilton/)3, [Kyle Ellrott](http://www.soe.ucsc.edu/people/kellrott)4, and [GCC2014 Hackathon Participants](/src/events/gcc2014/hackathon/)** 1 [Johns Hopkins University](http://jhu.edu/), Baltimore Maryland, United States
2 [Harvard University](http://harvard.edu), Cambridge, Massachusetts, United States
@@ -247,9 +247,9 @@ In this talk, we’ll very briefly describe our Galaxy Hackathon goals and provi ## More Options, Less Time: Streamlining Access to Reference Datasets -
Dan Blenkenberg
+
Dan Blenkenberg
-**[Daniel Blankenberg](/src/people/dan/index.md)1** and the [Galaxy Team](/src/galaxy-team/index.md)2 +**[Daniel Blankenberg](/people/dan/index.md)1** and the [Galaxy Team](/src/galaxy-team/)21 [Penn State University](http://psu.edu), State College, Pennsylvania, United States
2 [http://galaxyproject.org/](http://galaxyproject.org/) @@ -266,9 +266,9 @@ Here, we describe a new set of resources that aim to rectify this situation. The ## Building More Powerful Galaxy Workflows with Dataset Collections -
John Chilton
+
John Chilton
-**[John Chilton](/src/people/john-chilton/index.md)1** and the [Galaxy Team](/src/galaxy-team/index.md) +**[John Chilton](/people/john-chilton/index.md)1** and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu), State College, Pennsylvania, United States @@ -301,9 +301,9 @@ Dataset collections are a powerful new feature that greatly enhance the expressi ## Lab Specimen Tracking with Galaxy -
Martin Čech
+
Martin Čech
-**[Martin Čech](/src/people/marten/index.md)1**, [Pavel Švéda](http://www.linkedin.com/in/pavelsveda)1, [Ondřej Fabián](https://www.linkedin.com/pub/ondrej-fabian/33/6a5/1b8)1 and the [Galaxy Team](/src/galaxy-team/index.md) +**[Martin Čech](/people/marten/index.md)1**, [Pavel Švéda](http://www.linkedin.com/in/pavelsveda)1, [Ondřej Fabián](https://www.linkedin.com/pub/ondrej-fabian/33/6a5/1b8)1 and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu), State College, Pennsylvania, United States @@ -398,7 +398,7 @@ GI UV scales to truly extraordinary levels – today up to 2,560 physical cores
Olivier Inizan Mikael Loaec
-**[Olivier Inizan](https://urgi.versailles.inra.fr/About-us/Team/Genome-analysis/Olivier-Inizan)1, [Mikael Loaec](https://urgi.versailles.inra.fr/About-us/Team/Genome-analysis/Mikael-Loaec)1**, [Helena Rasche](/src/people/helena-rasche/index.md)2, [Hadi Quesneville](https://urgi.versailles.inra.fr/About-us/Team/Management-staff/Hadi-Quesneville)1 +**[Olivier Inizan](https://urgi.versailles.inra.fr/About-us/Team/Genome-analysis/Olivier-Inizan)1, [Mikael Loaec](https://urgi.versailles.inra.fr/About-us/Team/Genome-analysis/Mikael-Loaec)1**, [Helena Rasche](/people/helena-rasche/)2, [Hadi Quesneville](https://urgi.versailles.inra.fr/About-us/Team/Management-staff/Hadi-Quesneville)11 [URGI-INRA](https://urgi.versailles.inra.fr/), Versailles, France 2 [Center for Phage Technology](https://cpt.tamu.edu/), [Texas A&M University](http://tamu.edu), College Station, Texas, United States @@ -419,7 +419,7 @@ Here we describe our progress towards an automation process for the deployment o
Andrew Lonie
-**[Andrew Lonie](http://www.msi.unimelb.edu.au/people/andrew-lonie/)1**, [Enis Afgan](/src/people/enis-afgan/index.md)2,3, [Ron Horst](http://au.linkedin.com/pub/ron-horst/0/9a2/550)4, [Simon Gladman](http://www.vlsci.org.au/researcher/sgladman)5, [Clare Sloggett](http://www.vlsci.org.au/researcher/csloggett)1, [Nuwan Goonasekera](http://www.vlsci.org.au/researcher/ngoonasekera)1, Igor Manukin4, [Yousef Kowsar](http://www.vlsci.org.au/researcher/ykowsar)4 +**[Andrew Lonie](http://www.msi.unimelb.edu.au/people/andrew-lonie/)1**, [Enis Afgan](/people/enis-afgan/)2,3, [Ron Horst](http://au.linkedin.com/pub/ron-horst/0/9a2/550)4, [Simon Gladman](http://www.vlsci.org.au/researcher/sgladman)5, [Clare Sloggett](http://www.vlsci.org.au/researcher/csloggett)1, [Nuwan Goonasekera](http://www.vlsci.org.au/researcher/ngoonasekera)1, Igor Manukin4, [Yousef Kowsar](http://www.vlsci.org.au/researcher/ykowsar)41 [Life Sciences Computation Centre](http://www.vlsci.org.au/), [University of Melbourne](http://www.unimelb.edu.au/), Australia
2 [University of Melbourne](http://www.unimelb.edu.au/), Australia
@@ -462,7 +462,7 @@ This talk will be about our experiences while integrating Galaxy with GenomeClou
Nuwan Goonasekera
-[Enis Afgan](/src/people/enis-afgan/index.md)1,2, Derek Benson3, and **[Nuwan Goonasekera](http://www.vlsci.org.au/researcher/ngoonasekera)1** +[Enis Afgan](/people/enis-afgan/)1,2, Derek Benson3, and **[Nuwan Goonasekera](http://www.vlsci.org.au/researcher/ngoonasekera)1** 1 [VLSCI](http://www.vlsci.org.au/), University of Melbourne, Melbourne, Australia
2 CIR, RBI, Zagreb, Croatia
diff --git a/content/events/gcc2014/bofs/branch-release-merge/index.md b/content/events/gcc2014/bofs/branch-release-merge/index.md index 6dc2ad5092..19e331e101 100644 --- a/content/events/gcc2014/bofs/branch-release-merge/index.md +++ b/content/events/gcc2014/bofs/branch-release-merge/index.md @@ -49,7 +49,7 @@ Those managing a local Galaxy instance with code customizations. If you are interested, please add your name below and/or send an email to [Nikolay Aleksandrov Vazov](http://www.usit.uio.no/om/organisasjon/uav/itf/ft/ansatte/nikolaiv/index.html). * [Nikolay Aleksandrov Vazov](http://www.usit.uio.no/om/organisasjon/uav/itf/ft/ansatte/nikolaiv/index.html) -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * Peter Cock * ... diff --git a/content/events/gcc2014/bofs/galaxy-admins/index.md b/content/events/gcc2014/bofs/galaxy-admins/index.md index d4cc7e0e09..0a34a38281 100644 --- a/content/events/gcc2014/bofs/galaxy-admins/index.md +++ b/content/events/gcc2014/bofs/galaxy-admins/index.md @@ -15,7 +15,7 @@ When: **Wednesday, July 2, 5:45pm** Where: **Multipurpose Room 324** -Contact: [Dave Clements](/src/people/dave-clements/index.md) +Contact: [Dave Clements](/people/dave-clements/) # Description @@ -45,13 +45,13 @@ If you manage, or are about to manage, a Galaxy installation, then this is an ex # Attendees -If you are interested, please add your name below and/or send an email to [Dave Clements](/src/people/dave-clements/index.md) +If you are interested, please add your name below and/or send an email to [Dave Clements](/people/dave-clements/) -* [Dave Clements](/src/people/dave-clements/index.md) -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Dave Clements](/people/dave-clements/) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * Sebastian Schaaf -* [Helena Rasche](/src/people/helena-rasche/index.md) -* [Dan Blankenberg](/src/people/dan/index.md) +* [Helena Rasche](/people/helena-rasche/) +* [Dan Blankenberg](/people/dan/) * Christine Walls * Alistair Chilcott * Nathan Cole @@ -59,8 +59,8 @@ If you are interested, please add your name below and/or send an email to [Dave * David van Enckevort * Leon Mei * Melissa Cline -* [Dannon Baker](/src/people/dannon-baker/index.md) -* [James Taylor](/src/people/james-taylor/index.md) +* [Dannon Baker](/people/dannon-baker/) +* [James Taylor](/people/james-taylor/) * Kyle Elrott * Nikolay Vazov * Derek Benson @@ -75,7 +75,7 @@ If you are interested, please add your name below and/or send an email to [Dave * Ulf Schaefer * JJ Johnson * Ira Cooke -* [John Chilton](/src/people/john-chilton/index.md) +* [John Chilton](/people/john-chilton/) * Nuria Lozano-Garcia * Eric Petkau * Carsten Rundsten diff --git a/content/events/gcc2014/bofs/galaxy-end-users/index.md b/content/events/gcc2014/bofs/galaxy-end-users/index.md index 236871284b..86f11ab607 100644 --- a/content/events/gcc2014/bofs/galaxy-end-users/index.md +++ b/content/events/gcc2014/bofs/galaxy-end-users/index.md @@ -98,7 +98,7 @@ End-users of Galaxy who would like to share experiences (or listen to those of o * Anushka Brownley * Ben Busby * Brian Whalen -* [Carl Eberhard](/src/people/carl-eberhard/index.md) +* [Carl Eberhard](/people/carl-eberhard/) * David Hoover * Dawei Lin * Edwin Smith @@ -114,7 +114,7 @@ End-users of Galaxy who would like to share experiences (or listen to those of o * Maria Doyle * Marie Jacques Seignon * Mark Rose -* [Martin Cech](/src/people/marten/index.md) +* [Martin Cech](/people/marten/) * Michael R. Crusoe * Mo Heydarian * Morten Johansen diff --git a/content/events/gcc2014/bofs/heterogeneous/index.md b/content/events/gcc2014/bofs/heterogeneous/index.md index ea55c812ca..da1bca27b3 100644 --- a/content/events/gcc2014/bofs/heterogeneous/index.md +++ b/content/events/gcc2014/bofs/heterogeneous/index.md @@ -13,7 +13,7 @@ When: Tuesday, July 1, 5:45pm Where: Salon A -Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/src/people/john-chilton/index.md), [Nate Coraor](/src/people/nate/index.md), Carrie Ganote +Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/people/john-chilton/index.md), [Nate Coraor](/src/people/nate/), Carrie Ganote ## Description @@ -42,12 +42,12 @@ Anyone (users or admins) interested in leveraging remote or heterogeneous hardwa If you are interested, please add your name below and/or send an email to [Your Name](mailto:your AT email DOT address). * [Philip Blood](mailto:blood AT psc DOT edu) -* [John Chilton](/src/people/john-chilton/index.md) -* [nate Coraor](/src/people/nate/index.md) -* [Helena Rasche](/src/people/helena-rasche/index.md) +* [John Chilton](/people/john-chilton/) +* [nate Coraor](/people/nate/) +* [Helena Rasche](/people/helena-rasche/) * Ben Busby * Aaron Gardner -* [Dan Blankenberg](/src/people/dan/index.md) +* [Dan Blankenberg](/people/dan/) * [Michael R. Crusoe](mailto:mcrusoe AT msu DOT edu) * Cameron Smith * Carrie Ganote diff --git a/content/events/gcc2014/bofs/using-galaxy-ui-overview/index.md b/content/events/gcc2014/bofs/using-galaxy-ui-overview/index.md index 7256464138..2331f5f5ca 100644 --- a/content/events/gcc2014/bofs/using-galaxy-ui-overview/index.md +++ b/content/events/gcc2014/bofs/using-galaxy-ui-overview/index.md @@ -13,7 +13,7 @@ When: Wednesday, July 2, 12:15 pm (lunch) Where: East Room 304 -Contact: [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md) & Karen Reddy +Contact: [Jennifer Hillman-Jackson](/people/jennifer-jackson/) & Karen Reddy diff --git a/content/events/gcc2014/lightning/index.md b/content/events/gcc2014/lightning/index.md index cffaddf9a9..ba91b01834 100644 --- a/content/events/gcc2014/lightning/index.md +++ b/content/events/gcc2014/lightning/index.md @@ -175,7 +175,7 @@ Presented by **Gilda Le Corguillé1** ### Galaxy: Farm to Federation -**Kyle Ellrott1**, [Dannon Baker](/src/people/dannon-baker/index.md)2 +**Kyle Ellrott1**, [Dannon Baker](/people/dannon-baker/)21 UC Santa Cruz
2 John Hopkins University @@ -215,14 +215,14 @@ Lightning talks are your opportunity to give an impassioned and enthralling talk ## Slides -* Your slides (as PDF or PowerPoint) should be on the presentation computer before the session starts (talk to [Dave Clements](/src/people/dave-clements/index.md)) to minimize the risk of BYOD. +* Your slides (as PDF or PowerPoint) should be on the presentation computer before the session starts (talk to [Dave Clements](/people/dave-clements/)) to minimize the risk of BYOD. * You can BYOD (your own computer or whatever) but you are advised not to. * **If you do BYOD, we will start swapping out your device at 2 minutes left, rather than 1.** * Connection and fiddling time beyond the first minute comes out of your 5 minutes and ***is painful, for everyone.*** ## Gratuitous Advice -From [Ross Lazarus](/src/people/fubar/index.md), the (possibly former) *Benevolent Lightning Session Moderator for Life* +From [Ross Lazarus](/people/fubar/), the (possibly former) *Benevolent Lightning Session Moderator for Life* * Good lightning talks are well rehearsed and very, very focussed. * Plan on talking to 5 or 6 slides diff --git a/content/events/gcc2014/organizers/index.md b/content/events/gcc2014/organizers/index.md index 68651d128b..ec458e828b 100644 --- a/content/events/gcc2014/organizers/index.md +++ b/content/events/gcc2014/organizers/index.md @@ -11,7 +11,7 @@ title: Organizers The GCC2014 Organizing Committee is responsible for event planning. - **[Dave Clements](/src/people/dave-clements/index.md)** + **[Dave Clements](/people/dave-clements/)** [Johns Hopkins University](http://jhu.edu/)

**[Mohammad Heydarian](http://epigenetics.jhu.edu/?section=personnelPages&personID=26)** [Johns Hopkins University](http://jhu.edu/)

@@ -26,15 +26,15 @@ Questions? Send the organizers an [email](mailto:gcc2014 DASH org AT groups DOT The GCC2014 Scientific Program Committee is responsible for meeting content, including reviewing and accepting talks, posters, and lightning talks. - **[Jeremy Goecks](/src/people/jeremy-goecks/index.md)** + **[Jeremy Goecks](/people/jeremy-goecks/)** [George Washington University](http://www.gwu.edu/)

**[Jessica Kissinger](http://mango.ctegd.uga.edu/jkissingLab/)** [University of Georgia](http://uga.edu)

- **[Anton Nekrutenko](/src/people/anton/index.md)** + **[Anton Nekrutenko](/people/anton/)** [Penn State University](http://psu.edu/)

**[Karen Reddy](http://biolchem.bs.jhmi.edu/pages/facultydetail.aspx?FID=343)** [Johns Hopkins University](http://jhu.edu/)

- **[James Taylor](/src/people/james-taylor/index.md)** + **[James Taylor](/people/james-taylor/)** [Johns Hopkins University](http://jhu.edu/)

The Scientific Program Committee can [be reached via email](mailto:gcc2014 DASH org AT groups DOT galaxyproject DOT org). @@ -43,11 +43,11 @@ The Scientific Program Committee can [be reached via email](mailto:gcc2014 DASH The GCC2014 Hackathon Organizing Committee is responsible for making the [accompanying hackathon](/src/events/gcc2014/hackathon/index.md) happen. - **[Dannon Baker](/src/people/dannon-baker/index.md)** + **[Dannon Baker](/people/dannon-baker/)** [Johns Hopkins University](http://jhu.edu/)

**[Brad Chapman](http://bcbio.wordpress.com/about/)** [Harvard University](http://compbio.sph.harvard.edu/chb/)

- **[John Chilton](/src/people/john-chilton/index.md)** + **[John Chilton](/people/john-chilton/)** [Penn State University](http://psu.edu/)

**[Kyle Ellrott](https://twitter.com/kellrott)** [University of California Santa Cruz (UCSC)](http://www.soe.ucsc.edu/people/kellrott) diff --git a/content/events/gcc2014/program/index.md b/content/events/gcc2014/program/index.md index 54b01ba4c9..69434e1e45 100644 --- a/content/events/gcc2014/program/index.md +++ b/content/events/gcc2014/program/index.md @@ -40,10 +40,10 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - - - - + + + + @@ -53,8 +53,8 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - - + + @@ -65,9 +65,9 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - - - + + + @@ -197,11 +197,11 @@ Moderator: [Liisa Koski](https://www.linkedin.com/pub/liisa-koski/70/164/b0b), [
Instructors James Taylor, Emory University
Nate Coraor, Penn State University 		James Taylor, Emory University
Nate Coraor, Penn State University
Content
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
- + - +
1:15 State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
1:50 Update on Ion Torrent Sequencing – Accurate, Long Reads
Mike Lelivelt
Director of Bioinformatics and Software Products, Ion Torrent, part of Life Technologies
Platinum Sponsor Presentation 		Update on Ion Torrent Sequencing – Accurate, Long Reads
Mike Lelivelt
Director of Bioinformatics and Software Products, Ion Torrent, part of Life Technologies
Platinum Sponsor Presentation 		 Ion Torrent by Life Technologies
@@ -229,7 +229,7 @@ Moderator: [Ravi Madduri](http://www.mcs.anl.gov/person/ravi-madduri), [Argonne 4:00 - The Galaxy Tool Shed: A Framework for Building Galaxy Tools
Greg von Kuster, Penn State University
+ The Galaxy Tool Shed: A Framework for Building Galaxy Tools
Greg von Kuster, Penn State University
4:20 @@ -260,7 +260,7 @@ Moderator: [Ravi Madduri](http://www.mcs.anl.gov/person/ravi-madduri), [Argonne Ebiogenouest régional initiative : a use case for the structuration of the biologists community
Yvan Le Bras, CNRS, IRISA-INRIA
- Intergalactic travel: Sending usegalaxy.org through the wormhole
Nate Coraor, Galaxy Team, Penn State University
+ Intergalactic travel: Sending usegalaxy.org through the wormhole
Nate Coraor, Galaxy Team, Penn State University
@@ -315,15 +315,15 @@ Moderator: [Mohammad Heydarian](http://epigenetics.jhu.edu/?section=personnelPag 9:10 - The GCC2014 Hackathon
Dannon Baker, Brad Chapman, John Chilton, Kyle Ellrott, and GCC2014 Hackathon Participants
+ The GCC2014 Hackathon
Dannon Baker, Brad Chapman, John Chilton, Kyle Ellrott, and GCC2014 Hackathon Participants
9:30 - More Options, Less Time: Streamlining Access to Reference Datasets
Daniel Blankenberg, Penn State University
+ More Options, Less Time: Streamlining Access to Reference Datasets
Daniel Blankenberg, Penn State University
9:45 - Building More Powerful Galaxy Workflows with Dataset Collections
John Chilton, Penn State University
+ Building More Powerful Galaxy Workflows with Dataset Collections
John Chilton, Penn State University
10:05 @@ -352,7 +352,7 @@ Moderator: [Tom Bair](http://www.medicine.uiowa.edu/humangenetics/biostatistics/ 10:55 - Lab Specimen Tracking with Galaxy
Martin Čech, Penn State University
+ Lab Specimen Tracking with Galaxy
Martin Čech, Penn State University
11:10 @@ -427,7 +427,7 @@ Moderator: [Jessica Kissinger](http://mango.ctegd.uga.edu/jkissingLab/), [Univer
**Session 8**
-Moderator: [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [George Washington University](http://www.gwu.edu/)
+Moderator: [Jeremy Goecks](/people/jeremy-goecks/), [George Washington University](http://www.gwu.edu/)
diff --git a/content/events/gcc2014/training-day/admin-walkthrough/index.md b/content/events/gcc2014/training-day/admin-walkthrough/index.md index b8fbbf9276..4c9a409f61 100644 --- a/content/events/gcc2014/training-day/admin-walkthrough/index.md +++ b/content/events/gcc2014/training-day/admin-walkthrough/index.md @@ -9,7 +9,7 @@ title: "Tutorial: Galaxy Installation and Administration"
GCC2014 Training Day
-[Nate Coraor](/src/people/nate/index.md) and [John Chilton](/src/people/john-chilton/index.md) +[Nate Coraor](/people/nate/index.md) and [John Chilton](/src/people/john-chilton/)
diff --git a/content/events/gcc2014/training-day/index.md b/content/events/gcc2014/training-day/index.md index e8384bf3c4..fbe5b1c922 100644 --- a/content/events/gcc2014/training-day/index.md +++ b/content/events/gcc2014/training-day/index.md @@ -36,10 +36,10 @@ Meeting participants select which Training Day topics to attend when they [regis - - - - + + + + @@ -49,8 +49,8 @@ Meeting participants select which Training Day topics to attend when they [regis - - + + @@ -61,9 +61,9 @@ Meeting participants select which Training Day topics to attend when they [regis - - - + + + @@ -121,7 +121,7 @@ See each individual workshop's list of prerequisite for specifics.
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
- + @@ -212,7 +212,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Tom Bair, University of Iowa
Jennifer Jackson, Penn State University 		Tom Bair, University of Iowa
Jennifer Jackson, Penn State University
Content
- + @@ -257,7 +257,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Jeremy Goecks, George Washington University
Aysam Guerler, Johns Hopkins University 		Jeremy Goecks, George Washington University
Aysam Guerler, Johns Hopkins University
Content
- + @@ -306,7 +306,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Nate Coraor, Penn State University
John Chilton, Penn State University 		Nate Coraor, Penn State University
John Chilton, Penn State University
Content
- + @@ -329,7 +329,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University 		Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University
Content
- + @@ -353,7 +353,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Greg Von Kuster, Penn State University
Björn Grüning, University of Freiburg
Peter Cock, James Hutton Institute 		Greg Von Kuster, Penn State University
Björn Grüning, University of Freiburg
Peter Cock, James Hutton Institute
Content
- + @@ -377,7 +377,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors JJ Johnson, University of Minnesota
Dan Blankenberg, Penn State University 		JJ Johnson, University of Minnesota
Dan Blankenberg, Penn State University
Content
- + @@ -396,7 +396,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors James Taylor, Johns Hopkins University James Taylor, Johns Hopkins University
Content
- + diff --git a/content/events/gcc2015/bofs/data-management-challenges/index.md b/content/events/gcc2015/bofs/data-management-challenges/index.md index 08be4b2473..16146e035f 100644 --- a/content/events/gcc2015/bofs/data-management-challenges/index.md +++ b/content/events/gcc2015/bofs/data-management-challenges/index.md @@ -31,8 +31,8 @@ Wednesday, 8 July, 12:30 (Lunch), in the Franklin Room, JICCC If you are interested, please add your name below and/or send an email to [Brad Langhorst](mailto:langhorst@neb DOT com), **or just show up.** * Brad Langhorst -* [Nate Coraor](/src/people/nate/index.md) -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Nate Coraor](/people/nate/) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * Next Name ## Questions? diff --git a/content/events/gcc2015/bofs/fots/index.md b/content/events/gcc2015/bofs/fots/index.md index facdf6fda8..5a0341ef06 100644 --- a/content/events/gcc2015/bofs/fots/index.md +++ b/content/events/gcc2015/bofs/fots/index.md @@ -12,7 +12,7 @@ When: Tuesday, 7 July, 20:30 Where: we meet at the http://thecellarhouse.co.uk/ -Contact: [Martin Cech](/src/people/marten/index.md) +Contact: [Martin Cech](/people/marten/) ## Description @@ -20,7 +20,7 @@ Tools, dependencies, workflows, datatypes, visualizations, pages, histories, ana ## Audience -All are welcome, even [John](/src/people/john-chilton/index.md) +All are welcome, even [John](/people/john-chilton/) ## When and Where @@ -29,18 +29,18 @@ All are welcome, even [John](/src/people/john-chilton/index.md) ## Who is Participating -If you are interested, please add your name below and/or send an email to [Martin Cech](/src/people/marten/index.md). +If you are interested, please add your name below and/or send an email to [Martin Cech](/people/marten/). -* [Martin Cech](/src/people/marten/index.md) +* [Martin Cech](/people/marten/) * Helena Rasche * John Chilton * Peter Cock * Bjoern Gruening -* [Nate Coraor](/src/people/nate/index.md) -* [Daniel Blankenberg](/src/people/dan/index.md) -* [Nicola Soranzo](/src/people/nicola-soranzo/index.md) +* [Nate Coraor](/people/nate/) +* [Daniel Blankenberg](/people/dan/) +* [Nicola Soranzo](/people/nicola-soranzo/) * Next Name ## Questions? -Send them to [Martin Cech](/src/people/marten/index.md). +Send them to [Martin Cech](/people/marten/). diff --git a/content/events/gcc2015/bofs/galaxy-admins/index.md b/content/events/gcc2015/bofs/galaxy-admins/index.md index 514d73b2f6..52e80d3f2a 100644 --- a/content/events/gcc2015/bofs/galaxy-admins/index.md +++ b/content/events/gcc2015/bofs/galaxy-admins/index.md @@ -17,7 +17,7 @@ When:: Tuesday, 7 July, 18:20 Where:: Franklin Room, JICCC -Contact:: [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), [Dave Clements](/src/people/dave-clements/index.md) +Contact:: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), [Dave Clements](/src/people/dave-clements/) # Audience @@ -30,12 +30,12 @@ This BoF will meet on **Tuesday, 7 July at 18:20, in the Franklin Room, at the J # Participants -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) -* [Dave Clements](/src/people/dave-clements/index.md) -* [Helena Rasche](/src/people/helena-rasche/index.md) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) +* [Dave Clements](/people/dave-clements/) +* [Helena Rasche](/people/helena-rasche/) * Peter Briggs * Peter Cock -* [Nate Coraor](/src/people/nate/index.md) +* [Nate Coraor](/people/nate/) * Oleksandr Moskalenko * Simon Gladman * Aaron Petkau @@ -102,4 +102,4 @@ This BoF will meet on **Tuesday, 7 July at 18:20, in the Franklin Room, at the J # Questions? -Send them to [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/index.md) +Send them to [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/) diff --git a/content/events/gcc2015/bofs/galaxy-scientists/index.md b/content/events/gcc2015/bofs/galaxy-scientists/index.md index cc15611a4a..fd7fb05770 100644 --- a/content/events/gcc2015/bofs/galaxy-scientists/index.md +++ b/content/events/gcc2015/bofs/galaxy-scientists/index.md @@ -12,7 +12,7 @@ When:: Tuesday, 7 July, 12:30 (Lunch) Where:: Franklin Room, JICCC -Contact:: [JenniferJackson](/src/people/jennifer-jackson/index.md) & see [BoF](https://wiki.galaxyproject.org/Events/GCC2015/BoFs/GalaxyScientists) wiki +Contact:: [JenniferJackson](/people/jennifer-jackson/) & see [BoF](https://wiki.galaxyproject.org/Events/GCC2015/BoFs/GalaxyScientists) wiki
## Description @@ -38,7 +38,7 @@ If you are interested, please add your name below. * [jen@galaxyproject.org](mailto:jen@galaxyproject.org), Jennifer Hillman-Jackson * [kreddy4@jhmi.edu](mailto:kreddy4@jhmi.edu), Karen Reddy * Mo Heydarian -* [Dan Blankenberg](/src/people/dan/index.md) +* [Dan Blankenberg](/people/dan/) * Michael Sauria * Gergely Izrael (izi) * Christian Rausch diff --git a/content/events/gcc2015/bofs/galaxy-training-network/index.md b/content/events/gcc2015/bofs/galaxy-training-network/index.md index 5f33d49d42..57c965f1b1 100644 --- a/content/events/gcc2015/bofs/galaxy-training-network/index.md +++ b/content/events/gcc2015/bofs/galaxy-training-network/index.md @@ -11,7 +11,7 @@ When:: Monday, 6 July, 18:50 Where:: Franklin Room, JICCC -Contact:: [Dave Clements](/src/people/dave-clements/index.md), [Andrew Lonie](https://www.vlsci.org.au/researcher/alonie) +Contact:: [Dave Clements](/people/dave-clements/), [Andrew Lonie](https://www.vlsci.org.au/researcher/alonie) The **[Galaxy Training Network (GTN)](https://training.galaxyproject.org/)** will have an in-person [Birds of a Feather](/src/events/gcc2015/bofs/index.md) meetup at the [2015 Galaxy Community Conference (GCC2015)](http://gcc2015.tsl.ac.uk/), held in Norwich, UK, 4-8 July, 2015. @@ -40,10 +40,10 @@ This BoF will be held **Monday, 6 July, 18:50, in the Franklin Room.** ## Participants -* [Dave Clements](/src/people/dave-clements/index.md), organiser +* [Dave Clements](/people/dave-clements/), organiser * [Andrew Lonie](https://www.vlsci.org.au/researcher/alonie), organiser -* [Helena Rasche](/src/people/helena-rasche/index.md) -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Helena Rasche](/people/helena-rasche/) +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * Mark Fernandes * Catriona McInerney * Annette McGrath @@ -56,7 +56,7 @@ This BoF will be held **Monday, 6 July, 18:50, in the Franklin Room.** * Agata Smialowska * Jochen Bick * Brad Langhorst -* [Björn Grüning](/src/people/bjoern-gruening/index.md) +* [Björn Grüning](/people/bjoern-gruening/) * Daniel Sobral * Simon Gladman * Clare Sloggett @@ -147,4 +147,4 @@ Compiled from the [Working Minutes for this BoF](http://bit.ly/gcc2015gtn) and D ## Questions? -Send them to [Dave Clements](/src/people/dave-clements/index.md) and [Andrew Lonie](https://www.vlsci.org.au/researcher/alonie). +Send them to [Dave Clements](/people/dave-clements/) and [Andrew Lonie](https://www.vlsci.org.au/researcher/alonie). diff --git a/content/events/gcc2019/organizers/index.md b/content/events/gcc2019/organizers/index.md index f55897f5ad..329bc97528 100644 --- a/content/events/gcc2019/organizers/index.md +++ b/content/events/gcc2019/organizers/index.md @@ -5,14 +5,14 @@ GCC2019 is hosted by the [Freiburg Galaxy Project](http://www.bioinf.uni-freibur # GCC2019 Organizers * *[Bérénice Batut](http://research.bebatut.fr/)*, [University of Freiburg](https://www.uni-freiburg.de/) -* *[Dave Clements](/src/people/dave-clements/index.md)*, [Johns Hopkins University](https://jhu.edu/) +* *[Dave Clements](/people/dave-clements/)*, [Johns Hopkins University](https://jhu.edu/) * *[Frederik Coppens](https://www.psb.ugent.be/lab-members-and-alumni-frcop)*, [VIB](https://www.psb.ugent.be/), [UGent](https://www.ugent.be), [ELIXIR Belgium](https://www.elixir-belgium.org) * *[Monika Degen-Hellmuth](https://portal.uni-freiburg.de/iif/institut/Personen/direktor/sekretariat)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Rolf Backofen](http://www.bioinf.uni-freiburg.de/~backofen/)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Anika Erxleben](https://github.com/erxleben)*, [University of Freiburg](https://www.uni-freiburg.de/) -* *[Björn Grüning](/src/people/bjoern-gruening/index.md)*, [University of Freiburg](https://www.uni-freiburg.de/) -* *[Mo Heydarian](/src/people/mo-heydarian/index.md)*, [Johns Hopkins University](https://jhu.edu/) -* *[Helena Rasche](/src/people/helena-rasche/index.md)*, [University of Freiburg](https://www.uni-freiburg.de/) +* *[Björn Grüning](/people/bjoern-gruening/)*, [University of Freiburg](https://www.uni-freiburg.de/) +* *[Mo Heydarian](/people/mo-heydarian/)*, [Johns Hopkins University](https://jhu.edu/) +* *[Helena Rasche](/people/helena-rasche/)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Devon Ryan](https://www.researchgate.net/profile/Devon_Ryan)*, [Max Planck Institute of Immunobiology and Epigenetics](https://www.ie-freiburg.mpg.de/) We can be reached at *GCC2019 Organizers <gcc2019-org@lists.galaxyproject.org>* @@ -20,26 +20,26 @@ We can be reached at *GCC2019 Organizers <gcc2019-org@lists.galaxyproject.org # GCC2019 Scientific Program Committee * *[Matthias Bernt](https://www.ufz.de/index.php?en=43047)*, [Helmholtz Centre for Environmental Research – UFZ](https://www.ufz.de/) -* *[Dan Blankenberg](/src/people/dan/index.md)*, [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) +* *[Dan Blankenberg](/people/dan/)*, [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) * *[Gildas Le Corguillé](https://github.com/lecorguille)*, [Station Biologique de Roscoff](http://www.sb-roscoff.fr/) * *[Maria Doyle](https://www.researchgate.net/profile/Maria_Doyle4)*, [Peter MacCallum Cancer Centre](https://www.petermac.org/) * *[Anika Erxleben](https://github.com/erxleben)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Melanie Föll](https://github.com/foellmelanie)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Anne Claire Fouilloux](https://www.mn.uio.no/geo/english/people/adm/annefou/)*, [University of Oslo](https://www.uio.no/) * *[Carrie Ganote](https://www.researchgate.net/profile/Carrie_Ganote)*, [Indiana University](https://iu.edu/) -* *[Jeremy Goecks](/src/people/jeremy-goecks/index.md)*, [Oregon Health & Science University](https://www.ohsu.edu/) -* *[Björn Grüning](/src/people/bjoern-gruening/index.md)*, [University of Freiburg](https://www.uni-freiburg.de/) -* *[Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md)*, [Penn State University](https://www.psu.edu/) +* *[Jeremy Goecks](/people/jeremy-goecks/)*, [Oregon Health & Science University](https://www.ohsu.edu/) +* *[Björn Grüning](/people/bjoern-gruening/)*, [University of Freiburg](https://www.uni-freiburg.de/) +* *[Jennifer Hillman-Jackson](/people/jennifer-jackson/)*, [Penn State University](https://www.psu.edu/) * *[Saskia Hiltemann](https://github.com/shiltemann)*, [ErasmusMC](https://www.erasmusmc.nl/) -* *[Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md)*, [Friedrich Miescher Institute for Biomedical Research](https://fmi.ch/) +* *[Hans-Rudolf Hotz](/people/hansrudolf-hotz/)*, [Friedrich Miescher Institute for Biomedical Research](https://fmi.ch/) * *[Nancy Ide](https://www.cs.vassar.edu/~ide/)*, [Vassar College](https://www.vassar.edu/) * *[Pratik Jagtap](https://www.msi.umn.edu/group/mscls)*, [University of Minnesota](http://umn.edu/) * *[Yvan Le Bras](http://cesco.mnhn.fr/fr/annuaire/yvan-le-bras-6200)*, [Muséum national d’histoire naturelle](https://www.mnhn.fr/) * *[Thomas Manke](https://www.ie-freiburg.mpg.de/bioinformaticsfac)*, [Max Planck Institute of Immunobiology and Epigenetics](https://www.ie-freiburg.mpg.de/) * *[Pablo Moreno](https://www.ebi.ac.uk/about/people/pablo-moreno)*, [EMBL-EBI](https://www.ebi.ac.uk/) -* *[Anton Nekrutenko](/src/people/anton/index.md)*, [Penn State University](https://www.psu.edu/) +* *[Anton Nekrutenko](/people/anton/)*, [Penn State University](https://www.psu.edu/) * *[Krzysztof Poterlowicz](https://www.bradford.ac.uk/life-sciences/chemistry-and-biosciences/our-staff/dr-krzysztof-poterlowicz.php)*, [University of Bradford](https://bradford.ac.uk/external/) -* *[Helena Rasche](/src/people/helena-rasche/index.md)*, [University of Freiburg](https://www.uni-freiburg.de/) +* *[Helena Rasche](/people/helena-rasche/)*, [University of Freiburg](https://www.uni-freiburg.de/) * *[Devon Ryan](https://www.researchgate.net/profile/Devon_Ryan)*, [Max Planck Institute of Immunobiology and Epigenetics](https://www.ie-freiburg.mpg.de/) * *[Beata Scholtz](https://www.researchgate.net/profile/Beata_Scholtz)*, [University of Debrecen](https://unideb.hu/en) * *[Nicola Soranzo](http://www.earlham.ac.uk/nicola-soranzo)*, [Earlham Institute](http://www.earlham.ac.uk/) @@ -50,11 +50,11 @@ The SPC can be reached at *GCC2019 Scientifc Program Committee <gcc2019-sci@l # CollaborationFest Organizers -* *[Dannon Baker](/src/people/dannon-baker/index.md)*, [Johns Hopkins University](https://jhu.edu/) +* *[Dannon Baker](/people/dannon-baker/)*, [Johns Hopkins University](https://jhu.edu/) * *[Frederik Coppens](https://www.elixir-belgium.org/organisation/steeringgroup/frederik-coppens)*, [VIB](http://www.vib.be/) and [ELIXIR Belgium](https://www.elixir-belgium.org/) * *Maria Doyle*, [Peter MacCallum Cancer Centre](https://www.petermac.org/) -* *[Mo Heydarian](/src/people/mo-heydarian/index.md)*, [Johns Hopkins University](https://jhu.edu/) -* *[Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md)*, [Penn State University](http://www.bx.psu.edu) +* *[Mo Heydarian](/people/mo-heydarian/)*, [Johns Hopkins University](https://jhu.edu/) +* *[Jennifer Hillman-Jackson](/people/jennifer-jackson/)*, [Penn State University](http://www.bx.psu.edu) * *[Brad Langhorst](https://scholar.google.com/citations?user=75w73LQAAAAJ&hl=en)*, [New England Biolabs](https://www.neb.com/) * *[Marius van den Beek](https://github.com/mvdbeek)*, [Institut Curie](https://institut-curie.org/) diff --git a/content/events/gccbosc2018/collaboration/index.md b/content/events/gccbosc2018/collaboration/index.md index d3b2a7b6fd..b8ed03e38b 100644 --- a/content/events/gccbosc2018/collaboration/index.md +++ b/content/events/gccbosc2018/collaboration/index.md @@ -98,8 +98,8 @@ CollaborationFest will be at Reed College, the same location as other GCCBOSC 20 # CollaborationFest Organizers * *[Brad Chapman](http://bcb.io/)*, [Harvard T.H. Chan School of Public Health](https://www.hsph.harvard.edu/) -* *[Dannon Baker](/src/people/dannon-baker/index.md)*, [Johns Hopkins University](https://jhu.edu/) -* *[Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md)*, [Penn State University](http://www.bx.psu.edu) +* *[Dannon Baker](/people/dannon-baker/)*, [Johns Hopkins University](https://jhu.edu/) +* *[Jennifer Hillman-Jackson](/people/jennifer-jackson/)*, [Penn State University](http://www.bx.psu.edu) * *[Frederik Coppens](https://www.elixir-belgium.org/organisation/steeringgroup/frederik-coppens)*, [VIB](http://www.vib.be/) and [ELIXIR Belgium](https://www.elixir-belgium.org/) * *[Björn Grüning](https://github.com/bgruening)*, [University of Freiburg](http://www.uni-freiburg.de/) * *[Christian Schudoma](http://www.earlham.ac.uk/christian-schudoma)*, [Earlham Institute](http://www.earlham.ac.uk/) diff --git a/content/events/gccbosc2018/organizers/index.md b/content/events/gccbosc2018/organizers/index.md index 93a840682c..6e7ea18e24 100644 --- a/content/events/gccbosc2018/organizers/index.md +++ b/content/events/gccbosc2018/organizers/index.md @@ -31,7 +31,7 @@ If you have a community specific query you can contact: * *[Christopher Fields](http://hpcbio.illinois.edu/people)*, [University of Illinois](http://illinois.edu/) * *Maria Doyle*, [Peter MacCallum Cancer Centre](https://www.petermac.org/) * *[Peter Cock](http://www.hutton.ac.uk/staff/peter-cock),* [The James Hutton Institute](http://www.hutton.ac.uk/) -* *[Dave Clements](/src/people/dave-clements/index.md)*, [Johns Hopkins University](https://jhu.edu/), GCC2018 Co-Chair +* *[Dave Clements](/people/dave-clements/)*, [Johns Hopkins University](https://jhu.edu/), GCC2018 Co-Chair * *Andrew Chitty*, [Oregon Health and Science University (OHSU)](http://www.ohsu.edu/) * *[Brad Chapman](http://bcb.io/)*, [Harvard T.H. Chan School of Public Health](https://www.hsph.harvard.edu/), BOSC 2018 Co-Chair diff --git a/content/events/gdc2010/index.md b/content/events/gdc2010/index.md index 86803d9c94..4e527a7c8e 100644 --- a/content/events/gdc2010/index.md +++ b/content/events/gdc2010/index.md @@ -33,7 +33,7 @@ contact: Organizers #### Afternoon * [ZFS for NGS data analysis](https://depot.galaxyproject.org/hub/attachments/events/gdc2010/GDC2010_ZFS-for_NGS_Analysis.pdf) - Davide Cittaro -* [Do-It-Yourself Bioinformatics with the FMI Galaxy Server](https://depot.galaxyproject.org/hub/attachments/events/gdc2010/GDC2010DIY_Bioinf_FMI.pdf) - [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +* [Do-It-Yourself Bioinformatics with the FMI Galaxy Server](https://depot.galaxyproject.org/hub/attachments/events/gdc2010/GDC2010DIY_Bioinf_FMI.pdf) - [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * [Cistrome Project: An Integrative Platform to Analyze ChIP-chip/seq Data](https://depot.galaxyproject.org/hub/attachments/events/gdc2010/GDC2010_Cistrome.pdf) - Tao Liu * [Transcriptome Analysis with Galaxy](https://depot.galaxyproject.org/hub/attachments/events/gdc2010/Transcriptome_Analysis_with_Galaxy.pdf) - Gunnar Rätsch diff --git a/content/events/germany2014/index.md b/content/events/germany2014/index.md index 258378da81..40c80a4d9f 100644 --- a/content/events/germany2014/index.md +++ b/content/events/germany2014/index.md @@ -15,14 +15,14 @@ In addition to the [2nd Swiss Galaxy Workshop](/src/events/switzerland2014/index | Time | Speaker | Title | PDF | | ---- | -------- | ------ | ---- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | Introduction: Galaxy as Developer Platform | | -| 9:45 - 10:15 | [Nicola Soranzo](/src/people/nicola-soranzo/index.md) ([CRS4](http://www.crs4.it/)) | BioBlend and BioBlend.objects: high level API for scripting Galaxy analyses | [pdf](https://depot.galaxyproject.org/hub/attachments/documents/presentations/Soranzo_SG2014T.pdf +| 9:30 - 9:45 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | Introduction: Galaxy as Developer Platform | | +| 9:45 - 10:15 | [Nicola Soranzo](/people/nicola-soranzo/) ([CRS4](http://www.crs4.it/)) | BioBlend and BioBlend.objects: high level API for scripting Galaxy analyses | [pdf](https://depot.galaxyproject.org/hub/attachments/documents/presentations/Soranzo_SG2014T.pdf /tmp/AttchmentsWorking//events/germany2014/Soranzo_SG2014T.pdf) | | 10:15 - 10:45 | Jürgen Reymann | Automated Data Pipelines & Intelligent Microscopy | [pdf](https://depot.galaxyproject.org/hub/attachments/AutomatedDataPipelines_IntelligentMicroscopy_JürgenReymann.pdf) | | 11:15 - 11:45 | Sebastian Wilzbach | BioJS 2: taking biological visualization to the next level | [pdf](https://depot.galaxyproject.org/hub/attachments/events/germany2014/attachment_BioJS-Reusable_JavaScript_for_Life_Sciences.pdf), [video](https://www.youtube.com/watch?v=SkMKuj-Q0YI) | | 11:45 - 13:00 | Lunch Break (we will need to find some food nearby) | | 13:00 - 13:30 | Sebastian Schaaf | Galaxy deployment joy in Munich | | -| 13:30 - 14:00 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | Interactive Environments: IPython in Galaxy | | +| 13:30 - 14:00 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | Interactive Environments: IPython in Galaxy | | | 14:30 - 15:30| Open Discussion | | 15:30 - 16:00 | DEPARTURE (... and going to the city) | @@ -39,4 +39,4 @@ We have created a [small map of places to find food and drinks](https://mapsengi ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/germany2016/index.md b/content/events/germany2016/index.md index 3db0fc44aa..f659d0ee18 100644 --- a/content/events/germany2016/index.md +++ b/content/events/germany2016/index.md @@ -39,4 +39,4 @@ Please let us know what you are interesting in. ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/glasgow2015/index.md b/content/events/glasgow2015/index.md index 0f383c26f1..f8b941d66a 100644 --- a/content/events/glasgow2015/index.md +++ b/content/events/glasgow2015/index.md @@ -10,7 +10,7 @@ title: Introduction to Galaxy Workshop **8th - 9th June, 2015, 9:00-17:00** **Instructors**
-[Dave Clements](/src/people/dave-clements/index.md), Galaxy Project, [Johns Hopkins University](http://www.jhu.edu)
+[Dave Clements](/people/dave-clements/), Galaxy Project, [Johns Hopkins University](http://www.jhu.edu)
[Mani Mudaliar](http://www.polyomics.gla.ac.uk/biog-manimudaliar.html), [Glasgow Polyomics](http://www.polyomics.gla.ac.uk/), [University of Glasgow](http://www.gla.ac.uk/)
[Graham Hamilton](http://www.polyomics.gla.ac.uk/biog-ghamilton.html), [Glasgow Polyomics](http://www.polyomics.gla.ac.uk/), [University of Glasgow](http://www.gla.ac.uk/)
@@ -168,4 +168,4 @@ This workshop is supported by [Glasgow Polyomics](http://www.polyomics.gla.ac.uk ## Questions? -Contact [Amy Cattanach](http://www.gla.ac.uk/stafflist/?action=person&id=4cddece38a97) or [Dave Clements](/src/people/dave-clements/index.md). +Contact [Amy Cattanach](http://www.gla.ac.uk/stafflist/?action=person&id=4cddece38a97) or [Dave Clements](/people/dave-clements/). diff --git a/content/events/indiana-u2012/index.md b/content/events/indiana-u2012/index.md index be165641f9..c834e4dcdf 100644 --- a/content/events/indiana-u2012/index.md +++ b/content/events/indiana-u2012/index.md @@ -35,7 +35,7 @@ There will be three Galaxy-related events on the Indiana University Bloomington
**1:30pm-2:30pm, October 19, Jordan Hall 065**
-**[Dave Clements](/src/people/dave-clements/index.md)**
+**[Dave Clements](/people/dave-clements/)**
**Emory University**

[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2012_IndianaU.pdf) @@ -52,7 +52,7 @@ The talk is open to the public. No advance registration is required.
**3:00pm-4:30pm, October 19, Lindley 102**
-**[Dave Clements](/src/people/dave-clements/index.md)**
+**[Dave Clements](/people/dave-clements/)**
**Emory University**

[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2012IndianaUGalaxyForBiologists.pdf) @@ -107,10 +107,10 @@ This is a hands-on workshop. **Please bring a wifi-enabled laptop with a curren
**9:30am-11:30am (note new time), October 19, PTI 015** in the [Cyberinfrastructure Building](http://it.iu.edu/cib/)
-**[Dave Clements](/src/people/dave-clements/index.md)**
+**[Dave Clements](/people/dave-clements/)**
**Emory University**

-This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/src/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/src/people/nate/index.md) and [Dannon Baker](/src/people/dannon-baker/index.md) of the Galaxy development team. +This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/people/nate/) and [Dannon Baker](/src/people/dannon-baker/) of the Galaxy development team. *Registration is open to any member of the Indiana University community. The workshop is free, but space is limited and advanced registration is required.*
diff --git a/content/events/iowa-state2012/index.md b/content/events/iowa-state2012/index.md index 08dee90382..d14389dc10 100644 --- a/content/events/iowa-state2012/index.md +++ b/content/events/iowa-state2012/index.md @@ -8,7 +8,7 @@
Instructors Ntino Krampis, JCVI
Enis Afgan, Ruđer Bošković Institute (RBI)
Ravi Sanka, JCVI
Brad Chapman, Harvard University 		Ntino Krampis, JCVI
Enis Afgan, Ruđer Bošković Institute (RBI)
Ravi Sanka, JCVI
Brad Chapman, Harvard University
Content
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9am-5pm
[MBB](http://www.fpm.iastate.edu/maps/default.asp?zoom=2&xcenter=1471&ycenter=1605&xshow=1471&yshow=1605) [1340 (Computer Lab)](http://www.bb.iastate.edu/computing/1340Home.html) diff --git a/content/events/ismb-eccb-bosc2011/index.md b/content/events/ismb-eccb-bosc2011/index.md index 823a7b528b..7b968a1081 100644 --- a/content/events/ismb-eccb-bosc2011/index.md +++ b/content/events/ismb-eccb-bosc2011/index.md @@ -24,7 +24,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 14:50-:15:10 - Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool, Jeremy Goecks, Emory University + Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool, Jeremy Goecks, Emory University @@ -37,7 +37,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 Saturday July 16 BOSC 12:05-12:15 - Enabling NGS Analysis with(out) the Infrastructure, Enis Afgan, Emory University + Enabling NGS Analysis with(out) the Infrastructure, Enis Afgan, Emory University Abstract PDF @@ -91,7 +91,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 ISMB/ECCB Workshops 14:30-16:25 - W6: Genomics for Non-Model Organisms, Dave Clements, Emory University. This Galaxy organized workshop features these talks: + W6: Genomics for Non-Model Organisms, Dave Clements, Emory University. This Galaxy organized workshop features these talks: Abstracts @@ -99,7 +99,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 PDF - Using RNA-seq for gene annotation, quantitation, and function in non-model organisms, Jeremy Goecks, Emory University + Using RNA-seq for gene annotation, quantitation, and function in non-model organisms, Jeremy Goecks, Emory University PDF @@ -119,7 +119,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 ISMB/ECCB Tech Track 16:00-16:25 - TT59: The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool, Jeremy Goecks, Emory University + TT59: The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool, Jeremy Goecks, Emory University Abstract diff --git a/content/events/ismb2012/index.md b/content/events/ismb2012/index.md index 1f02abe7ad..1c1728dc49 100644 --- a/content/events/ismb2012/index.md +++ b/content/events/ismb2012/index.md @@ -19,7 +19,7 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B Wednesday July 11 OpenBio Codefest 2012 All Day - Enis Afgan and Dannon Baker of the the Galaxy Team will participate. + Enis Afgan and Dannon Baker of the the Galaxy Team will participate. Report @@ -47,17 +47,17 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B 11:00-11:15 - Galaxy Project Update, Dannon Baker, Emory University + Galaxy Project Update, Dannon Baker, Emory University slides 11:15-11:30 - Zero to a Bioinformatics Analysis Platform in 4 Minutes, Enis Afgan, Ruđer Bošković Institute (RBI) and Victorian Life Science Computation Initiative (VLSCI) + Zero to a Bioinformatics Analysis Platform in 4 Minutes, Enis Afgan, Ruđer Bošković Institute (RBI) and Victorian Life Science Computation Initiative (VLSCI) slides 2:40-2:55 - A Framework for Interactive Visual Analysis of NGS Data using Galaxy, Jeremy Goecks, Emory University + A Framework for Interactive Visual Analysis of NGS Data using Galaxy, Jeremy Goecks, Emory University slides @@ -72,12 +72,12 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B 2:30-2:55 - TT08: Interactive Visual Analysis of NGS Data using Trackster and Galaxy, Jeremy Goecks, Emory University + TT08: Interactive Visual Analysis of NGS Data using Trackster and Galaxy, Jeremy Goecks, Emory University Slides 3:00-3:25 - TT10: The first biomedical AppStore: Galaxy Tool Shed, Greg von Kuster, Penn State University + TT10: The first biomedical AppStore: Galaxy Tool Shed, Greg von Kuster, Penn State University Slides @@ -92,7 +92,7 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B 11:45-12:10 - WK3 - Part C: Running a Bioinformatics Help Desk: from drawing colorful plasmid maps to working with Hi Seq Data, Hans-Rudolf Hotz, Friedrich Miescher Institute + WK3 - Part C: Running a Bioinformatics Help Desk: from drawing colorful plasmid maps to working with Hi Seq Data, Hans-Rudolf Hotz, Friedrich Miescher Institute Slides diff --git a/content/events/ismb2013/index.md b/content/events/ismb2013/index.md index 19479aa1eb..a3a8d94242 100644 --- a/content/events/ismb2013/index.md +++ b/content/events/ismb2013/index.md @@ -21,7 +21,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 19 July Mass Spectrometry SIG (MS-SIG) 11:30-11:45 - Innovative, Reproducible MS-based Proteomic Informatics in the Cloud for Emerging Applications with Galaxy-P and CloudBioLinux, John Chilton + Innovative, Reproducible MS-based Proteomic Informatics in the Cloud for Emerging Applications with Galaxy-P and CloudBioLinux, John Chilton Prezi @@ -34,7 +34,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 20 July BOSC 10-45-11:10 - BioBlend - Enabling Pipeline Dreams, Enis Afgan + BioBlend - Enabling Pipeline Dreams, Enis Afgan Slides @@ -44,7 +44,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 13:30-13:45 - Towards Enabling Big Data and Federated Computing in the Cloud, Enis Afgan + Towards Enabling Big Data and Federated Computing in the Cloud, Enis Afgan Slides @@ -54,7 +54,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 14:15-14:30 - Open Source Configuration of Bioinformatics Infrastructure, John Chilton + Open Source Configuration of Bioinformatics Infrastructure, John Chilton Prezi, Slides, Video @@ -64,14 +64,14 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 16:25-16:40 - Understanding Cancer Genomes Using Galaxy, Jeremy Goecks
This will also be presented as poster 19.
+ Understanding Cancer Genomes Using Galaxy, Jeremy Goecks
This will also be presented as poster 19.
Slides, Graphic, Video 21 July ISMB/ECCB Technology Track 14:10-14:35 - TT09: Understanding Cancer Genomes Using Galaxy, Jeremy Goecks + TT09: Understanding Cancer Genomes Using Galaxy, Jeremy Goecks Slides @@ -100,14 +100,14 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 - O097: An Integrated Systems Biology Platform for Complete Proteogenomic Analysis, John Chilton + O097: An Integrated Systems Biology Platform for Complete Proteogenomic Analysis, John Chilton Poster 23 July ISMB/ECCB Workshop 10:30-12:25 - Bioconductor and Galaxy: examples of successful bioinformatics networks, Wolfgang Huber and Jeremy Goecks; part of The “How To Guide” for Establishing a Successful Bioinformatics Network + Bioconductor and Galaxy: examples of successful bioinformatics networks, Wolfgang Huber and Jeremy Goecks; part of The “How To Guide” for Establishing a Successful Bioinformatics Network Slides @@ -131,7 +131,7 @@ Galaxy had a significant presence at [ISMB/ECCB](http://www.iscb.org/ismbeccb201 ISMB/ECCB Workshop 14:10-16:05 - Integrated Visualization and Computing for Biomedical Research, Nils Gehlenborg, Jeremy Goecks + Integrated Visualization and Computing for Biomedical Research, Nils Gehlenborg, Jeremy Goecks diff --git a/content/events/ismb2014/index.md b/content/events/ismb2014/index.md index 4f388b88c6..babaa38f2d 100644 --- a/content/events/ismb2014/index.md +++ b/content/events/ismb2014/index.md @@ -28,13 +28,13 @@ Galaxy has a significant presence at [ISMB 2014](http://www.iscb.org/ismb2014) a July 11 11:57 - Galaxy as an Extensible Job Execution Platform
John Chilton
+ Galaxy as an Extensible Job Execution Platform
John Chilton
Slides, Video July 12 2:36 - Enhancing the Galaxy Experience through Community Involvement
Daniel Blankenberg
+ Enhancing the Galaxy Experience through Community Involvement
Daniel Blankenberg
Slides , Video @@ -56,7 +56,7 @@ Galaxy has a significant presence at [ISMB 2014](http://www.iscb.org/ismb2014) a July 13 3:05 Room 309 - TT03: Interactive Visual Analysis with Galaxy Charts
Aysam Guerler + TT03: Interactive Visual Analysis with Galaxy Charts
Aysam Guerler Slides @@ -96,7 +96,7 @@ Galaxy has a significant presence at [ISMB 2014](http://www.iscb.org/ismb2014) a July 15 11:00 Room 313 - TT24: From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser
Daniel Blankenberg
+ TT24: From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser
Daniel Blankenberg
Slides @@ -108,7 +108,7 @@ Galaxy has a significant presence at [ISMB 2014](http://www.iscb.org/ismb2014) a 2:00 Room 310 - TT29: Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude
John Chilton
+ TT29: Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude
John Chilton
Slides diff --git a/content/events/ismb2015/index.md b/content/events/ismb2015/index.md index 9d96bfdac5..d9cf2ff51f 100644 --- a/content/events/ismb2015/index.md +++ b/content/events/ismb2015/index.md @@ -38,12 +38,12 @@ Galaxy has a significant presence at [ISMB/ECCB 2015](http://www.iscb.org/ismbec 14:34 - Demystifying the Interoperability of Disparate Genomic Resources
Daniel Blankenberg
+ Demystifying the Interoperability of Disparate Genomic Resources
Daniel Blankenberg
Slides, Video 14:51 - Increasing the utility of Galaxy workflows
John Chilton
+ Increasing the utility of Galaxy workflows
John Chilton
Slides (PDF), Video @@ -53,12 +53,12 @@ Galaxy has a significant presence at [ISMB/ECCB 2015](http://www.iscb.org/ismbec 15:15 - Evolution of the Galaxy tool ecosystem - happier developers, happier users
Martin Čech
+ Evolution of the Galaxy tool ecosystem - happier developers, happier users
Martin Čech
Slides (PDF), Video 17:15 - Building successful open-source bioinformatics developer communities (Part 1)
Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
+ Building successful open-source bioinformatics developer communities (Part 1)
Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
Video @@ -67,17 +67,17 @@ Galaxy has a significant presence at [ISMB/ECCB 2015](http://www.iscb.org/ismbec 11 July 12:05 - The perfect fit for reproducible interactive research: Galaxy, Docker, IPython
Björn Grüning + The perfect fit for reproducible interactive research: Galaxy, Docker, IPython
Björn Grüning Video 16:45 - BioaRchive: enabling reproducibility of Bioconductor package versions
Nitesh Turaga
+ BioaRchive: enabling reproducibility of Bioconductor package versions
Nitesh Turaga
Slides, Poster. Video 17:15 - Building successful open-source bioinformatics developer communities (Part 2)
Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
+ Building successful open-source bioinformatics developer communities (Part 2)
Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
@@ -118,13 +118,13 @@ Galaxy has a significant presence at [ISMB/ECCB 2015](http://www.iscb.org/ismbec 11 July 13:30 - AKES 05: Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training
Dave Clements
+ AKES 05: Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training
Dave Clements
12 July 15:30 - Experience Exchange: Focus on the NGS Course
Francis Ouellette, Gabriella Rustici, Annette McGrath, Dave Clements
Part of WK01: Workshop on Education in Bioinformatics: Unlocking the super teacher inside you - Becoming competent in delivering bioinformatics training
+ Experience Exchange: Focus on the NGS Course
Francis Ouellette, Gabriella Rustici, Annette McGrath, Dave Clements
Part of WK01: Workshop on Education in Bioinformatics: Unlocking the super teacher inside you - Becoming competent in delivering bioinformatics training
@@ -150,7 +150,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2015](http://www.iscb.org/ismbec 14 July 12:00 - TT16: What’s new in the Galaxy (Project)?
Dave Clements
+ TT16: What’s new in the Galaxy (Project)?
Dave Clements
Slides diff --git a/content/events/ismb2016/index.md b/content/events/ismb2016/index.md index 7da1f7c0f9..886d379a56 100644 --- a/content/events/ismb2016/index.md +++ b/content/events/ismb2016/index.md @@ -32,17 +32,17 @@ Galaxy has a significant presence at [ISMB 2016](http://www.iscb.org/ismb2016) a 11:57 - Planemo – A Scientific Workflow SDK
John Chilton
+ Planemo – A Scientific Workflow SDK
John Chilton
Slides, Video 12:03 - Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics
Daniel Blankenberg
+ Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics
Daniel Blankenberg
Slides, Video 16:00 - Panel: Growing and sustaining open source communities
John Chilton
+ Panel: Growing and sustaining open source communities
John Chilton
@@ -107,7 +107,7 @@ Galaxy has a significant presence at [ISMB 2016](http://www.iscb.org/ismb2016) a July 12 2:40 - TT23: Large Scale Analysis with Galaxy
John Chilton + TT23: Large Scale Analysis with Galaxy
John Chilton Slides diff --git a/content/events/ismms2016/index.md b/content/events/ismms2016/index.md index e2c1858a41..5e9d8c4d80 100644 --- a/content/events/ismms2016/index.md +++ b/content/events/ismms2016/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
January 21, 2016, and
January 22, 2016
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-5:00

Location: Large Classroom (Thursday), Small Classroom (Friday)
[Levy Library](http://icahn.mssm.edu/about-us/services-and-resources/levy-library) (11th floor)
Annenberg Building. 1468 Madison Ave.
diff --git a/content/events/johns-hopkins2012/index.md b/content/events/johns-hopkins2012/index.md index 550a034898..a72722e0c5 100644 --- a/content/events/johns-hopkins2012/index.md +++ b/content/events/johns-hopkins2012/index.md @@ -3,7 +3,7 @@ **A workshop for the Johns Hopkins community -Instructor: [Dave Clements](/src/people/dave-clements/index.md) +Instructor: [Dave Clements](/people/dave-clements/) 9:00am-4:30pm
612 Physiology
diff --git a/content/events/johns-hopkins2013/index.md b/content/events/johns-hopkins2013/index.md index e85038be4e..ce716b45ce 100644 --- a/content/events/johns-hopkins2013/index.md +++ b/content/events/johns-hopkins2013/index.md @@ -3,7 +3,7 @@ **Workshops for the Johns Hopkins community -Instructors: [Dave Clements](/src/people/dave-clements/index.md), [Mo Heydarian](http://epigenetics.jhu.edu/?section=personnelPages&personID=26) +Instructors: [Dave Clements](/people/dave-clements/), [Mo Heydarian](http://epigenetics.jhu.edu/?section=personnelPages&personID=26) 9:00am-4:30pm
Rangos 490
diff --git a/content/events/meetups/baltimore/2015-01-22/index.md b/content/events/meetups/baltimore/2015-01-22/index.md index 579c9c1cdc..2097e71cc0 100644 --- a/content/events/meetups/baltimore/2015-01-22/index.md +++ b/content/events/meetups/baltimore/2015-01-22/index.md @@ -13,7 +13,7 @@ The first Galaxy meetup or social gathering held in Baltimore was sold out. It w The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis](/src/people/enis-afgan/index.md) & [Nitesh](/src/people/nitesh-turaga/index.md) +[Enis](/people/enis-afgan/index.md) & [Nitesh](/src/people/nitesh-turaga/) ## There's a meetup! @@ -21,7 +21,7 @@ Hey Everyone, We are looking forward to kicking off our first [Galaxy Project](http://galaxyproject.org) Meetup! We will meet at one of the Galaxy project hubs - the Department of Biology of Johns Hopkins University for a general introduction to Galaxy in form of a social gathering. This will be an informal meeting open to anyone interested in data analysis, tools, computer infrastructure, programming - regardless. -[Enis Afgan](/src/people/enis-afgan/index.md) and [Nitesh Turaga](/src/people/nitesh-turaga/index.md) of the [Galaxy team](/src/galaxy-team/index.md) will be kicking things off with a discussion on Galaxy and how researchers around the world are leveraging it. +[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be kicking things off with a discussion on Galaxy and how researchers around the world are leveraging it. Thanks and hope to see you there! diff --git a/content/events/meetups/baltimore/2015-02-18/index.md b/content/events/meetups/baltimore/2015-02-18/index.md index 36ca7f9f5b..6b6e769d58 100644 --- a/content/events/meetups/baltimore/2015-02-18/index.md +++ b/content/events/meetups/baltimore/2015-02-18/index.md @@ -12,7 +12,7 @@ Hey Everyone, We are looking forward to a [follow-up Meetup](https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22) by the [Galaxy Project](http://galaxyproject.org)! We will meet at one of the Galaxy project hubs - the Department of Biology of Johns Hopkins University. This time around, we will briefly take a look at how to get started using Galaxy. Again, this will be an informal meeting open to anyone interested in data analysis, tools, computer infrastructure, programming. -[Enis Afgan](/src/people/enis-afgan/index.md) and [Nitesh Turaga](/src/people/nitesh-turaga/index.md) of the [Galaxy team](/src/galaxy-team/index.md) will be delivering a short introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint (and will be available for any additional questions). +[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be delivering a short introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint (and will be available for any additional questions). Thanks and hope to see you there! diff --git a/content/events/meetups/psu/2015-03/index.md b/content/events/meetups/psu/2015-03/index.md index 8e862d1f34..c3a6fde365 100644 --- a/content/events/meetups/psu/2015-03/index.md +++ b/content/events/meetups/psu/2015-03/index.md @@ -8,7 +8,7 @@ title: March 2015 Penn State Using Galaxy Workshop Hey Everyone, This will be an informal meeting open to anyone interested in data analysis, genomic tools and biology workflows. -[Anton Nekrutenko](/src/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/index.md) will be delivering an introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint. Multiple Galaxy Team members will be available for any additional questions. +[Anton Nekrutenko](/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint. Multiple Galaxy Team members will be available for any additional questions. Thanks and hope to see you there! diff --git a/content/events/meetups/psu/2015-05/index.md b/content/events/meetups/psu/2015-05/index.md index 5fe7c48121..5b574083ad 100644 --- a/content/events/meetups/psu/2015-05/index.md +++ b/content/events/meetups/psu/2015-05/index.md @@ -12,7 +12,7 @@ title: May 2015 Penn State RNA-Seq Galaxy Workshop Hey Everyone, This meeting is open to anyone interested in RNA-Seq analysis and biology workflows. -[Anton Nekrutenko](/src/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/index.md) will be delivering an introduction to RNA-Seq resources available at Galaxy from a practitioner's viewpoint. +[Anton Nekrutenko](/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to RNA-Seq resources available at Galaxy from a practitioner's viewpoint. [Galaxy Team members](/src/galaxy-team/index.md) will be available for any additional questions. diff --git a/content/events/missouri2013/index.md b/content/events/missouri2013/index.md index 00a625ff87..88d0fafbe8 100644 --- a/content/events/missouri2013/index.md +++ b/content/events/missouri2013/index.md @@ -3,7 +3,7 @@
Introduction to Galaxy
Thursday May 2, 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) +**Instructor: [Dave Clements](/people/dave-clements/), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) 9:00am-5:00pm
[Bond Life Sciences Center](http://map.missouri.edu/?bldg=37156),
Room 572 ** (note room change)
diff --git a/content/events/ncsu2013/index.md b/content/events/ncsu2013/index.md index d76f2da372..dde66bb186 100644 --- a/content/events/ncsu2013/index.md +++ b/content/events/ncsu2013/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
July 22, 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-4:45
[3503 Thomas Hall (The Stephens Room)](http://harvest.cals.ncsu.edu/caat/index.cfm?pageID=1331)
diff --git a/content/events/niehs2013/index.md b/content/events/niehs2013/index.md index d0874ed6c7..d578d957eb 100644 --- a/content/events/niehs2013/index.md +++ b/content/events/niehs2013/index.md @@ -8,7 +8,7 @@
Galaxy
July 18, 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-5:00
NIEHS Rall Room 101/A262
diff --git a/content/events/northwestern-u-2015/index.md b/content/events/northwestern-u-2015/index.md index 5a571db8fd..2a1a77c201 100644 --- a/content/events/northwestern-u-2015/index.md +++ b/content/events/northwestern-u-2015/index.md @@ -2,7 +2,7 @@
Northwestern University -
Introduction to Galaxy
February 27, 2015, 9:00-4:00

Instructors: Dave Clements, Matt Schipma

Galter Health Sciences Library, Learning Resources Center
Northwestern University Feinberg School of Medicine campus
Chicago, Illinois, United States +
Introduction to Galaxy
February 27, 2015, 9:00-4:00

Instructors: Dave Clements, Matt Schipma

Galter Health Sciences Library, Learning Resources Center
Northwestern University Feinberg School of Medicine campus
Chicago, Illinois, United States diff --git a/content/events/pag-gmod-2014/index.md b/content/events/pag-gmod-2014/index.md index 032bedc3b7..70e4f16487 100644 --- a/content/events/pag-gmod-2014/index.md +++ b/content/events/pag-gmod-2014/index.md @@ -82,7 +82,7 @@ Galaxy had a strong presence at the [Plant and Animal Genome XXII (PAG 2014)](ht Galaxy for NGS Data Analysis: A Hands-on Workshop Workshops
California Room
Slides1, Slides2 - Dave Clements, Anushka Brownley + Dave Clements, Anushka Brownley @@ -99,7 +99,7 @@ Galaxy had a strong presence at the [Plant and Animal Genome XXII (PAG 2014)](ht 11:50-12:30 Galaxy CloudMan: A Gentle Introduction to Data Analysis on the Cloud Slides - Dave Clements + Dave Clements @@ -121,7 +121,7 @@ The [GMOD 2014](http://gmod.org/wiki/Jan_2014_GMOD_Meeting) meeting schedule has Thursday
January 16 Galaxy Project Update Slides - Dave Clements + Dave Clements Friday
January 17 diff --git a/content/events/pag2012/index.md b/content/events/pag2012/index.md index 41faff9241..7640397954 100644 --- a/content/events/pag2012/index.md +++ b/content/events/pag2012/index.md @@ -50,7 +50,7 @@ Galaxy had a strong presence at [Plant and Animal Genome XX (PAG 2012)](http://w 10:30-11:30 Galaxy (slides: PDF) GMOD Workshop - Dave Clements + Dave Clements 11:35-11:50 diff --git a/content/events/pag2016/index.md b/content/events/pag2016/index.md index b5403b129a..b3db51e327 100644 --- a/content/events/pag2016/index.md +++ b/content/events/pag2016/index.md @@ -64,7 +64,7 @@ Galaxy will be at [Plant and Animal Genome XXIV (PAG 2016)](http://www.intlpag.o Galaxy for SNP and Variant Data Analysis Workshop, California Room Slides - Dave Clements + Dave Clements Wednesday
January 13 @@ -72,6 +72,6 @@ Galaxy will be at [Plant and Animal Genome XXIV (PAG 2016)](http://www.intlpag.o Galaxy Community Update GMOD, Golden West Slides - Dave Clements + Dave Clements diff --git a/content/events/pag2017/index.md b/content/events/pag2017/index.md index df37645909..1d7bda3316 100644 --- a/content/events/pag2017/index.md +++ b/content/events/pag2017/index.md @@ -124,7 +124,7 @@ Galaxy will have a strong presence at [Plant and Animal Genome XXIV (PAG 2017)]( Genome Annotation with Galaxy Workshop, California Room Slides - Jeremy Goecks + Jeremy Goecks @@ -136,7 +136,7 @@ Galaxy will have a strong presence at [Plant and Animal Genome XXIV (PAG 2017)]( GMOD, Golden West [Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2017-pag-gmod-community-update.pdf) - Dave Clements + Dave Clements 2:00-2:25 diff --git a/content/events/psu-medicine2015/index.md b/content/events/psu-medicine2015/index.md index 1c008bdeb7..7ed96f4e9f 100644 --- a/content/events/psu-medicine2015/index.md +++ b/content/events/psu-medicine2015/index.md @@ -7,7 +7,7 @@ title: Introduction to Galaxy for Next Generation Sequencing Analysis **May 27, 2015, 10:00-4:00**
-Instructor: [Anton Nekrutenko](/src/people/anton/index.md), Penn State University

+Instructor: [Anton Nekrutenko](/people/anton/), Penn State University

Room 302C, [Conference Center](http://www.pennstatehershey.org/c/document_library/get_file?folderId=11516&name=DLFE-17612.pdf)
[Penn State Hershey](http://www.pennstatehershey.org/)
Hershey, Pennsylvania, United States
diff --git a/content/events/purdue2012/index.md b/content/events/purdue2012/index.md index 49622770a6..7c02c0c5ec 100644 --- a/content/events/purdue2012/index.md +++ b/content/events/purdue2012/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
October 22, 2012
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9am-5pm
Room: MRGN 129 (new location)
diff --git a/content/events/rochester2016/index.md b/content/events/rochester2016/index.md index e4141a7897..7fe7f37840 100644 --- a/content/events/rochester2016/index.md +++ b/content/events/rochester2016/index.md @@ -11,7 +11,7 @@ **[Kathryn W. Nesbit Classroom #2](https://www.urmc.rochester.edu/libraries/miner/teaching_and_learning/classrooms.cfm), [Edward G. Miner Library](https://www.urmc.rochester.edu/libraries/miner/index.cfm)
[University of Rochester Medical Center](https://www.urmc.rochester.edu/) -Instructor: [Dave Clements](/src/people/dave-clements/index.md) +Instructor: [Dave Clements](/people/dave-clements/) **
@@ -167,4 +167,4 @@ We will ask for it! ## Questions? -Contact [John Ashton](https://www.urmc.rochester.edu/people/26567020-john-m-ashton) or [Dave Clements](/src/people/dave-clements/index.md). +Contact [John Ashton](https://www.urmc.rochester.edu/people/26567020-john-m-ashton) or [Dave Clements](/people/dave-clements/). diff --git a/content/events/sao-paulo2014/index.md b/content/events/sao-paulo2014/index.md index 7849a54822..ad3b7d07bc 100644 --- a/content/events/sao-paulo2014/index.md +++ b/content/events/sao-paulo2014/index.md @@ -6,7 +6,7 @@ title: DNA Sequence Bioinformatics Analysis with the Galaxy Platform -**Instructors: [Dave Clements](/src/people/dave-clements/index.md), Robson Francisco de Souza, José Belizario +**Instructors: [Dave Clements](/people/dave-clements/), Robson Francisco de Souza, José Belizario 28th July - 1st August 2014
9:00-17:00**
diff --git a/content/events/sdsu2014/index.md b/content/events/sdsu2014/index.md index f0a615521c..d9facd5102 100644 --- a/content/events/sdsu2014/index.md +++ b/content/events/sdsu2014/index.md @@ -2,7 +2,7 @@
San Diego State University -
Galaxy Workshops
January 15, 2015

9:00-11:00: Introductory
 1:30- 3:30: Advanced

Instructor: Dave Clements
Location TBD
San Diego State University
San Diego, California, United States +
Galaxy Workshops
January 15, 2015

9:00-11:00: Introductory
 1:30- 3:30: Advanced

Instructor: Dave Clements
Location TBD
San Diego State University
San Diego, California, United States diff --git a/content/events/sg2014/index.md b/content/events/sg2014/index.md index ee9a38c00b..bbd4c87495 100644 --- a/content/events/sg2014/index.md +++ b/content/events/sg2014/index.md @@ -10,7 +10,7 @@ title: Swiss German Galaxy Tour 2014 There will be a *Swiss-German Galaxy Tour* this fall featuring a range of events over 3 days in two locations. ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Events @@ -39,4 +39,4 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/src/people/hansru ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/sg2016/index.md b/content/events/sg2016/index.md index 49a2546dc5..7b5bafcb39 100644 --- a/content/events/sg2016/index.md +++ b/content/events/sg2016/index.md @@ -51,4 +51,4 @@ The [second day](/src/events/germany2016/index.md), October 21st, is ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/slu2013/index.md b/content/events/slu2013/index.md index 7f2f7ad41e..42405da18c 100644 --- a/content/events/slu2013/index.md +++ b/content/events/slu2013/index.md @@ -3,7 +3,7 @@
Introduction to Galaxy
Tuesday April 30, 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) +**Instructor: [Dave Clements](/people/dave-clements/), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) 9:00am-5:00pm
[Caroline Building](http://www.slu.edu/campusmap/pdf_maps/section_3_of_3.pdf), Room 204** diff --git a/content/events/switzerland2012/index.md b/content/events/switzerland2012/index.md index f7d7fec48d..b7cd721c09 100644 --- a/content/events/switzerland2012/index.md +++ b/content/events/switzerland2012/index.md @@ -23,12 +23,12 @@ The workshop is part of the [SyBIT Tech Day series](https://wiki.systemsx.ch/dis | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | | | | 9:30 - 9:40 | Peter Kunszt ([SyBIT](https://wiki.systemsx.ch/display/SyBIT)) | Welcome and usual news | | -| 9:40 - 9:50 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Switzerland2012_hrh_intro.pdf) | -| 9:50 - 10:30 | [Dannon Baker](/src/people/dannon-baker/index.md) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/baker_swiss_galaxy_day.pdf) | +| 9:40 - 9:50 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Switzerland2012_hrh_intro.pdf) | +| 9:50 - 10:30 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/baker_swiss_galaxy_day.pdf) | | 10:30 - 11:00 | BREAK | | | | 11:00 - 11:15 | Mark Robinson ([IMLS, University of Zurich](http://www.imls.uzh.ch/research/robinson.html)) | edgeR and Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/edgeR_galaxy_robinson.pptx.pdf) | | 11:15 - 11:30 | Tim Roloff ([FMI](http://www.fmi.ch/)) | Microarray analaysis | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Affy_analysis_TCRH.pdf) | -| 11:30 - 11:45 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | NGS analysis | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Switzerland2012_hrh_NGS_at_FMI.pdf) | +| 11:30 - 11:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | NGS analysis | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Switzerland2012_hrh_NGS_at_FMI.pdf) | | 11:45 - 12:00 | Manuel Kohler ([D-BSSE, ETH Zurich](http://www.bsse.ethz.ch/)) | openBIS and Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Galaxy_workshop_Bern_2012_MK.pdf) | | 12:00 - 13:45 | LUNCH Break (lunch will be at 12:15) | | | | 13:45 - 14:00 | Nikolai Vazov ([USIT, University of Oslo](http://www.usit.uio.no/english/)) | Installing Galaxy on a cluster : issues around DB server, queuing system, external authentication, etc. | [odp](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/Swiss_Galaxy_Workshop_NikolaiVazov.odp) | @@ -38,7 +38,7 @@ The workshop is part of the [SyBIT Tech Day series](https://wiki.systemsx.ch/dis | 15:15 - 15:30 | Grainne Kerr ([DKFZ, Heidelberg](http://www.dkfz.de)) | Galaxy and a high throughput screening lab | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/GalaxyAndHighThroughputScreeningLab.pptx.pdf) | | 15:30 - 15:45 | Björn Grüning ([University of Freiburg](http://www.uni-freiburg.de/)) | Chemical Tool Box | [html5](https://depot.galaxyproject.org/hub/attachments/events/switzerland2012/ChemicalToolBoX.tar.bz2) | | 15:45 - 16:00 | Sveinung Gundersen (The Norwegian Radium Hospital) | [Genomic HyperBrowser](http://hyperbrowser.uio.no/hb/) | [pdf](https://depot.galaxyproject.org/hub/attachmentsrimary or operator) | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | concluding remarks | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | concluding remarks | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | | | @@ -64,7 +64,7 @@ This workshop is generously supported by [SyBIT](https://wiki.systemsx.ch/displa ## Registration -The workshop is full, and registration is closed. Please contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) in order to get informed in case places become available again. +The workshop is full, and registration is closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) in order to get informed in case places become available again. ## Links @@ -72,4 +72,4 @@ The workshop is full, and registration is closed. Please contact [Hans-Rudolf Ho ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) diff --git a/content/events/switzerland2014/index.md b/content/events/switzerland2014/index.md index 093f4b482e..6fbc2d7e70 100644 --- a/content/events/switzerland2014/index.md +++ b/content/events/switzerland2014/index.md @@ -27,7 +27,7 @@ Following the workshop, we organise a [Developers Day](/src/events/germany2014/i ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Preliminary Schedule @@ -35,20 +35,20 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/src/people/hansru | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | -| 9:45 - 10:30 | [Dannon Baker](/src/people/dannon-baker/index.md) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/SG2014T__State_of_the_Galaxy.pdf) | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | +| 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/SG2014T__State_of_the_Galaxy.pdf) | | 10:30 - 10:50 | coffee Break | -| 10:50 - 11:40 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | Galaxy: putting pieces together | [whiteboard](/src/events/switzerland2014/Bjoern_whiteboard.jpg) | +| 10:50 - 11:40 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | Galaxy: putting pieces together | [whiteboard](/src/events/switzerland2014/Bjoern_whiteboard.jpg) | | 11:40 - 12:00 | Nikolay Vazov ([USIT, University of Oslo](http://www.usit.uio.no/english/)) | Authentication in Galaxy : let's use what is out there - National Identity Providers | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Auth-tutorial-vazov.pdf) | | 12:00 - 13:30 | Lunch Break (lunch will be at 12:15) | | 13:30 - 13:40 | Jeevan Karloss ([CIGENE, Norwegian University of Life Sciences](http://www.cigene.no/)) | Elixir Norway and Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Elixir_Norway_011014.pdf) | | 13:40 - 14:00 | Marco Antonio Mendoza ([IGBMC Strasbourg](http://www.igbmc.fr/)) | NGS-QC Generator: A quality control system for ChIP-seq and enrichment-related NGS datasets | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Marco_Galaxy_Bern_October_2014_final.pdf) | | 14:00 - 14:30 | Sarah Diehl ([MPI-IE](https://www.ie-freiburg.mpg.de/) Freiburg) | deepTools: a flexible platform for exploring deep-sequencing data | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/deepTools_SG14_v3.pdf) | | 14:30 - 15:00 | coffee Break | -| 15:00 - 15:30 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | Using Galaxy for NGS analysis in a collaborative environment | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/hrh_20141001.pdf) | +| 15:00 - 15:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Using Galaxy for NGS analysis in a collaborative environment | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/hrh_20141001.pdf) | | 15:30 - 15:45 | Tim-Christoph Roloff ([FMI](http://www.fmi.ch/)) | Genomics analysis at FMI | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Galaxy_Workshop_Bern_2014_Tim_Roloff.pdf) | | 15:45 - 16:00 | Torsten Houwaart ([University of Freiburg](http://www.uni-freiburg.de/)) | RNA structure visualized in Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Torsten_Bern01.10.2014.pdf) | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | @@ -69,4 +69,4 @@ This workshop is generously supported by [SyBIT](https://wiki.systemsx.ch/displa ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/switzerland2014/trainingday/index.md b/content/events/switzerland2014/trainingday/index.md index 69b52f4b49..26575abf6a 100644 --- a/content/events/switzerland2014/trainingday/index.md +++ b/content/events/switzerland2014/trainingday/index.md @@ -27,18 +27,18 @@ Topics covered: | Time | Speaker | Title | Type | Slides | | ---- | -------- | ------ | ----- | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:40 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | -| 9:40 - 9:50 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | demo | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/intro_20140930.pdf) | -| 9:50 - 10:30 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | datatypes, histories, datasets, tools, data sharing | hands-on | | +| 9:30 - 9:40 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | +| 9:40 - 9:50 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | demo | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/intro_20140930.pdf) | +| 9:50 - 10:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | datatypes, histories, datasets, tools, data sharing | hands-on | | | 10:30 - 11:00 | coffee Break | -| 11:00 - 12:00 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)) | simple text manipulations, workflows | hands-on | | +| 11:00 - 12:00 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | simple text manipulations, workflows | hands-on | | | 12:00 - 13:30 | Lunch Break (lunch will be at 12:15) | -| 13:30 - 14:10 | [Dannon Baker](/src/people/dannon-baker/index.md) ([Galaxy Project](http://galaxyproject.org)) | installing and administering your own Galaxy on the cloud | hands-on | | -| 14:10 - 14:40 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | toolshed | hands-on | | +| 13:30 - 14:10 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | installing and administering your own Galaxy on the cloud | hands-on | | +| 14:10 - 14:40 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | toolshed | hands-on | | | 14:40 - 15:00| coffee Break | -| 15:00 - 15:30 | [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | NGS-analaysis: a Chip-Seq example | hands-on | | -| 15:30 - 16:00 | [Dannon Baker](/src/people/dannon-baker/index.md) ([Galaxy Project](http://galaxyproject.org)) | visualizations | hands-on | | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | +| 15:00 - 15:30 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | NGS-analaysis: a Chip-Seq example | hands-on | | +| 15:30 - 16:00 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | visualizations | hands-on | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | This schedule will most likely change. It will be adapted according to the progress we make during the day @@ -50,7 +50,7 @@ The training day will be held in the [UniS-Building (room: A -119) of the Univer ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you.
diff --git a/content/events/switzerland2016/index.md b/content/events/switzerland2016/index.md index e503f3e787..6186a0833c 100644 --- a/content/events/switzerland2016/index.md +++ b/content/events/switzerland2016/index.md @@ -20,11 +20,11 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/index.md) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | -| 9:45 - 10:30 | [Dannon Baker](/src/people/dannon-baker/index.md) | State of the Galaxy Project - priorities, plans, and community | | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | +| 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) | State of the Galaxy Project - priorities, plans, and community | | | 10:30 - 11:00 | Coffee Break | | 11:00 - 11:20 | Nicola Soranzo | News from the [IUC](/src/iuc/index.md) and the Galaxy tool ecosystem | | -| 11:20 - 11:40 | [Björn Grüning](/src/people/bjoern-gruening/index.md) | Fixing Bioinformatic Infrastructure | | +| 11:20 - 11:40 | [Björn Grüning](/people/bjoern-gruening/) | Fixing Bioinformatic Infrastructure | | | 11:40 - 12:00 | Bérénice Batut | [Galaxy Training Network](https://training.galaxyproject.org/) - rebooted | | | 12:00 - 13:30 | Lunch Break in nearby restaurants | | 13:30 - 13:50 | TBA | Debian Med - Debian for medicine and life sciences | | @@ -35,7 +35,7 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | 15:20 - 15:40 | Nikolay Vazov | Customizing Galaxy for Large Institutions | | | 15:40 - 16:00 | TBA | | | | 16:00 - 17:00 | lightening talks | | | -| 17:00 - 17:01 | [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md) | concluding remarks | | +| 17:00 - 17:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), [Björn Grüning](/src/people/bjoern-gruening/) | concluding remarks | | | 17:01 - 17:15 | ...going to the pub | @@ -45,4 +45,4 @@ The workshop will be held at the Universität of Freiburg in Germany (see the [m ## Questions? -Contact [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/index.md) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/tgac2013/index.md b/content/events/tgac2013/index.md index 3be5493b30..33c460f211 100644 --- a/content/events/tgac2013/index.md +++ b/content/events/tgac2013/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
11 April 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-16:30
IT Training Theatre
diff --git a/content/events/tokyo2015/index.md b/content/events/tokyo2015/index.md index 9eb11f92bf..f2f7a24089 100644 --- a/content/events/tokyo2015/index.md +++ b/content/events/tokyo2015/index.md @@ -87,7 +87,7 @@ The preparation hands-on is optional. To attend this hands-on, please bring your 13:25-13:30 Message from Galaxy Team - Dave Clements (Johns Hopkins University) + Dave Clements (Johns Hopkins University) - pdf video diff --git a/content/events/u-cape-town2013/index.md b/content/events/u-cape-town2013/index.md index 2ce32195e2..9474d01ae1 100644 --- a/content/events/u-cape-town2013/index.md +++ b/content/events/u-cape-town2013/index.md @@ -6,7 +6,7 @@ title: NGS Data Analysis and Galaxy Workshop -**Instructors: [Dave Clements](/src/people/dave-clements/index.md), [Gerrit Botha](http://www.cbio.uct.ac.za/people/5-gerrit-botha.html) +**Instructors: [Dave Clements](/people/dave-clements/), [Gerrit Botha](http://www.cbio.uct.ac.za/people/5-gerrit-botha.html) 21-25 October 2013
9:00-17:00**
diff --git a/content/events/u-maryland2012/index.md b/content/events/u-maryland2012/index.md index 8e189c9d41..83744e51ff 100644 --- a/content/events/u-maryland2012/index.md +++ b/content/events/u-maryland2012/index.md @@ -21,7 +21,7 @@ title: Introduction to Galaxy **A workshop for the University of Maryland community -Instructor: [Dave Clements](/src/people/dave-clements/index.md) +Instructor: [Dave Clements](/people/dave-clements/) 1:30-5:00pm, April 11
Bioscience Research Building, Room 1103** diff --git a/content/events/u-pretoria2013/index.md b/content/events/u-pretoria2013/index.md index 8f0990b9ea..116ce346f3 100644 --- a/content/events/u-pretoria2013/index.md +++ b/content/events/u-pretoria2013/index.md @@ -11,7 +11,7 @@ title: NGS Data Analysis and Galaxy Workshop -**Instructors: [Dave Clements](/src/people/dave-clements/index.md), [Burger van Jaarsveld](https://www.linkedin.com/pub/burger-van-jaarsveld/4a/561/566), [Fourie Joubert](http://science.up.ac.za/html/fourie_joubert.html) +**Instructors: [Dave Clements](/people/dave-clements/), [Burger van Jaarsveld](https://www.linkedin.com/pub/burger-van-jaarsveld/4a/561/566), [Fourie Joubert](http://science.up.ac.za/html/fourie_joubert.html) 14-18 October 2013
8:30-16:30
diff --git a/content/events/u-utah-workshop/index.md b/content/events/u-utah-workshop/index.md index e437aa4f78..0ac3719ef7 100644 --- a/content/events/u-utah-workshop/index.md +++ b/content/events/u-utah-workshop/index.md @@ -4,7 +4,7 @@ title: Introduction to Galaxy
University of Utah

-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) November 16, 2016
9:00-5:00

diff --git a/content/events/uga2014/index.md b/content/events/uga2014/index.md index be82c6a2f9..5cc77649e5 100644 --- a/content/events/uga2014/index.md +++ b/content/events/uga2014/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
March 7, 2014
-**Instructors
[Carl Eberhard](/src/people/carl-eberhard/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) +**Instructors
[Carl Eberhard](/people/carl-eberhard/index.md), [Dave Clements](/people/dave-clements/), [Dannon Baker](/src/people/dannon-baker/), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) 8:30-17:00
[University of Georgia](http://www.uga.edu/), Athens, GA** diff --git a/content/events/uiowa2012/index.md b/content/events/uiowa2012/index.md index 69ce578209..475bf75a3a 100644 --- a/content/events/uiowa2012/index.md +++ b/content/events/uiowa2012/index.md @@ -15,7 +15,7 @@ title: Introduction to Galaxy **A workshop for the University of Iowa community -Instructor: [Dave Clements](/src/people/dave-clements/index.md) +Instructor: [Dave Clements](/people/dave-clements/) April 19: Two workshops:** @@ -101,7 +101,7 @@ No programming or Linux command line experience is required. ## Slides -* [Introduction to Galaxy](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2012_UIowaIntroToGalaxy.pdf), [Dave Clements](/src/people/dave-clements/index.md) +* [Introduction to Galaxy](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2012_UIowaIntroToGalaxy.pdf), [Dave Clements](/people/dave-clements/) * [University of Iowa Custom Galaxy Deployment](https://depot.galaxyproject.org/hub/attachments/documents/presentations/2012_UIowaCustomGalaxyDeployment.pdf), Ann Black-Ziegelbein ## Support diff --git a/content/events/uiuc2012/index.md b/content/events/uiuc2012/index.md index 3ae2cd05e0..ae951f81a6 100644 --- a/content/events/uiuc2012/index.md +++ b/content/events/uiuc2012/index.md @@ -7,7 +7,7 @@
Introduction to Galaxy
October 16-17, 2012
-**Instructors: [Dave Clements](/src/people/dave-clements/index.md)** with **Christopher Fields** +**Instructors: [Dave Clements](/people/dave-clements/)** with **Christopher Fields** **1pm - 5pm
Location - 1040 NCSA** @@ -108,7 +108,7 @@ One week before this workshop there will be an Institute for Genomic Biology Sem **[Addressing Irreproducibility of Biomedical Research](http://www.igb.illinois.edu/sites/default/files/upload/Nekrutenko-1.pdf)** -[Anton Nekrutenko](/src/people/anton/index.md), Ph.D.
+[Anton Nekrutenko](/people/anton/), Ph.D.
Associate Professor of Biochemistry and Molecular Biology
Penn State University diff --git a/content/events/uk-may2014/igmm-workshop/index.md b/content/events/uk-may2014/igmm-workshop/index.md index f1e3379f47..be70b642ac 100644 --- a/content/events/uk-may2014/igmm-workshop/index.md +++ b/content/events/uk-may2014/igmm-workshop/index.md @@ -9,7 +9,7 @@ Western General Hospital, Crewe Road, Edinburgh, United Kingdom**
[Directions](http://www.igmm.ac.uk/contact.htm)

-**Instructor**
[Dave Clements](/src/people/dave-clements/index.md), [Johns Hopkins University](http://www.jhu.edu/)
+**Instructor**
[Dave Clements](/people/dave-clements/), [Johns Hopkins University](http://www.jhu.edu/)
## Registration diff --git a/content/events/uk-may2014/tgac-workshop/index.md b/content/events/uk-may2014/tgac-workshop/index.md index 248ba70a89..3ef6e11c05 100644 --- a/content/events/uk-may2014/tgac-workshop/index.md +++ b/content/events/uk-may2014/tgac-workshop/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
9 May 2014
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-16:00
Genome Seminar Room
diff --git a/content/events/uk-may2014/u-edinburgh/index.md b/content/events/uk-may2014/u-edinburgh/index.md index cd1e1405d6..3c128086ce 100644 --- a/content/events/uk-may2014/u-edinburgh/index.md +++ b/content/events/uk-may2014/u-edinburgh/index.md @@ -13,7 +13,7 @@ Room 4325D, [James Clerk Maxwell Building (JCMB)](http://www.ph.ed.ac.uk/about/l [University of Edinburgh](http://www.ed.ac.uk/), Edinburgh, United Kingdom
-Instructors
[Dave Clements](/src/people/dave-clements/index.md), [Johns Hopkins University](http://www.jhu.edu/)
[Shaun Webb](http://www.research.ed.ac.uk/portal/en/persons/shaun-webb(f89f2a63-6811-473c-aa8a-5e9df97bea3a)/publications.html), [University of Edinburgh](http://www.ed.ac.uk/)
+Instructors
[Dave Clements](/people/dave-clements/), [Johns Hopkins University](http://www.jhu.edu/)
[Shaun Webb](http://www.research.ed.ac.uk/portal/en/persons/shaun-webb(f89f2a63-6811-473c-aa8a-5e9df97bea3a)/publications.html), [University of Edinburgh](http://www.ed.ac.uk/)
[Bert Overduin](https://www.linkedin.com/pub/bert-overduin/21/233/129), [University of Edinburgh](http://www.ed.ac.uk/) ** diff --git a/content/events/unc2013/index.md b/content/events/unc2013/index.md index 06f7cc660b..97bb065fa1 100644 --- a/content/events/unc2013/index.md +++ b/content/events/unc2013/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
July 19, 2013
-**Instructor: [Dave Clements](/src/people/dave-clements/index.md) +**Instructor: [Dave Clements](/people/dave-clements/) 9:00-4:30
Health Sciences Library Biogen-Idec Classroom (#307)
diff --git a/content/events/vsu2014/index.md b/content/events/vsu2014/index.md index 766b8cefb4..444ac65c6e 100644 --- a/content/events/vsu2014/index.md +++ b/content/events/vsu2014/index.md @@ -2,7 +2,7 @@ - +

Virginia State University
Introduction to Galaxy
December 12, 2014, 10:00-3:00

Instructor: Dave Clements
VSU Engineering Building, Room 205
Virginia State University
Petersburg, Virginia, United States
Introduction to Galaxy
December 12, 2014, 10:00-3:00

Instructor: Dave Clements
VSU Engineering Building, Room 205
Virginia State University
Petersburg, Virginia, United States
diff --git a/content/events/wash-u2013/index.md b/content/events/wash-u2013/index.md index 592961ca13..dafcbb773a 100644 --- a/content/events/wash-u2013/index.md +++ b/content/events/wash-u2013/index.md @@ -5,7 +5,7 @@ **Workshops for the Washington University community -Instructor: [Dave Clements](/src/people/dave-clements/index.md), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) +Instructor: [Dave Clements](/people/dave-clements/), [Galaxy Project](http://galaxyproject.org), [Emory University](http://emory.edu) 9:00am-5:00pm (both days)** diff --git a/content/galaxy-qa/index.md b/content/galaxy-qa/index.md index eebbba6142..a636c6276a 100644 --- a/content/galaxy-qa/index.md +++ b/content/galaxy-qa/index.md @@ -18,7 +18,7 @@ The Galaxy Q&A and [BioStar](http://www.biostars.org/) source code is open-sourc * [Galaxy Q&A source code](https://github.com/galaxyQandA) * [BioStar source code](https://github.com/ialbert/biostar-central) -**For Galaxy team:** A mail has been sent for the meeting the *08/29/2012* with all the credentials to access to Galaxy Q&A, the object of the mail is ***"[galaxy-lab] Tasks"*** from [Anton Nekrutenko](/src/people/anton/index.md) +**For Galaxy team:** A mail has been sent for the meeting the *08/29/2012* with all the credentials to access to Galaxy Q&A, the object of the mail is ***"[galaxy-lab] Tasks"*** from [Anton Nekrutenko](/people/anton/) ## Set up Galaxy Q&A diff --git a/content/galaxy-team/index.md b/content/galaxy-team/index.md index 0e47382801..80120394e5 100644 --- a/content/galaxy-team/index.md +++ b/content/galaxy-team/index.md @@ -7,72 +7,72 @@ Galaxy is developed by the [Nekrutenko lab](http://nekrut.bx.psu.edu) in the [Ce
-[![Enis Afgan](/src/images/people/EnisAfgan.jpg)](/src/people/enis-afgan/index.md) +[![Enis Afgan](/src/images/people/EnisAfgan.jpg)](/people/enis-afgan/) -[Enis Afgan](/src/people/enis-afgan/index.md) +[Enis Afgan](/people/enis-afgan/) [Johns Hopkins](http://www.jhu.edu)
-[![Dannon Baker](/src/images/people/dannon.jpg)](/src/people/dannon-baker/index.md) -[Dannon Baker](/src/people/dannon-baker/index.md) +[![Dannon Baker](/src/images/people/dannon.jpg)](/people/dannon-baker/) +[Dannon Baker](/people/dannon-baker/) [Johns Hopkins](http://www.jhu.edu)
-[![Dan Blankenberg](/src/images/people/dan.jpg)](/src/people/dan/index.md) -[Dan Blankenberg](/src/people/dan/index.md) +[![Dan Blankenberg](/src/images/people/dan.jpg)](/people/dan/) +[Dan Blankenberg](/people/dan/) [The Cleveland Clinic](https://www.lerner.ccf.org/)
-[![Dave Bouvier](/src/galaxy-team/davebouvierflag.jpg)](/src/people/dave-bouvier/index.md) -[Dave Bouvier](/src/people/dave-bouvier/index.md) +[![Dave Bouvier](/src/galaxy-team/davebouvierflag.jpg)](/people/dave-bouvier/) +[Dave Bouvier](/people/dave-bouvier/) [Penn State](http://www.bx.psu.edu)
-[![Marten Cech](/src/people/marten/marten.jpg)](/src/people/marten/index.md) -[Martin Cech](/src/people/marten/index.md) +[![Marten Cech](/people/marten/marten.jpg)](/src/people/marten/) +[Martin Cech](/people/marten/) [Penn State](http://www.bx.psu.edu)
-[![John Chilton](/src/images/people/JohnChiltonSmaller.jpg)](/src/people/john-chilton/index.md) -[John Chilton](/src/people/john-chilton/index.md) +[![John Chilton](/src/images/people/JohnChiltonSmaller.jpg)](/people/john-chilton/) +[John Chilton](/people/john-chilton/) [Penn State](http://www.bx.psu.edu)
-[![Dave Clements](/src/galaxy-team/Clements.jpg)](/src/people/dave-clements/index.md) -[Dave Clements](/src/people/dave-clements/index.md) +[![Dave Clements](/src/galaxy-team/Clements.jpg)](/people/dave-clements/) +[Dave Clements](/people/dave-clements/) [Johns Hopkins](http://www.jhu.edu)
-[![Nate Coraor](/src/galaxy-team/nate.jpg)](/src/people/nate/index.md) -[Nate Coraor](/src/people/nate/index.md) +[![Nate Coraor](/src/galaxy-team/nate.jpg)](/people/nate/) +[Nate Coraor](/people/nate/) [Penn State](http://www.bx.psu.edu)
-[![Jeremy Goecks](/src/images/people/jgoecks-banff-small.png)](/src/people/jeremy-goecks/index.md) -[Jeremy Goecks](/src/people/jeremy-goecks/index.md) +[![Jeremy Goecks](/src/images/people/jgoecks-banff-small.png)](/people/jeremy-goecks/) +[Jeremy Goecks](/people/jeremy-goecks/) [OHSU](http://www.ohsu.edu)
-[![Sergey Golitsynskiy](/src/galaxy-team/sergey.jpg)](/src/people/sergey/index.md) -[Sergey Golitsynskiy](/src/people/sergey/index.md) +[![Sergey Golitsynskiy](/src/galaxy-team/sergey.jpg)](/people/sergey/) +[Sergey Golitsynskiy](/people/sergey/) [Johns Hopkins](http://www.jhu.edu)
@@ -87,57 +87,57 @@ Qiang Gu
-[![Aysam Guerler](/src/galaxy-team/guerler.jpg)](/src/people/guerler/index.md) -[Aysam Guerler](/src/people/guerler/index.md) +[![Aysam Guerler](/src/galaxy-team/guerler.jpg)](/people/guerler/) +[Aysam Guerler](/people/guerler/) [Johns Hopkins](http://www.jhu.edu)
-[![Mo Heydarian](/src/galaxy-team/mheydarian.jpg)](/src/people/mo-heydarian/index.md) -[Mo Heydarian](/src/people/mo-heydarian/index.md) +[![Mo Heydarian](/src/galaxy-team/mheydarian.jpg)](/people/mo-heydarian/) +[Mo Heydarian](/people/mo-heydarian/) [Johns Hopkins](http://www.jhu.edu)
-[![Jen Jackson](/src/galaxy-team/jenhjackson.png)](/src/people/jennifer-jackson/index.md) -[Jennifer Hillman Jackson](/src/people/jennifer-jackson/index.md) +[![Jen Jackson](/src/galaxy-team/jenhjackson.png)](/people/jennifer-jackson/) +[Jennifer Hillman Jackson](/people/jennifer-jackson/) [Penn State](http://www.bx.psu.edu)
-[![Vahid Jalili](/src/galaxy-team/Vahid.jpg)](/src/people/vahid-jalili/index.md) -[Vahid Jalili](/src/people/vahid-jalili/index.md) +[![Vahid Jalili](/src/galaxy-team/Vahid.jpg)](/people/vahid-jalili/) +[Vahid Jalili](/people/vahid-jalili/) [OHSU](http://www.ohsu.edu)
-[![DelphineLariviere](/src/galaxy-team/DelphineLariviere.jpg)](/src/people/delphine-lariviere/index.md) -[Delphine Lariviere](/src/people/delphine-lariviere/index.md) +[![DelphineLariviere](/src/galaxy-team/DelphineLariviere.jpg)](/people/delphine-lariviere/) +[Delphine Lariviere](/people/delphine-lariviere/) [Penn State](http://www.bx.psu.edu)
-[![Alexandru Mahmoud](/src/galaxy-team/almahmoud.jpg)](/src/people/almahmoud/index.md) -[Alexandru Mahmoud](/src/people/almahmoud/index.md) +[![Alexandru Mahmoud](/src/galaxy-team/almahmoud.jpg)](/people/almahmoud/) +[Alexandru Mahmoud](/people/almahmoud/) [Johns Hopkins](http://www.jhu.edu)
-[![Anton Nekrutenko](/src/images/people/anton.jpg)](/src/people/anton/index.md) -[Anton Nekrutenko](/src/people/anton/index.md) +[![Anton Nekrutenko](/src/images/people/anton.jpg)](/people/anton/) +[Anton Nekrutenko](/people/anton/) [Penn State](http://www.bx.psu.edu)
-[![Alex Ostrovsky](/src/galaxy-team/ostrovsky.jpg)](/src/people/alex-ostrovsky/index.md) -[Alex Ostrovsky](/src/people/alex-ostrovsky/index.md) +[![Alex Ostrovsky](/src/galaxy-team/ostrovsky.jpg)](/people/alex-ostrovsky/) +[Alex Ostrovsky](/people/alex-ostrovsky/) [Johns Hopkins](http://www.jhu.edu)
@@ -157,8 +157,8 @@ Luke Sargent
-[![James Taylor](/src/images/people/james.jpg)](/src/people/james-taylor/index.md) -[James Taylor](/src/people/james-taylor/index.md) +[![James Taylor](/src/images/people/james.jpg)](/people/james-taylor/) +[James Taylor](/people/james-taylor/) [Johns Hopkins](http://www.jhu.edu)
@@ -171,8 +171,8 @@ Luke Sargent
-[![Matthias Bernt](/src/galaxy-team/matthias.jpg)](/src/people/matthias/index.md) -[Matthias Bernt](/src/people/matthias/index.md) +[![Matthias Bernt](/src/galaxy-team/matthias.jpg)](/people/matthias/) +[Matthias Bernt](/people/matthias/) [UFZ Leipzig](https://www.ufz.de/)
@@ -242,7 +242,7 @@ Luke Sargent
![Greg von Kuster](/src/images/people/greg.png) -[Greg von Kuster](/src/people/greg_vonkuster/index.md) +[Greg von Kuster](/people/greg_vonkuster/) [Penn State](http://www.bx.psu.edu)
@@ -270,23 +270,23 @@ Luke Sargent * Ramkrishna Chakrabarty * Wen-Yu Chung * Fabio Cumbo -* [Carl Eberhard](/src/people/carl-eberhard/index.md) +* [Carl Eberhard](/people/carl-eberhard/) * Dorine Francheteau * Mallory Freeberg * Belinda Giardine * Jianbin He -* [Mo Heydarian](/src/people/mo-heydarian/index.md) +* [Mo Heydarian](/people/mo-heydarian/) * Radesh Kamath * Ross Lazarus * Kanwei Li -* [Rémi Marenco](/src/people/remi-marenco/index.md) +* [Rémi Marenco](/people/remi-marenco/) * Scott McManus * Arjun Nath * Chinmay Rao * Prachi Shah * Ian Schenck * Kelly Vincent -* [Nitesh Turaga](/src/people/nitesh-turaga/index.md) +* [Nitesh Turaga](/people/nitesh-turaga/) * Yi Zhang ## Past Contributors diff --git a/content/galaxy-updates/2012-02/index.md b/content/galaxy-updates/2012-02/index.md index f3463ea68b..f354e5d628 100644 --- a/content/galaxy-updates/2012-02/index.md +++ b/content/galaxy-updates/2012-02/index.md @@ -1,7 +1,7 @@ --- title: February 2012 Galaxy Update --- -
**Looking for the [March 2012 Galaxy Update](/src/galaxy-updates/2012-03/index.md)? Click [here](/src/galaxy-updates/2012-03/index.md).**
Sorry about the bad link in the email announcement! [Dave C](/src/people/dave-clements/index.md)
+
**Looking for the [March 2012 Galaxy Update](/src/galaxy-updates/2012-03/index.md)? Click [here](/src/galaxy-updates/2012-03/index.md).**
Sorry about the bad link in the email announcement! [Dave C](/people/dave-clements/)
@@ -18,7 +18,7 @@ New papers of note for the Galaxy community: * Thomas Hentrich, Julia M. Schulze, Eldon Emberly, and Michael S. Kobor, "[CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures](http://bioinformatics.oxfordjournals.org/content/early/2012/01/10/bioinformatics.bts007.short)." *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* -* Jeremy Goecks, Kanwei Li, [Dave Clements](/src/people/dave-clements/index.md), The [Galaxy Team](/src/galaxy-team/index.md), James Taylor, "[The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool](http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6094046)." *[Biological Data Visualization (BioVis), 2011 IEEE Symposium on](http://www.biovis.net/)* +* Jeremy Goecks, Kanwei Li, [Dave Clements](/people/dave-clements/index.md), The [Galaxy Team](/src/galaxy-team/), James Taylor, "[The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool](http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6094046)." *[Biological Data Visualization (BioVis), 2011 IEEE Symposium on](http://www.biovis.net/)* Plus [27 other papers](http://www.citeulike.org/group/16008/library) that use, reference, or are about Galaxy. @@ -62,7 +62,7 @@ Abstract submission for the [2012 Galaxy Community Conference (GCC2012)](/src/ev April 5-6 April 2012 GMOD Meeting Washington DC, immediately following Biocuration 2012 - Dave Clements + Dave Clements July 13-17 @@ -74,7 +74,7 @@ Abstract submission for the [2012 Galaxy Community Conference (GCC2012)](/src/ev July 25-27 2012 Galaxy Community Conference Chicago, Illinois, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2012-03/index.md b/content/galaxy-updates/2012-03/index.md index a08745a5cd..47506e222a 100644 --- a/content/galaxy-updates/2012-03/index.md +++ b/content/galaxy-updates/2012-03/index.md @@ -73,7 +73,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr April 5-6 April 2012 GMOD Meeting
Including a Galaxy Workshop on evening of April 5. Early registration ends March 7. Washington DC, immediately following Biocuration 2012 - Dave Clements + Dave Clements April 24-26 @@ -85,7 +85,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore - James Taylor + James Taylor June 11-12 @@ -103,13 +103,13 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 13-17 Bioinformatics Software Interoperability SIG (BSI-SIG) ISMB 2012, Long Beach, California, United States - Anton Nekrutenko + Anton Nekrutenko July 25-27 2012 Galaxy Community Conference
Abstract submission is now open, and Training Day topics are set. Chicago, Illinois, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2012-04/index.md b/content/galaxy-updates/2012-04/index.md index eafdcc459a..73de7c81c3 100644 --- a/content/galaxy-updates/2012-04/index.md +++ b/content/galaxy-updates/2012-04/index.md @@ -86,7 +86,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr April 5-6 April 2012 GMOD Meeting
Including a Galaxy Workshop on evening of April 5 Washington DC, immediately following Biocuration 2012 - Dave Clements + Dave Clements April 24-26 @@ -98,7 +98,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore - James Taylor + James Taylor June 11-12 @@ -122,13 +122,13 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 13-17 Bioinformatics Software Interoperability SIG (BSI-SIG) ISMB 2012, Long Beach, California, United States - Anton Nekrutenko + Anton Nekrutenko July 25-27 2012 Galaxy Community Conference
Early registration and abstract submission are now open. Chicago, Illinois, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2012-05/index.md b/content/galaxy-updates/2012-05/index.md index 4e38996768..f7bccf3b44 100644 --- a/content/galaxy-updates/2012-05/index.md +++ b/content/galaxy-updates/2012-05/index.md @@ -38,7 +38,7 @@ Also, if you are interested in presenting a topic, especially a "how to use Gala
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/src/people/nate/index.md), [Anton Nekrutenko](/src/people/anton/index.md) and [James Taylor](/src/people/james-taylor/index.md). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/index.md), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See [Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md) for details and links. @@ -122,7 +122,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr May 8-12 Staying on top of evolving best practices with Galaxy, Poster The Biology of Genomes, Cold Spring Harbor Laboratory, New York, United States - Dan Blankenberg + Dan Blankenberg http://gmod.org/wiki/|GMOD in the Cloud, Poster @@ -130,7 +130,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr Integrative venomics reveals different infection strategies for parasitic wasps, poster - Jeremy Goecks + Jeremy Goecks May 28 - June 1 @@ -142,7 +142,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore - James Taylor + James Taylor June 11-12 @@ -166,13 +166,13 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 13-17 Bioinformatics Software Interoperability SIG (BSI-SIG) ISMB 2012, Long Beach, California, United States - Anton Nekrutenko + Anton Nekrutenko July 25-27 2012 Galaxy Community Conference
Early registration is now open. Chicago, Illinois, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2012-06/index.md b/content/galaxy-updates/2012-06/index.md index aa375ad4f4..5287fd69d0 100644 --- a/content/galaxy-updates/2012-06/index.md +++ b/content/galaxy-updates/2012-06/index.md @@ -111,7 +111,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll p
-There are June application and early registration deadlines for [GCC2012](/src/events/gcc2012/register/index.md), [ISMB 2012](/src/events/ismb2012/index.md), SciPy, and the Winter School in Mathematical and Computational Biology, and an abstract deadline for ASHG 2012. It's also a big month for conferences and courses, including Arthropod Genomics, Bio-IT World Asia ([James Taylor](/src/people/james-taylor/index.md) will be speaking), SocBIN, [Next-gen sequencing in evolutionary biology](https://academy.nescent.org/wiki/Next-gen_sequencing) Course at NESCent (Sergei Kosakovsky-Pond will cover Galaxy), [Informatics on High Throughput Sequencing Data Workshop](http://www.bioinformatics.ca/workshops/high_throughput) (Francis Ouellette will cover Galaxy), Copenhagenomics, SMBE 2012, and, ESHG 2012, *to name just a few.* +There are June application and early registration deadlines for [GCC2012](/src/events/gcc2012/register/index.md), [ISMB 2012](/src/events/ismb2012/index.md), SciPy, and the Winter School in Mathematical and Computational Biology, and an abstract deadline for ASHG 2012. It's also a big month for conferences and courses, including Arthropod Genomics, Bio-IT World Asia ([James Taylor](/people/james-taylor/) will be speaking), SocBIN, [Next-gen sequencing in evolutionary biology](https://academy.nescent.org/wiki/Next-gen_sequencing) Course at NESCent (Sergei Kosakovsky-Pond will cover Galaxy), [Informatics on High Throughput Sequencing Data Workshop](http://www.bioinformatics.ca/workshops/high_throughput) (Francis Ouellette will cover Galaxy), Copenhagenomics, SMBE 2012, and, ESHG 2012, *to name just a few.* See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?src=mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com) for details on these and other events. @@ -128,7 +128,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore - James Taylor + James Taylor June 11-12 @@ -164,7 +164,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 25-27 2012 Galaxy Community Conference
Early registration ends June 11.
University of Illinois Chicago, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2012-07/index.md b/content/galaxy-updates/2012-07/index.md index 6c2733de5d..9b9d1608db 100644 --- a/content/galaxy-updates/2012-07/index.md +++ b/content/galaxy-updates/2012-07/index.md @@ -52,9 +52,9 @@ Welcome to the July 2012 edition of *[Galaxy Update](/src/galaxy-updates/index.m These papers may be of interest to the Galaxy community: -* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/src/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/index.md), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. +* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. -* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Daniel Blankenberg](/src/people/dan/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), [Galaxy Team](/src/galaxy-team/index.md), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. +* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. These papers were among [31 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md) (for a total of 348 papers in the last ~16 months). The new papers are spread [across 8 categories](http://www.citeulike.org/group/16008/tags). @@ -126,7 +126,7 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 5-6 Atelier Galaxy Le Centre de Génomique Fonctionnelle Bordeaux - Anton Nekrutenko + Anton Nekrutenko July 11 @@ -144,19 +144,19 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr July 25-27 2012 Galaxy Community Conference
Registration deadline is July 18
University of Illinois Chicago, United States - Dave Clements + Dave Clements August 25-29 2012 GMOD Summer School
Application deadline is July 9 US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States - Dave Clements + Dave Clements September 3-4 Galaxy Workshop
Application deadline is June 30
University of Pretoria, Pretoria, South Africa - Dave Clements + Dave Clements September 6-7 @@ -166,19 +166,19 @@ See the [Galaxy Events Google Calendar](https://www.google.com/calendar/embed?sr September 10-11 Systems Bioinformatics Workshop
Early registration deadline is June 30
Institute for Systems Biology
Seattle, Washington, United States - James Taylor + James Taylor September 10-12 Transparent, accessible, reproducible analysis with Galaxy
Early registration deadline is July 1
South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa - Dave Clements + Dave Clements September 27-29 Beyond the Genome 2012 Harvard Medical School, Boston, Massachusetts - James Taylor + James Taylor @@ -212,7 +212,7 @@ A new version of CloudMan was [Released in June](/src/news/new-cloudman-release/ 1. Several new videos, screencasts, and tutorials were posted: * [OpenHelix Video Tip of the Week: Visualizing the Galaxy](http://blog.openhelix.eu/?p=12439) * [Using PhyloTastic Tools inside Galaxy](http://www.youtube.com/watch?v=kMME658xOu4&feature=youtu.be), by Rutger Vos - * [Getting Started with the CloudMan Platform Using BioCloudCentral](http://www.youtube.com/watch?v=AKu_CbbgEj0), by [Enis Afgan](/src/people/enis-afgan/index.md) + * [Getting Started with the CloudMan Platform Using BioCloudCentral](http://www.youtube.com/watch?v=AKu_CbbgEj0), by [Enis Afgan](/people/enis-afgan/) * [Using Galaxy for NGS Analysis](http://chagall.med.cornell.edu/galaxy/), by [Luce Skrabanek](mailto:las2017 AT med DOT cornell DOT edu) * [RNA-Seq Course v1.0 documentation](http://training.bioinformatics.ucdavis.edu/docs/2012/05/RNA/index.html), by [UC Davis Bioinformatics Professional Training Program](http://training.bioinformatics.ucdavis.edu/) * [Cloud Computing for Bioinformatics](http://training.bioinformatics.ucdavis.edu/docs/2012/05/AWS/index.html) (using AWS and Galaxy, but not using CloudMan), by [UC Davis Bioinformatics Professional Training Program](http://training.bioinformatics.ucdavis.edu/) diff --git a/content/galaxy-updates/2012-08/index.md b/content/galaxy-updates/2012-08/index.md index 19ca65c119..a2611961eb 100644 --- a/content/galaxy-updates/2012-08/index.md +++ b/content/galaxy-updates/2012-08/index.md @@ -133,13 +133,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the August 25-29 http://gmod.org/wiki/2012 GMOD Summer School US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States - Dave Clements + Dave Clements September 3-4 Galaxy Workshop University of Pretoria, Pretoria, South Africa - Dave Clements + Dave Clements September 6-7 @@ -149,31 +149,31 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the September 10-11 Systems Bioinformatics Workshop Institute for Systems Biology
Seattle, Washington, United States - James Taylor + James Taylor September 10-12 Transparent, accessible, reproducible analysis with Galaxy South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa - Dave Clements + Dave Clements September 27-29 Beyond the Genome 2012 Harvard Medical School, Boston, Massachusetts - James Taylor + James Taylor October 3 (first Swiss) Galaxy Workshop SyBIT Tech Day, Bern, Switzerland - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-12 Extending High-Performance Computing Beyond its Traditional User Communities Workshop 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States - James Taylor + James Taylor diff --git a/content/galaxy-updates/2012-09/index.md b/content/galaxy-updates/2012-09/index.md index fc096ccacb..7ab0b9ed3d 100644 --- a/content/galaxy-updates/2012-09/index.md +++ b/content/galaxy-updates/2012-09/index.md @@ -50,7 +50,7 @@ Welcome to the September 2012 edition of *[Galaxy Update](/src/galaxy-updates/in These papers may be of interest to the Galaxy community: -* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/src/people/anton/index.md) & [Taylor](/src/people/james-taylor/index.md), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) +* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/people/anton/index.md) & [Taylor](/src/people/james-taylor/), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) * "[IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis](https://doi.org/10.1186/1471-2105-13-S14-S5)", by Merelli, Viti, Milanesi, *BMC Bioinformatics*, Vol. 13, No. Suppl 14. (2011), S5 @@ -116,7 +116,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the September 3-4 Galaxy Workshop University of Pretoria, Pretoria, South Africa - Dave Clements + Dave Clements September 6-7 @@ -126,13 +126,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the September 10-11 Systems Bioinformatics Workshop Institute for Systems Biology
Seattle, Washington, United States - James Taylor + James Taylor September 10-12 Transparent, accessible, reproducible analysis with Galaxy South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa - Dave Clements + Dave Clements Assembling a cassava transcriptome using Galaxy on a high performance computing cluster @@ -154,19 +154,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the September 27-29 Informatics Workshop Beyond the Genome 2012, Harvard Medical School, Boston, Massachusetts - James Taylor + James Taylor October 3 (first Swiss) Galaxy Workshop SyBIT Tech Day, Bern, Switzerland - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-12 Extending High-Performance Computing Beyond its Traditional User Communities Workshop 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States - James Taylor + James Taylor October 9-11 @@ -178,19 +178,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the October 31 - November 6 Computaional & Comparative Genomics Course Cold Spring Harbor Laboratory, New York, United States - William Pearson, James Taylor + William Pearson, James Taylor October 28 - November 2 Genomic Virtual Laboratory Workshop eResearch Australasia, Sydney, Australia - Enis Afgan + Enis Afgan November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States - Jennifer Jackson, Jeremy Goecks + Jennifer Jackson, Jeremy Goecks Working with High-Throughput Data and Data Visualization @@ -258,7 +258,7 @@ The most recent Galaxy distribution was [released on July 20, 2012](/src/archive * [Upgrading Galaxy](http://www.agapow.net/science/bioinformatics/galaxy/upgrading-galaxy) * [Setting up a Galaxy toolshed](http://www.agapow.net/science/bioinformatics/galaxy/setting-up-a-galaxy-toolshed) * [Ntino Krampis BioTechniques interview](http://www.biotechniques.com/multimedia/podcasts/#.UD6V2VTYNUO) on doing bioinformatics on the cloud, including CloudMan. -* [Jeremy Goecks](/src/people/jeremy-goecks/index.md) updated his [RNA-seq Analysis Exercise Galaxy Page](https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise) to cover quality control through CuffDiff: paired-end data, iGenomes gtf, answer key, and bonus resources +* [Jeremy Goecks](/people/jeremy-goecks/) updated his [RNA-seq Analysis Exercise Galaxy Page](https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise) to cover quality control through CuffDiff: paired-end data, iGenomes gtf, answer key, and bonus resources * [Slides and videos](http://bit.ly/QGxVJU) for the Iowa Initiative in Human Genetics [Bioinformatics Course](http://bit.ly/QGxVJU) * A few summaries of the recent [2012 Galaxy Community Conference (GCC2012)](/src/events/gcc2012/index.md) have been posted online: * Peter Li's [GigaBlog post](http://blogs.biomedcentral.com/gigablog/2012/08/06/enabling-bioinformatics-tools-to-smoke-the-peace-pipe-together/) diff --git a/content/galaxy-updates/2012-10/index.md b/content/galaxy-updates/2012-10/index.md index 1250ea8ff6..924fcfce6c 100644 --- a/content/galaxy-updates/2012-10/index.md +++ b/content/galaxy-updates/2012-10/index.md @@ -53,7 +53,7 @@ Welcome to the October 2012 edition of *[Galaxy Update](/src/galaxy-updates/inde These papers may be of interest to the Galaxy community: -* [Turning pipe dreams into reality](https://doi.org/10.1186/gb4039) by Peter Li, [Jeremy Goecks](/src/people/jeremy-goecks/index.md), Tin L. Lee, *Genome Biology*, Vol. 13, No. 8. (2012), 318. +* [Turning pipe dreams into reality](https://doi.org/10.1186/gb4039) by Peter Li, [Jeremy Goecks](/people/jeremy-goecks/), Tin L. Lee, *Genome Biology*, Vol. 13, No. 8. (2012), 318. * [Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome](https://doi.org/10.1002/0471250953.bi1502s39), by Belinda M. Giardine, Cathy Riemer, Richard Burhans, Aakrosh Ratan, Webb Miller; in *Current Protocols in Bioinformatics* 39:15.2.1-15.2.27 @@ -114,13 +114,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the October 3 (first Swiss) Galaxy Workshop SyBIT Tech Day, Bern, Switzerland - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-12 Lessons from Galaxy, a Web-based Platform for High-throughput Genomic Analyses Extending High-Performance Computing Beyond its Traditional User Communities Workshop, part of 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States - Jeremy Goecks + Jeremy Goecks October 9-11 @@ -138,25 +138,25 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the October 18-30 Advanced Sequencing Technologies and Applications Course Cold Spring Harbor Laboratory, New York, United States - Anton Nekrutenko + Anton Nekrutenko October 31 - November 6 Computaional & Comparative Genomics Course Cold Spring Harbor Laboratory, New York, United States - William Pearson, James Taylor + William Pearson, James Taylor October 28 - November 2 Genomic Virtual Laboratory Workshop eResearch Australasia, Sydney, Australia - Enis Afgan + Enis Afgan November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States - Jennifer Jackson, Jeremy Goecks + Jennifer Jackson, Jeremy Goecks Working with High-Throughput Data and Data Visualization diff --git a/content/galaxy-updates/2012-11/index.md b/content/galaxy-updates/2012-11/index.md index b81ba94253..eeadde32ca 100644 --- a/content/galaxy-updates/2012-11/index.md +++ b/content/galaxy-updates/2012-11/index.md @@ -60,11 +60,11 @@ These papers may be of interest to the Galaxy community: * "[Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing](https://doi.org/10.1242/dev.083931)," Nikolaus Obholzer, Ian A. Swinburne, Evan Schwab, Alex V. Nechiporuk, Teresa Nicolson, Sean G. Megason; *[Development](http://dev.biologists.org/)* (10 October 2012)
→ *The [MegaMapper](http://bit.ly/QupZs1) package is implemented in Galaxy and [is available as a VirtualBox VM and an Amazon AMI](http://bit.ly/QupZs1).*

-* "[CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences](https://doi.org/10.1534/genetics.112.144204)," Gregory Minevich, Danny S. Park, [Daniel Blankenberg](/src/people/dan/index.md), Richard J. Poole, Oliver Hobert, *[Genetics](http://www.genetics.org/)* (10 October 2012)

+* "[CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences](https://doi.org/10.1534/genetics.112.144204)," Gregory Minevich, Danny S. Park, [Daniel Blankenberg](/people/dan/), Richard J. Poole, Oliver Hobert, *[Genetics](http://www.genetics.org/)* (10 October 2012)

* "[G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes](https://doi.org/10.1186/1471-2105-13-253)," Danielle Lemay, William Martin, Angie Hinrichs, Monique Rijnkels, J. German, Ian Korf, Katherine Pollard, *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)*, Vol. 13, No. 1. (28 September 2012), 253

-* "[Creating re-usable tools from scripts: The Galaxy Tool Factory](https://doi.org/10.1093/bioinformatics/bts573)," [Ross Lazarus](/src/people/fubar/index.md), Antony Kaspi, Mark Ziemann, [The Galaxy Team](/src/galaxy-team/index.md), *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* (28 September 2012) +* "[Creating re-usable tools from scripts: The Galaxy Tool Factory](https://doi.org/10.1093/bioinformatics/bts573)," [Ross Lazarus](/people/fubar/index.md), Antony Kaspi, Mark Ziemann, [The Galaxy Team](/src/galaxy-team/), *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* (28 September 2012) These papers were among [44 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md). @@ -131,13 +131,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the October 28 - November 2 Genomic Virtual Laboratory Workshop eResearch Australasia, Sydney, Australia - Enis Afgan + Enis Afgan November 6-10 Galaxy 101: Data Integration, Analysis and Sharing
Sold out
American Society of Human Genetics (ASHG), San Francisco, California, United States - Jennifer Jackson, Jeremy Goecks + Jennifer Jackson, Jeremy Goecks Working with High-Throughput Data and Data Visualization
Sold out
@@ -158,7 +158,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the November 28 - December 4 Computaional & Comparative Genomics Course
This was rescheduled due to hurricane Sandy
Cold Spring Harbor Laboratory, New York, United States - William Pearson, James Taylor + William Pearson, James Taylor @@ -167,7 +167,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the January 12-16 Plant and Animal Genome (PAG 2013) San Diego, California, United States - Dave Clements + Dave Clements January 28 - February 1 diff --git a/content/galaxy-updates/2012-12/index.md b/content/galaxy-updates/2012-12/index.md index 229a11e4fd..5c42e4bfeb 100644 --- a/content/galaxy-updates/2012-12/index.md +++ b/content/galaxy-updates/2012-12/index.md @@ -45,8 +45,8 @@ These papers may be of interest to the Galaxy community:
-* [Enis Afgan](/src/people/enis-afgan/index.md), Brad Chapman and [James Taylor](/src/people/james-taylor/index.md), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

-* [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [Nate Coraor](/src/people/nate/index.md), [The Galaxy Team](/src/galaxy-team/index.md), [Anton Nekrutenko](/src/people/anton/index.md) & [James Taylor](/src/people/james-taylor/index.md), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

+* [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman and [James Taylor](/src/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

+* [Jeremy Goecks](/people/jeremy-goecks/index.md), [Nate Coraor](/people/nate/index.md), [The Galaxy Team](/src/galaxy-team/index.md), [Anton Nekrutenko](/src/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

* Samantha Baldwin, Roopashree Revanna, Susan Thomson, *et al.*, "[A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)](https://doi.org/10.1186/1471-2164-13-637)," *BMC Genomics*, Vol. 13, No. 1. (2012), 637

* Jeremy C. Morgan, Robert W. Chapman, Paul E. Anderson, "[A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources](https://doi.org/10.1145/2382936.2383033). Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

* Bo Liu, Borja Sotomayor, Ravi Madduri, Kyle Chard, "[Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision](http:// bit.ly/UPBbRI)." [Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012)](http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/) @@ -109,13 +109,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the January 12-16 Galaxy Part of the GMOD Workshop at Plant and Animal Genome (PAG 2013), San Diego, California, United States - Jennifer Jackson + Jennifer Jackson January 16 Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan January GalaxyAdmins Web Meetup - John Chilton, Srinivas Maddhi, Dave Clements + John Chilton, Srinivas Maddhi, Dave Clements January 14-18 @@ -133,19 +133,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the March 2-5 SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis and
W6: Community Resource Solutions to Analyzing Large Genomic Data Sets ABRF 2013
Palm Springs, California, United States - Dave Clements + Dave Clements April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 - Dave Clements + Dave Clements April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom - Dave Clements, Suzanna Lewis + Dave Clements, Suzanna Lewis June 30 - July 2 @@ -241,8 +241,8 @@ Several new repositories were added to, and existing repositories updated in the * [GCC2013](/src/events/gcc2013/index.md) is coming. Help [get the word out](/src/events/gcc2013/promotion/index.md)! * [Training Day Topic Nominations](/src/events/gcc2013/training-day/index.md) for [GCC2013](/src/events/gcc2013/index.md) will open in December. Please start thinking of ideas now. -* Slides and Screencast from [November GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2012-11-14/index.md) are online. The next [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/index.md) will be on [January 16](/src/community/galaxy-admins/meetups/2013-01-16/index.md) and feature [John Chilton](/src/people/john-chilton/index.md) discussing "Deploying Galaxy on OpenStack with CloudBioLinux & CloudMan" +* Slides and Screencast from [November GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2012-11-14/index.md) are online. The next [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/index.md) will be on [January 16](/src/community/galaxy-admins/meetups/2013-01-16/index.md) and feature [John Chilton](/people/john-chilton/) discussing "Deploying Galaxy on OpenStack with CloudBioLinux & CloudMan" * New Tutorial: *[Analysis of ChIP-seq data in Galaxy](http://jura.wi.mit.edu/bio/education/hot_topics/galaxy/GalaxyNov2012_ChIP-seq_toPost.pdf)* from the [BaRC, Whitehead Institute](http://jura.wi.mit.edu/bio/education/hot_topics/) -* [A short "Getting started with JGalaxy"](http://bit.ly/SkW2yU) document (with screenshots), by [John Chilton](/src/people/john-chilton/index.md) +* [A short "Getting started with JGalaxy"](http://bit.ly/SkW2yU) document (with screenshots), by [John Chilton](/people/john-chilton/) * [生物人的電腦教室：高通量定序分析一次搞定](http://bit.ly/Sc4LDN) including Galaxy, by Eric Lee * [Batch Workflow starting using the Galaxy API : Practical Example](http://bit.ly/TjTj6X) by Geert Vandeweyer diff --git a/content/galaxy-updates/2013-01/index.md b/content/galaxy-updates/2013-01/index.md index d78ff2f4fd..e9af47d04f 100644 --- a/content/galaxy-updates/2013-01/index.md +++ b/content/galaxy-updates/2013-01/index.md @@ -146,13 +146,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the January 12-16 Galaxy Part of the GMOD Workshop at Plant and Animal Genome (PAG 2013), San Diego, California, United States - Jennifer Jackson + Jennifer Jackson January 16 Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan January GalaxyAdmins Web Meetup - John Chilton, Srinivas Maddhi, Dave Clements + John Chilton, Srinivas Maddhi, Dave Clements January 14-18 @@ -164,7 +164,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the March 2-5 SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis and
W6: Community Resource Solutions to Analyzing Large Genomic Data Sets ABRF 2013
Palm Springs, California, United States - Dave Clements + Dave Clements March 26-28 @@ -176,19 +176,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 - Dave Clements + Dave Clements April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom - Dave Clements, Suzanna Lewis + Dave Clements, Suzanna Lewis June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 30 - July 2 diff --git a/content/galaxy-updates/2013-02/index.md b/content/galaxy-updates/2013-02/index.md index 2b737dc336..f218596bda 100644 --- a/content/galaxy-updates/2013-02/index.md +++ b/content/galaxy-updates/2013-02/index.md @@ -168,7 +168,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the March 2-5 Accessible, Transparent and Reproducible Analysis With Galaxy, part of
SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis
Galaxy for Core Facilities, part of
"W6: Community Resource Solutions to Analyzing Large Genomic Data Sets"
ABRF 2013
Palm Springs, California, United States - Dave Clements + Dave Clements March 26-28 @@ -180,19 +180,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 - Dave Clements + Dave Clements April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom - Dave Clements, Suzanna Lewis + Dave Clements, Suzanna Lewis May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States - Anton Nekrutenko + Anton Nekrutenko June 6-7 @@ -204,7 +204,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 30 - July 2 diff --git a/content/galaxy-updates/2013-03/index.md b/content/galaxy-updates/2013-03/index.md index 65619761ea..999a7633f3 100644 --- a/content/galaxy-updates/2013-03/index.md +++ b/content/galaxy-updates/2013-03/index.md @@ -146,7 +146,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the March 2-5 Accessible, Transparent and Reproducible Analysis With Galaxy, part of
SW1: Application of NGS Platforms for Whole Transcriptome and Genome Analysis
Galaxy for Core Facilities, part of
"W6: Community Resource Solutions to Analyzing Large Genomic Data Sets"
ABRF 2013
Palm Springs, California, United States - Dave Clements + Dave Clements March 8 @@ -176,19 +176,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 - Dave Clements + Dave Clements April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom - Dave Clements, Suzanna Lewis + Dave Clements, Suzanna Lewis May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States - Anton Nekrutenko + Anton Nekrutenko June 6-7 @@ -200,7 +200,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 30 - July 2 diff --git a/content/galaxy-updates/2013-04/index.md b/content/galaxy-updates/2013-04/index.md index f47cd54ae0..7ff06a9955 100644 --- a/content/galaxy-updates/2013-04/index.md +++ b/content/galaxy-updates/2013-04/index.md @@ -198,7 +198,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 - Dave Clements + Dave Clements April 7-8 @@ -210,7 +210,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom - Dave Clements, Suzanna Lewis + Dave Clements, Suzanna Lewis April 9-11 @@ -237,19 +237,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 11 Introduction to Galaxy Workshop The Genome Analysis Centre, Norwich, United Kingdom - Dave Clements + Dave Clements May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States - Anton Nekrutenko + Anton Nekrutenko May 16-17 Galaxy Workflows for Bioinformatics Analysis, and
Workshop 1A – Galaxy Workflows for Bioinformatics Analysis Workshop in Next-Generation Sequence Analysis and Metabolomics (WiNGS), UNC-Charlotte, North Carolina, United States - James Taylor + James Taylor May 28-31 @@ -275,13 +275,13 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 13-14 Genomics and Epigenomics with Deep Sequencing, the 24th CDB Meeting RIKEN, CDB, Kobe, Japan - Anton Nekrutenko + Anton Nekrutenko June 30 - July 2 @@ -298,7 +298,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the ### March 2013 Meetup -Slides and the screencast from the [March GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-03-20/index.md) are [now available](/src/community/galaxy-admins/meetups/2013-03-20/index.md) [Hailiang "Leon" Mei](mailto:hailiang DOT mei AT nbic DOT nl) spoke on *[NBIC Galaxy deployment](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/).* [NBIC Galaxy (Andromeda)](http://galaxy.nbic.nl/) was migrated to a HPC cloud hosted by Surfsara in September 2012. Leon discussed the setup of this HPC cloud and the architecture of NBIC Galaxy and shared their experiences installing the NBIC Galaxy using the Cloudman scripts. The presentation finished with a list of issues and our possible future plans. [Dan Blankenberg](/src/people/dan/index.md) also discussed the new Galaxy release process, and the upcoming Data Manager enhancements. +Slides and the screencast from the [March GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-03-20/index.md) are [now available](/src/community/galaxy-admins/meetups/2013-03-20/index.md) [Hailiang "Leon" Mei](mailto:hailiang DOT mei AT nbic DOT nl) spoke on *[NBIC Galaxy deployment](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/).* [NBIC Galaxy (Andromeda)](http://galaxy.nbic.nl/) was migrated to a HPC cloud hosted by Surfsara in September 2012. Leon discussed the setup of this HPC cloud and the architecture of NBIC Galaxy and shared their experiences installing the NBIC Galaxy using the Cloudman scripts. The presentation finished with a list of issues and our possible future plans. [Dan Blankenberg](/people/dan/) also discussed the new Galaxy release process, and the upcoming Data Manager enhancements. ### GalaxyAdmins Future Directions diff --git a/content/galaxy-updates/2013-05/index.md b/content/galaxy-updates/2013-05/index.md index 22d6f14eb1..1e24df6395 100644 --- a/content/galaxy-updates/2013-05/index.md +++ b/content/galaxy-updates/2013-05/index.md @@ -49,7 +49,7 @@ Welcome to the May 2013 *[Galaxy Update](/src/galaxy-updates/index.md)*, a month 39 new papers were added to the Galaxy CiteULike Group in April, including: -* [BioBlend: automating pipeline analyses within Galaxy and CloudMan](https://doi.org/10.1093/bioinformatics/btt199), by Clare Sloggett, Nuwan Goonasekera, [Enis Afgan](/src/people/enis-afgan/index.md), Bioinformatics (28 April 2013) +* [BioBlend: automating pipeline analyses within Galaxy and CloudMan](https://doi.org/10.1093/bioinformatics/btt199), by Clare Sloggett, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/), Bioinformatics (28 April 2013) There are now over [950 papers in the Galaxy CiteULike Group](http://www.citeulike.org/group/16008/). @@ -131,19 +131,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States - Anton Nekrutenko + Anton Nekrutenko May 15 GalaxyAdmins May 2013 Meetup GalaxyAdmins web meetup - Srinivas Maddhi, Dave Clements + Srinivas Maddhi, Dave Clements May 16-17 Galaxy Workflows for Bioinformatics Analysis, and
Workshop 1A – Galaxy Workflows for Bioinformatics Analysis Workshop in Next-Generation Sequence Analysis and Metabolomics (WiNGS), UNC-Charlotte, North Carolina, United States - James Taylor + James Taylor May 24
June 19 @@ -181,25 +181,25 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 9-13 61st ASMS Conference on Mass Spectrometry and Allied Topics
Includes at least 1 workshop and 9 posters either about or utilizing Galaxy
Minneapolis, Minnesota, United States - John Chilton + John Chilton June 13-14 Genomics and Epigenomics with Deep Sequencing, the 24th CDB Meeting RIKEN, CDB, Kobe, Japan - Anton Nekrutenko + Anton Nekrutenko June 20-22 W1: Next-generation sequencing data analysis with GenomeSpace and Galaxy FGED Conference, Seattle, Washington - Dave Clements + Dave Clements June 30 - July 2 diff --git a/content/galaxy-updates/2013-06/index.md b/content/galaxy-updates/2013-06/index.md index 375f233e77..80a9bcd78c 100644 --- a/content/galaxy-updates/2013-06/index.md +++ b/content/galaxy-updates/2013-06/index.md @@ -193,25 +193,25 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 9-13 61st ASMS Conference on Mass Spectrometry and Allied Topics
Includes at least 1 workshop and 9 posters either about or utilizing Galaxy
Minneapolis, Minnesota, United States - John Chilton + John Chilton June 13-14 Genomics and Epigenomics with Deep Sequencing, the 24th CDB Meeting RIKEN, CDB, Kobe, Japan - Anton Nekrutenko + Anton Nekrutenko June 20-22 W1: Next-generation sequencing data analysis with GenomeSpace and Galaxy FGED Conference, Seattle, Washington - Dave Clements + Dave Clements June 21 @@ -235,7 +235,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the July 19-23 The “How To Guide” for Establishing a Successful Bioinformatics Network ISMB/ECCB 2013 & BOSC 2013, Berlin, Germany - JeremyGoecks + JeremyGoecks Integrated Visualization and Computing for Biomedical Research @@ -244,7 +244,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the July 18-23 Introduction to Galaxy Workshop
National Institute of Environmental Health Sciences (NIEHS)
2013 Research Triangle Workshop Tour, North Carolina, United States - Dave Clements + Dave Clements Introduction to Galaxy Workshop
University of North Carolina, Chapel Hill
@@ -278,7 +278,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the
GalaxyAdmins
-The [May GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-05-15/index.md) featured Andrew Warren of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech speaking on their Galaxy deployment *[RNA Rocket](http://rnaseq.pathogenportal.org/)* for [Pathogen Portal](http://pathogenportal.org). [Dannon Baker](/src/people/dannon-baker/index.md)also gave a Galaxy Project update. Slides and a screencast are now available. +The [May GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-05-15/index.md) featured Andrew Warren of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech speaking on their Galaxy deployment *[RNA Rocket](http://rnaseq.pathogenportal.org/)* for [Pathogen Portal](http://pathogenportal.org). [Dannon Baker](/people/dannon-baker/)also gave a Galaxy Project update. Slides and a screencast are now available.
diff --git a/content/galaxy-updates/2013-07/index.md b/content/galaxy-updates/2013-07/index.md index a6f471b9bf..5533c17554 100644 --- a/content/galaxy-updates/2013-07/index.md +++ b/content/galaxy-updates/2013-07/index.md @@ -126,7 +126,7 @@ This installation of Galaxy has been configured such that anonymous users can op A record 53 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in June. These papers may be particularly interesting to the Galaxy community -* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [Carl Eberhard](/src/people/carl-eberhard/index.md), Tomithy Too, [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/people/james-taylor/index.md), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 +* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/index.md), [Carl Eberhard](/people/carl-eberhard/index.md), Tomithy Too, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 * "[Detection of non-coding RNA in Bacteria and Archaea using the DETR’PROK Galaxy pipeline](https://doi.org/10.1016/j.ymeth.2013.06.003)" by Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret, *[Methods](http://www.sciencedirect.com/science/journal/10462023)* (June 2013) * "[Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data](https://doi.org/10.1002/gepi.21739)" by Nicholas A. Davis, Caleb A. Lareau, Bill C. White, *et al.* *Genetic Epidemiology* (June 2013) * "[A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America](https://doi.org/10.1093/bib/bbt033)" by Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza, *Briefings in Bioinformatics* (30 May 2013) @@ -321,7 +321,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the July 18-23 Introduction to Galaxy Workshop
National Institute of Environmental Health Sciences (NIEHS)
2013 Research Triangle Workshop Tour, North Carolina, United States - Dave Clements + Dave Clements Introduction to Galaxy Workshop
University of North Carolina, Chapel Hill
@@ -356,19 +356,19 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Jennifer Jackson, Ross Lazarus + Jennifer Jackson, Ross Lazarus October 1-3 Beyond the Genome 2013 San Francisco, California, United States - James Taylor + James Taylor October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States - James Taylor, Jennifer Jackson + James Taylor, Jennifer Jackson diff --git a/content/galaxy-updates/2013-08/index.md b/content/galaxy-updates/2013-08/index.md index 90cef4ae21..57294317d4 100644 --- a/content/galaxy-updates/2013-08/index.md +++ b/content/galaxy-updates/2013-08/index.md @@ -103,7 +103,7 @@ The QBRC galaxy server tools are constantly being updated. Please contact author 47 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in July. These papers may be particularly interesting to the Galaxy community -* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), [Nate Coraor](/src/people/nate/index.md), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) +* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/people/james-taylor/index.md), [Anton Nekrutenko](/people/anton/), [Nate Coraor](/src/people/nate/), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) * "[Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE](https://doi.org/10.1186/1471-2164-14-494)" by Quang Trinh, Fei Y. Jen, Ziru Zhou, *et al.*, *BMC Genomics,* Vol. 14, No. 1. (2013), 494 * "[The Banana Genome Hub](https://doi.org/10.1093/database/bat035)" by Droc, *et al.*, *Database*, Vol. 2013 (01 January 2013), @@ -125,7 +125,7 @@ The Galaxy community now has a [mailing list dedicated to proteomics](https://li See [the complete list of mailing lists](/src/mailing-lists/index.md) for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. -Many thanks to Ira Cooke and [John Chilton](/src/people/john-chilton/index.md) for suggesting this and taking the lead in gathering the Galaxy Proteomics community. +Many thanks to Ira Cooke and [John Chilton](/people/john-chilton/) for suggesting this and taking the lead in gathering the Galaxy Proteomics community.
@@ -193,29 +193,29 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Jennifer Jackson, Ross Lazarus + Jennifer Jackson, Ross Lazarus September 30 - October 2 TBA, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States - James Taylor + James Taylor October 1-3 Galaxy Beyond the Genome 2013,San Francisco, California, United States - Jeremy Goecks + Jeremy Goecks October 7-8 TBD NGS & Bioinformatics Summit Europe - Anton Nektutenko + Anton Nektutenko Using Galaxy to Provide a NGS Analysis Platform - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-11 @@ -233,7 +233,7 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson diff --git a/content/galaxy-updates/2013-09/index.md b/content/galaxy-updates/2013-09/index.md index 292b844b0f..1c036ce627 100644 --- a/content/galaxy-updates/2013-09/index.md +++ b/content/galaxy-updates/2013-09/index.md @@ -121,7 +121,7 @@ The [ZBIT Bioinformatics Toolbox](http://webservices.cs.uni-tuebingen.de/) enabl 30 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in August. This paper may be particularly interesting to the Galaxy community: -* Richard LeDuc, Matthew Vaughn, John M Fonner, Michael Sullivan, James G Williams, Philip D Blood, [James Taylor](/src/people/james-taylor/index.md), William Barnett, "[Leveraging the national cyberinfrastructure for biomedical research](https://doi.org/10.1136/amiajnl-2013-002059)," in *[Journal of the American Medical Informatics Association (JAMIA)](http://jamia.bmj.com/)*, doi:10.1136/amiajnl-2013-002059 +* Richard LeDuc, Matthew Vaughn, John M Fonner, Michael Sullivan, James G Williams, Philip D Blood, [James Taylor](/people/james-taylor/), William Barnett, "[Leveraging the national cyberinfrastructure for biomedical research](https://doi.org/10.1136/amiajnl-2013-002059)," in *[Journal of the American Medical Informatics Association (JAMIA)](http://jamia.bmj.com/)*, doi:10.1136/amiajnl-2013-002059
@@ -180,29 +180,29 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg September 30 - October 2 TBA, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States - James Taylor + James Taylor October 1-3 Galaxy Beyond the Genome 2013,San Francisco, California, United States - Jeremy Goecks + Jeremy Goecks October 7-8 TBD NGS & Bioinformatics Summit Europe, Berlin, Germany - Anton Nektutenko + Anton Nektutenko Using Galaxy to Provide a NGS Analysis Platform - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-11 @@ -224,19 +224,19 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu High Throughput Data Analysis and Visualization with Galaxy' - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson January 11-15 Plant and Animal Genome XXII (PAG 2014) San Diego, California, United States - Dave Clements + Dave Clements January 16-17 2014 GMOD Meeting San Diego, California, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2013-10/index.md b/content/galaxy-updates/2013-10/index.md index b7354a669a..babb4244e7 100644 --- a/content/galaxy-updates/2013-10/index.md +++ b/content/galaxy-updates/2013-10/index.md @@ -186,7 +186,7 @@ In the next 3 months there are no less than 13 talks and workshops at at least 5 September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg October 13-16 @@ -279,13 +279,13 @@ And don't worry, you won't have to travel to Australia during its spring just to September 30 - October 2 Analysis of Genomic Sequence Data With Galaxy, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States - James Taylor + James Taylor October 1-3 Galaxy as a platform for High-throughput Genomics Beyond the Genome 2013, San Francisco, California, United States - Jeremy Goecks + Jeremy Goecks Development of a genomic region database and analysis tool for the Galaxy platform @@ -295,11 +295,11 @@ And don't worry, you won't have to travel to Australia during its spring just to October 7-8 Next-Generation Sequencing Data Interpretation: Enhancing Reproducibility and Accessibility NGS & Bioinformatics Summit Europe, Berlin, Germany - Anton Nektutenko + Anton Nektutenko Using Galaxy to Provide a NGS Analysis Platform - Hans-Rudolf Hotz + Hans-Rudolf Hotz October 8-11 @@ -317,7 +317,7 @@ And don't worry, you won't have to travel to Australia during its spring just to October 14-18 NGS Data Analysis and Galaxy Workshop
University of Pretoria
2013 South Africa Galaxy Workshop Tour
Application deadline is 17 September
- Dave Clements + Dave Clements October 21-25 @@ -327,7 +327,7 @@ And don't worry, you won't have to travel to Australia during its spring just to October 22 Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson, Anushka Brownley + Anton Nekrutenko, Jennifer Jackson, Anushka Brownley October 22-26 @@ -337,7 +337,7 @@ And don't worry, you won't have to travel to Australia during its spring just to High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
- Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders @@ -365,19 +365,19 @@ And don't worry, you won't have to travel to Australia during its spring just to November 6-12 Computational and Comparative Genomics Course
Application Deadline: July 15, 2013
Cold Spring Harbor Laboratory, New York, United States - James Taylor + James Taylor January 11-15 Plant and Animal Genome XXII (PAG 2014) San Diego, California, United States - Dave Clements + Dave Clements January 16-17 2014 GMOD Meeting San Diego, California, United States - Dave Clements + Dave Clements diff --git a/content/galaxy-updates/2013-11/index.md b/content/galaxy-updates/2013-11/index.md index f78d906642..8d41f78d27 100644 --- a/content/galaxy-updates/2013-11/index.md +++ b/content/galaxy-updates/2013-11/index.md @@ -97,7 +97,7 @@ And ... ## Ten Simple Rules for Reproducible Computational Research -[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/people/james-taylor/index.md), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October. +[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/people/anton/index.md), [James Taylor](/src/people/james-taylor/), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October.
PLoS Computational Biology: Ten Simple Rules for Reproducible Computational Research
@@ -263,7 +263,7 @@ Enrollment for each bootcamp will be capped at 24 students. Please enroll early November 20 November GalaxyAdmins Meetup Online - Dave Clements, Srinivas Maddhi + Dave Clements, Srinivas Maddhi November 22 @@ -308,19 +308,19 @@ Enrollment for each bootcamp will be capped at 24 students. Please enroll early January 11-15 Plant and Animal Genome XXII (PAG 2014) San Diego, California, United States - Dave Clements + Dave Clements January 16-17 2014 GMOD Meeting San Diego, California, United States - Dave Clements + Dave Clements May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 30 - July 2 diff --git a/content/galaxy-updates/2013-12/index.md b/content/galaxy-updates/2013-12/index.md index f675819ed4..9b55fa13e6 100644 --- a/content/galaxy-updates/2013-12/index.md +++ b/content/galaxy-updates/2013-12/index.md @@ -273,7 +273,7 @@ Enrollment for each bootcamp is capped at 24 students. Please enroll early to be December 11 Using Galaxy to Understand Cancer Genomics National Cancer Institute, Rockville, Maryland, United States - Jeremy Goecks + Jeremy Goecks 2014 @@ -282,17 +282,17 @@ Enrollment for each bootcamp is capped at 24 students. Please enroll early to be January 11-15 Galaxy for NGS Data Analysis: A Hands-on Computer Demo Plant and Animal Genome XXII (PAG 2014), San Diego, California, United States - Dave Clements, Anushka Brownley + Dave Clements, Anushka Brownley Galaxy Cloudman: A Gentle Introduction to Data Analysis on the Cloud
Part of the GMOD Workshop
- Dave Clements, Scott Cain + Dave Clements, Scott Cain January 16-17 2014 GMOD Meeting San Diego, California, United States - Dave Clements, Scott Cain + Dave Clements, Scott Cain February 10-14 @@ -304,7 +304,7 @@ Enrollment for each bootcamp is capped at 24 students. Please enroll early to be May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 30 - July 2 diff --git a/content/galaxy-updates/2014-01/index.md b/content/galaxy-updates/2014-01/index.md index 0aa4931bad..be78987f49 100644 --- a/content/galaxy-updates/2014-01/index.md +++ b/content/galaxy-updates/2014-01/index.md @@ -250,11 +250,11 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too January 11-15 Galaxy for NGS Data Analysis: A Hands-on Computer Demo Plant and Animal Genome XXII (PAG 2014), San Diego, California, United States - Dave Clements, Anushka Brownley + Dave Clements, Anushka Brownley Galaxy Cloudman: A Gentle Introduction to Data Analysis on the Cloud
Part of the GMOD Workshop
- Dave Clements, Scott Cain + Dave Clements, Scott Cain Plus 2 more talks and 4 posters @@ -264,7 +264,7 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too January 16-17 2014 GMOD Meeting San Diego, California, United States - Dave Clements, Scott Cain + Dave Clements, Scott Cain February 10-14 @@ -282,7 +282,7 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too February 12-15 Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States - Anton Nekrutenko + Anton Nekrutenko February 26-28 @@ -306,13 +306,13 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 9-10 diff --git a/content/galaxy-updates/2014-02/index.md b/content/galaxy-updates/2014-02/index.md index 00540a9316..793ab1365e 100644 --- a/content/galaxy-updates/2014-02/index.md +++ b/content/galaxy-updates/2014-02/index.md @@ -193,13 +193,13 @@ GMOD Malaysia 2014 is made possible by the generous support of the [National Evo February 12-15 Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States - Anton Nekrutenko + Anton Nekrutenko February 26-28 GMOD Malaysia 2014 Kuala Lumpur, Malaysia - Amelia Ireland, Dave Clements + Amelia Ireland, Dave Clements February 27 @@ -217,13 +217,13 @@ GMOD Malaysia 2014 is made possible by the generous support of the [National Evo March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 9-10 @@ -381,7 +381,7 @@ bringing the number of log entries to 12. # Galaxy is now at Johns Hopkins and GWU (and Penn State!) -In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/src/galaxy-team/index.md) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/src/people/james-taylor/index.md) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/index.md), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. +In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/src/galaxy-team/index.md) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/index.md) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are [still hiring](/src/galaxy-is-hiring/index.md), but now at three universities instead of two. diff --git a/content/galaxy-updates/2014-03/index.md b/content/galaxy-updates/2014-03/index.md index 3561a5ca4a..e52e39f0f3 100644 --- a/content/galaxy-updates/2014-03/index.md +++ b/content/galaxy-updates/2014-03/index.md @@ -9,7 +9,7 @@ Welcome to the March 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *54 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in Febrary. Some papers that may be particularly interesting to the Galaxy community: -* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/src/people/dan/index.md), [Von Kuster](/src/people/greg_vonkuster/index.md), [Bouvier](/src/people/dave-bouvier/index.md), [Baker](/src/people/dannon-baker/index.md), [Afgan](/src/people/enis-afgan/index.md), Stoler, the [Galaxy Team](/src/galaxy-team/index.md), [Taylor](/src/people/james-taylor/index.md) and [Nekrutenko](/src/people/anton/index.md), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 +* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/index.md), [Von Kuster](/people/greg_vonkuster/index.md), [Bouvier](/people/dave-bouvier/index.md), [Baker](/people/dannon-baker/index.md), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/src/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 * [Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis](https://doi.org/10.1371/journal.pone.0087301), by Khushi, *et al.,* *PLoS ONE*, Vol. 9, No. 2. (12 February 2014), e87301, doi:10.1371/journal.pone.0087301 @@ -188,7 +188,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson April 15-17 @@ -204,11 +204,11 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon W4: Analyzing NGS Data in Galaxy - Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski + Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski W14: Running a Local Galaxy Instance - Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney + Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs @@ -220,25 +220,25 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy - Jeremy Goecks + Jeremy Goecks May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom - Dave Clements + Dave Clements May 9 Galaxy Workshop The Genome Analysis Centre (TGAC), Norwich, United Kingdom - Dave Clements + Dave Clements May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 9-10 @@ -287,7 +287,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-04/index.md b/content/galaxy-updates/2014-04/index.md index 74a70f9ec9..de21ce1b9f 100644 --- a/content/galaxy-updates/2014-04/index.md +++ b/content/galaxy-updates/2014-04/index.md @@ -9,9 +9,9 @@ Welcome to the April 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *63 papers* (a new monthly record) were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in March. Some papers that may be particularly interesting to the Galaxy community: -* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/src/people/dan/index.md), James E. Johnson, [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 +* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/people/dan/index.md), James E. Johnson, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 -* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/src/people/dan/index.md), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/index.md), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) +* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/people/dan/index.md), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) * "[Orione, a web-based framework for NGS analysis in microbiology](https://doi.org/10.1093/bioinformatics/btu135)," Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia, *Bioinformatics* (Oxford, England) (10 March 2014), doi:10.1093/bioinformatics/btu135 @@ -178,7 +178,7 @@ A similar workshop, [using command line interfaces to perform the analysis](http April 15-17 Biosciences/Genomics Program GlobusWorld, Chicago, Illinois, United States - Globus Outreach, John Chilton + Globus Outreach, John Chilton April 29 -
May 1 @@ -188,11 +188,11 @@ A similar workshop, [using command line interfaces to perform the analysis](http W4: Analyzing NGS Data in Galaxy - Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski + Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski W14: Running a Local Galaxy Instance - Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney + Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs @@ -204,25 +204,25 @@ A similar workshop, [using command line interfaces to perform the analysis](http Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy - Jeremy Goecks + Jeremy Goecks May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom - Dave Clements + Dave Clements May 9 Galaxy Workshop The Genome Analysis Centre (TGAC), Norwich, United Kingdom - Dave Clements + Dave Clements May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 9-10 diff --git a/content/galaxy-updates/2014-05/index.md b/content/galaxy-updates/2014-05/index.md index d97bd710f2..5bd56aec07 100644 --- a/content/galaxy-updates/2014-05/index.md +++ b/content/galaxy-updates/2014-05/index.md @@ -41,9 +41,9 @@ Galaxy Biostar was launched on April 23. We hope you like the change and look f *47 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in April. Some papers that may be particularly interesting to the Galaxy community: -* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/src/people/dan/index.md) and [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 +* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/people/dan/index.md) and [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 -* "[Support for data-intensive computing with CloudMan](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6596260)," Yousef Kowsar and [Enis Afgan](/src/people/enis-afgan/index.md), *[Information & Communication Technology Electronics & Microelectronics (MIPRO), 2013 36th International Convention on](http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6588635),* (May 2013), pp. 243-248 +* "[Support for data-intensive computing with CloudMan](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6596260)," Yousef Kowsar and [Enis Afgan](/people/enis-afgan/), *[Information & Communication Technology Electronics & Microelectronics (MIPRO), 2013 36th International Convention on](http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6588635),* (May 2013), pp. 243-248 * "[Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines](http://www.biomedcentral.com/1471-2164/15/120)," Morten Rye, Geir Kjetil Sandve, Carsten O Daub, Hideya Kawaji, Piero Carninci, Alistair RR Forrest, Finn Drabløs and the FANTOM consortium, *[BMC Genomics](http://www.biomedcentral.com/bmcgenomics/)*, Vol. 15, No. 1. (26 March 2014), 120, doi:10.1186/1471-2164-15-120 @@ -224,7 +224,7 @@ And don't worry if you are not near Norwich or Edinburgh in May. There are [at May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom - Dave Clements + Dave Clements May 9 @@ -267,13 +267,13 @@ And don't worry if you are not near Norwich or Edinburgh in May. There are [at May 19-23 Installing Galaxy Workshop
Application deadline: April 28
GMOD Online Training - Carl Eberhard, Amelia Ireland + Carl Eberhard, Amelia Ireland May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia - Enis Afgan + Enis Afgan June 2-3 diff --git a/content/galaxy-updates/2014-06/index.md b/content/galaxy-updates/2014-06/index.md index aaa75c9d43..aaf710d3ec 100644 --- a/content/galaxy-updates/2014-06/index.md +++ b/content/galaxy-updates/2014-06/index.md @@ -183,7 +183,7 @@ There are [at least 13 other Galaxy related events](/src/events/index.md) in the July 28 - August 1 Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform University of São Paulo (USP), São Paulo, Brazil - Dave Clements + Dave Clements @@ -192,7 +192,7 @@ There are [at least 13 other Galaxy related events](/src/events/index.md) in the *49 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in May. Some papers that may be particularly interesting to the Galaxy community: -* [Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory](https://doi.org/10.1186/1756-0500-7-314), by Getiria Onsongo, Jesse Erdmann, Michael D Spears, [John Chilton](/src/people/john-chilton/index.md), Kenneth B Beckman, Adam Hauge, Sophia Yohe, Matthew Schomaker, Matthew Bower, Kevin A T Silverstein and Bharat Thyagarajan, *BMC Research Notes*, Vol. 7, No. 1. (2014), 314, doi:10.1186/1756-0500-7-314 +* [Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory](https://doi.org/10.1186/1756-0500-7-314), by Getiria Onsongo, Jesse Erdmann, Michael D Spears, [John Chilton](/people/john-chilton/), Kenneth B Beckman, Adam Hauge, Sophia Yohe, Matthew Schomaker, Matthew Bower, Kevin A T Silverstein and Bharat Thyagarajan, *BMC Research Notes*, Vol. 7, No. 1. (2014), 314, doi:10.1186/1756-0500-7-314 * [deepTools: a flexible platform for exploring deep-sequencing data](https://doi.org/10.1093/nar/gku365), by Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke, *Nucleic Acids Research* (05 May 2014), gku365, doi:10.1093/nar/gku365 diff --git a/content/galaxy-updates/2014-07/index.md b/content/galaxy-updates/2014-07/index.md index 45c479f799..ebedc7056f 100644 --- a/content/galaxy-updates/2014-07/index.md +++ b/content/galaxy-updates/2014-07/index.md @@ -28,12 +28,12 @@ Fifteen [Training sessions on 12 topics](/src/events/gcc2014/training-day/index. There will be at least six talks and five posters related to Galaxy at [ISMB and BOSC 2014](/src/events/ismb2014/index.md) this year. Talks include -* *Galaxy as an Extensible Job Execution Platform*, [John Chilton](/src/people/john-chilton/index.md) -* *Enhancing the Galaxy Experience through Community Involvement*, [Daniel Blankenberg](/src/people/dan/index.md) -* *[TT03: Interactive Visual Analysis with Galaxy Charts](http://www.iscb.org/uploaded/css/166/29988.pdf)*, [Sam Guerler](/src/people/guerler/index.md) -* *[TT24: From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser](http://www.iscb.org/uploaded/css/166/30137.pdf)*, [Daniel Blankenberg](/src/people/dan/index.md) +* *Galaxy as an Extensible Job Execution Platform*, [John Chilton](/people/john-chilton/) +* *Enhancing the Galaxy Experience through Community Involvement*, [Daniel Blankenberg](/people/dan/) +* *[TT03: Interactive Visual Analysis with Galaxy Charts](http://www.iscb.org/uploaded/css/166/29988.pdf)*, [Sam Guerler](/people/guerler/) +* *[TT24: From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser](http://www.iscb.org/uploaded/css/166/30137.pdf)*, [Daniel Blankenberg](/people/dan/) * *[TT27: Bioinformatics and Computer Biology Systems design applied to Medical Molecular Nanobiotechnology](http://www.iscb.org/uploaded/css/166/30125.pdf)*, Allan Orozco -* *[TT29: Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude](http://www.iscb.org/uploaded/css/166/30134.pdf)*, [John Chilton](/src/people/john-chilton/index.md) +* *[TT29: Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude](http://www.iscb.org/uploaded/css/166/30134.pdf)*, [John Chilton](/people/john-chilton/) ## Other Events @@ -92,7 +92,7 @@ Over the rest of the summer there are other [Galaxy related events](/src/events/ July 28 - August 1 Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform University of São Paulo (USP), São Paulo, Brazil - Dave Clements + Dave Clements August 25-27 @@ -116,7 +116,7 @@ Over the rest of the summer there are other [Galaxy related events](/src/events/ September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-08/index.md b/content/galaxy-updates/2014-08/index.md index b233dfb00d..9c17189f09 100644 --- a/content/galaxy-updates/2014-08/index.md +++ b/content/galaxy-updates/2014-08/index.md @@ -189,7 +189,7 @@ Over the rest of the few months there are many [Galaxy related events](/src/even September 19 The Great GigaScience and Galaxy (G3) Workshop The University of Melbourne, Melbourne, Australia - Nick Wong, Ross Lazarus + Nick Wong, Ross Lazarus September 30 - October 2 @@ -201,7 +201,7 @@ Over the rest of the few months there are many [Galaxy related events](/src/even September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-09/index.md b/content/galaxy-updates/2014-09/index.md index 1e2fd0f107..f2f91114a1 100644 --- a/content/galaxy-updates/2014-09/index.md +++ b/content/galaxy-updates/2014-09/index.md @@ -94,7 +94,7 @@ These events are a great way to meet other Galaxy users and developers and learn September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-10/index.md b/content/galaxy-updates/2014-10/index.md index 8d9a6002a7..38a1155d17 100644 --- a/content/galaxy-updates/2014-10/index.md +++ b/content/galaxy-updates/2014-10/index.md @@ -61,7 +61,7 @@ There are [upcoming events](/src/events/index.md) in Switzerland, Germany, Austr September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-11/index.md b/content/galaxy-updates/2014-11/index.md index ad692ce35d..0a89b307fe 100644 --- a/content/galaxy-updates/2014-11/index.md +++ b/content/galaxy-updates/2014-11/index.md @@ -119,7 +119,7 @@ There are [upcoming events](/src/events/index.md) in France, Germany, Australia, November 5-8 Rapidly bringing software to biologists with Galaxy and Docker Biological Data Science, Cold Spring Harbor Laboratory, New York, United States - John Chilton + John Chilton Building Galaxy Japan community
(See Pitagora Galaxy) @@ -129,7 +129,7 @@ There are [upcoming events](/src/events/index.md) in France, Germany, Australia, November 16 Deciphering Big Data Stacks: An Overview of Big Data Tools Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-14), Supercomputing 2014 (SC14), New Orleans, Louisiana, United States - Enis Afgan + Enis Afgan November 18-20 @@ -147,7 +147,7 @@ There are [upcoming events](/src/events/index.md) in France, Germany, Australia, November 21 Galaxy Cluster to Cloud - Genomics at Scale GCE: The 9th Gateway Computing Environments Workshop, Supercomputing 2014 (SC14), New Orleans, Louisiana, United States - Enis Afgan + Enis Afgan November 26-28 @@ -186,7 +186,7 @@ There are [upcoming events](/src/events/index.md) in France, Germany, Australia, January 10-14 Galaxy for SNP and Variant Data Analysis Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States - Dave Clements + Dave Clements February 9-13 @@ -198,7 +198,7 @@ There are [upcoming events](/src/events/index.md) in France, Germany, Australia, February 16-18 Managing and Disseminating Tools and Data in Galaxy Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States - James Taylor + James Taylor July 6-8 @@ -448,6 +448,6 @@ In no particular order: * Have you ever wanted to improve a Galaxy tool? Large number of tools are [now awaiting your pull requests at GitHub](https://github.com/galaxyproject/tools-devteam). * [On the awesomeness of the BOSC/OpenBio Codefest 2014](http://etalog.blogspot.com/2014/10/on-awesomeness-of-boscopenbio-codefest.html) -* [Björn Grüning's](/src/people/bjoern-gruening/index.md) [Galaxy Docker image](https://github.com/bgruening/docker-galaxy-stable/commits/master) now bundles FTP & SLURM and allows targeting external Galaxy directories. +* [Björn Grüning's](/people/bjoern-gruening/) [Galaxy Docker image](https://github.com/bgruening/docker-galaxy-stable/commits/master) now bundles FTP & SLURM and allows targeting external Galaxy directories. * An IPython notebook demonstrating an [interactive cummeRbund analysis embedded in Galaxy](http://nbviewer.ipython.org/github/jmchilton/ipython_notebooks/blob/master/cummerbund_galaxy_1.ipynb). * [GUGGO tutorial](http://bit.ly/ZQ7mdu): how to activate Docker functionality in Galaxy; create a Docker image and install Stacks on that image; and integrate a Stacks Galaxy tool using that image. diff --git a/content/galaxy-updates/2014-12/index.md b/content/galaxy-updates/2014-12/index.md index bf58aa82ae..23318ff0bf 100644 --- a/content/galaxy-updates/2014-12/index.md +++ b/content/galaxy-updates/2014-12/index.md @@ -101,7 +101,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G December 12 Introduction to Galaxy Workshop Virginia State University, Petersburg, Virginia, United States - Glenn Harris, Dave Clements + Glenn Harris, Dave Clements December 16-19 @@ -116,7 +116,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G January 10-14 Galaxy for SNP and Variant Data Analysis Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States - Dave Clements + Dave Clements February 9-13 @@ -128,7 +128,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G February 16-18 Accessible and Reproducible Large-Scale Analysis with Galaxy Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States - James Taylor + James Taylor Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic @@ -153,7 +153,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G **96 papers** (a new record) referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in November. That's a new record. Some of those papers are: -* "[Galaxy Cluster to Cloud - Genomics at Scale](https://doi.org/10.1109/GCE.2014.13)" by [Enis Afgan](/src/people/enis-afgan/index.md), *et al.* in [Proceedings of the 9th Gateway Computing Environments Workshop (2014)](http://dl.acm.org/citation.cfm?id=2690887&picked=prox&cfid=603148869&cftoken=86409151), pp. 47-50, doi:10.1109/gce.2014.13 +* "[Galaxy Cluster to Cloud - Genomics at Scale](https://doi.org/10.1109/GCE.2014.13)" by [Enis Afgan](/people/enis-afgan/), *et al.* in [Proceedings of the 9th Gateway Computing Environments Workshop (2014)](http://dl.acm.org/citation.cfm?id=2690887&picked=prox&cfid=603148869&cftoken=86409151), pp. 47-50, doi:10.1109/gce.2014.13 * "[Automatically exposing OpenLifeData via SADI semantic Web Services](https://doi.org/10.1186/2041-1480-5-46)" by Alejandro Gonzalez, *et al.* *Journal of Biomedical Semantics*, Vol. 5, No. 1. (2014), 46, doi:10.1186/2041-1480-5-46 diff --git a/content/galaxy-updates/2015-01/index.md b/content/galaxy-updates/2015-01/index.md index 044b278ad6..c23a236899 100644 --- a/content/galaxy-updates/2015-01/index.md +++ b/content/galaxy-updates/2015-01/index.md @@ -138,19 +138,19 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G January 10-14 Galaxy for SNP and Variant Data Analysis Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States - Dave Clements + Dave Clements January 15 Galaxy Workshops San Diego State University, San Diego, California, United States - Dave Clements + Dave Clements January 15-16 Accessible and Reproducible Genomics at Scale with Galaxy Revolutionizing Next-Generation Sequencing: Tools and Technologies, Leuven, Belgium - James Taylor + James Taylor January 19-20 @@ -168,7 +168,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G February 16-18 Accessible and Reproducible Large-Scale Analysis with Galaxy Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States - James Taylor + James Taylor Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic @@ -183,7 +183,7 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G May 25-29 MIPRO Opatija, Croatia - Enis Afgan + Enis Afgan July 6-8 @@ -200,13 +200,13 @@ There are [upcoming events](/src/events/index.md) on two continents. See the [G *We just don't know exactly when, yet ...* -Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Well, thanks to the efforts of [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) the GalaxyAdmins group *is back.* Starting this month, we will resume our bi-monthly conference calls. +Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Well, thanks to the efforts of [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) the GalaxyAdmins group *is back.* Starting this month, we will resume our bi-monthly conference calls. *Galaxy-Admins* is a discussion group for Galaxy community members who are responsible for large Galaxy installations. In an effort to better serve the global community we will rotate the time of the call in different months to be convenient for different parts of the world. To help us pick the best set of times for the calls, **please take a few minutes and fill out this [Doodle poll](http://doodle.com/dq3bexyuihs59h3c).** It covers every hour in a 72 hour period. *Please don't forget to select the timezone before you start filling it out.* -The likely presentation for the January meetup will be a summary of the Galaxy Community Survey last fall, presented by [Dave Clements](/src/people/dave-clements/index.md). The survey covered both Galaxy usage and deployment. The survey results will be published online before the call. +The likely presentation for the January meetup will be a summary of the Galaxy Community Survey last fall, presented by [Dave Clements](/people/dave-clements/). The survey covered both Galaxy usage and deployment. The survey results will be published online before the call. @@ -404,5 +404,5 @@ In no particular order: * [Bioinformatics WikiBook Collaborative Workshop](http://bit.ly/15PpUxA) 24-26 February at TGAC. And we encourage contributions [about Galaxy](http://bit.ly/1zS0PuW) to the [NGS WikiBook](http://bit.ly/NGSWikiBook). * [PDACS: a portal for data analysis services for cosmological simulations](http://bit.ly/1s0gMLe), Chard *et al.* *PDACS is a Galaxy implementation for cosmology.* And PDACS slides are [here](http://bit.ly/1pYSlSN). -* Just scheduled: Intro to variant calling for pathologists and laboratory managers, Sydney, 22 June. [Ross Lazarus](/src/people/fubar/index.md) & Andrew Lonie +* Just scheduled: Intro to variant calling for pathologists and laboratory managers, Sydney, 22 June. [Ross Lazarus](/people/fubar/) & Andrew Lonie * [ASH: A Galaxy VM](http://bit.ly/ASH_VM) from Erasmus Medical Centre for Automated Selection of Hotspots in cancer. diff --git a/content/galaxy-updates/2015-02/index.md b/content/galaxy-updates/2015-02/index.md index 329eefbfc4..a7e85f26fe 100644 --- a/content/galaxy-updates/2015-02/index.md +++ b/content/galaxy-updates/2015-02/index.md @@ -19,11 +19,11 @@ Welcome to the February *[Galaxy Update](/src/galaxy-updates/index.md)*, a summa 55 new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in January. Some highlights: * [Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines](https://doi.org/10.1002/cam4.360) - [Jeremy Goecks](/src/people/jeremy-goecks/index.md), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/src/people/james-taylor/index.md), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 + [Jeremy Goecks](/people/jeremy-goecks/index.md), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/src/people/james-taylor/), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 * [Merging OpenLifeData with SADI services using Galaxy and Docker](http://www.biorxiv.org/content/biorxiv/early/2015/01/10/013615) Mikel E. Aranguren, *bioRxiv* * [NCBI BLAST+ integrated into Galaxy](http://www.biorxiv.org/content/early/2015/01/21/014043) - Peter J. A. Cock, [John M. Chilton](/src/people/john-chilton/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), James E. Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md), *bioRxiv* + Peter J. A. Cock, [John M. Chilton](/people/john-chilton/index.md), [Björn Grüning](/people/bjoern-gruening/), James E. Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/), *bioRxiv* * [SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations](http://www.gigasciencejournal.com/content/4/1/1/abstract) Wilfried M Guiblet, Kai Zhao, Stephen J O'Brien, Steven E Massey, Alfred L Roca and Taras K Oleksyk, *[GigaScience](http://www.gigasciencejournal.com/)* 2015, 4:1
[Supplementary materials](http://gigagalaxy.net/u/gigascience/g/wguiblet2014) (as a Galaxy Page) @@ -162,7 +162,7 @@ Please let the organisers know if you are interested in helping make this event The first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) will happen online on Thursday, 19 February. [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/src/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) will lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/index.md) direction*. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) will lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. @@ -174,7 +174,7 @@ The [first Baltimore Area Galaxy meetup](/src/events/meetups/baltimore/2015-01-2 The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis Afgan](/src/people/enis-afgan/index.md) & [Nitesh Turaga](/src/people/nitesh-turaga/index.md) +[Enis Afgan](/people/enis-afgan/index.md) & [Nitesh Turaga](/src/people/nitesh-turaga/) ## Other Events @@ -208,7 +208,7 @@ There are [upcoming events](/src/events/index.md) in 5 countries on 4 continents - + @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 5 countries on 4 continents - + @@ -386,7 +386,7 @@ Several *critical* security vulnerabilities were recently discovered by Bartlomi **IPython Integration** -Thanks to the awesome work of community members [Björn Grüning](/src/people/bjoern-gruening/index.md) and [Helena Rasche](/src/people/helena-rasche/index.md), [Galaxy now features integration with the popular IPython project](/src/archive/dev-news-briefs/2015-01-13/index.md#ipython-integration). The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. +Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/index.md) and [Helena Rasche](/people/helena-rasche/), [Galaxy now features integration with the popular IPython project](/src/archive/dev-news-briefs/2015-01-13/#ipython-integration). The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. ** Tool Form Upgrade (for Beta Testing) ** @@ -428,8 +428,8 @@ Version 0.2.0 of [Planemo](https://github.com/galaxyproject/planemo/blob/master/ * Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. ([Pull Request 56](https://github.com/galaxyproject/planemo/pull/56)) * Allow setting various test output options in ``~/.planemo.yml`` and disabling JSON output. * More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See [this presentation](http://bit.ly/gxbrew1) for more details. -* Fix ``project_init`` for BSD tar (thanks to [Nitesh Turaga](/src/people/nitesh-turaga/index.md) for the bug report.) -* Documentation fixes for tool linting command (thanks to [Nicola Soranzo](/src/people/nicola-soranzo/index.md)). +* Fix ``project_init`` for BSD tar (thanks to [Nitesh Turaga](/people/nitesh-turaga/) for the bug report.) +* Documentation fixes for tool linting command (thanks to [Nicola Soranzo](/people/nicola-soranzo/)). ## BioBlend @@ -463,20 +463,20 @@ In no particular order: * [snpsift_dbnsfp_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_datatypes): Galaxy applicable data formats for SnpSift. snpsift_dbnsfp tool Allows for the creation of a snpsift dbnsfp Galaxy dataset from a tabular file that can be used by SnpSift dbnsfp to annotate a vcf formatted file. * [snpeff_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpeff_datatypes): Galaxy applicable data formats for SnpEff tools Galaxy applicable data formats for SnpEff tools. The snpeffdb datatype provides the means to represent a SnpEff genome database in a Galaxy dataset. * [snpsift_dbnsfp](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp): snpEff SnpSift dbnsfp tool from Pablo Cingolani Annotates variants on genes using the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.) http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift): snpEff SnpSift tools from Pablo Cingolani Variant annotation and effect prediction tools. It annotates and predicts the effects of variants on genes. This repository should manage tool dependencies. There are data managers for the Galaxy admin to download genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed /
* [snpsift_genesets](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_genesets): snpEff SnpSift genesets tool from Pablo Cingolani Annotates variants with GeneSets, such as Gene Ontology (GO), KEGG, Reactome, etc.; http://snpeff.sourceforge.net/SnpSift.html#geneSets !SnpEff and !SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift_dbnsfp_generic](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_generic): snpEff SnpSift dbnsfp tool that can use any dbnsfp-like annotation data Annotates variants on genes using a tabular set of annotation values such as those from the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.)
This tool determines the available annotations from the input, so it can be used for other organisms other than human or other annotation values than available from dbNSFP. http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP
SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * *From [amawla](https://toolshed.g2.bx.psu.edu/view/amawla):* @@ -532,7 +532,7 @@ In no particular order: * *From [iuc](https://toolshed.g2.bx.psu.edu/view/iuc/): * * [data_manager_snpeff](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_snpeff): Manage SnpEff genome reference data Data managers for the Galaxy admin to download SnpEff genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ ### Packages / Tool Dependency Definitions @@ -544,25 +544,25 @@ In no particular order: * *From [iuc](https://toolshed.g2.bx.psu.edu/view/iuc):* * [package_vienna_rna_1_8](https://toolshed.g2.bx.psu.edu/view/iuc/package_vienna_rna_1_8): Imported from capsule None Contains a tool dependency definition that downloads and compiles version 1.8 of the Vienna RNA package. The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
http://www.tbi.univie.ac.at/RNA /
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [package_perl_pdf_api2_2_023](https://toolshed.g2.bx.psu.edu/view/iuc/package_perl_pdf_api2_2_023): Contains a tool dependency definition that downloads and compiles version 2.023 of the perl PDF API * [package_randfold_2_0](https://toolshed.g2.bx.psu.edu/view/iuc/package_randfold_2_0): Contains a tool dependency definition that downloads and compiles version 2.0 of randfold. This is RANDFOLD version 2. The software compute the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md) & Cameron Smith
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/) & Cameron Smith
Repository-Development: https://github.com/bgruening/galaxytools * [package_boost_1_55](https://toolshed.g2.bx.psu.edu/view/iuc/package_boost_1_55): Tool dependency definition that downloads and compiles version 1.55 of the boost C++ libraries Boost provides free peer-reviewed portable C++ source libraries.
http://www.boost.org /
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [package_rhmm_1_5_0](https://toolshed.g2.bx.psu.edu/view/iuc/package_rhmm_1_5_0): Installs the RHmm CRAN library. Discrete, univariate or multivariate gaussian, mixture of univariate or multivariate gaussian HMM functions for simulation and estimation. * [package_snpeff_4_0](https://toolshed.g2.bx.psu.edu/view/iuc/package_snpeff_4_0): Contains a tool dependency definition that installs version 4.0 SnpEff, a variant annotation and effect prediction tool. SnpEff is a variant annotation and effect prediction tool by Pablo Cingolani.
It annotates and predicts the effects of variants on genes (such as amino acid changes).
SnpEff and SnpSift ( http://snpeff.sourceforge.net/ ) * [package_bedtools_2_22](https://toolshed.g2.bx.psu.edu/view/iuc/package_bedtools_2_22): Contains a tool dependency definition that downloads and compiles version 2.22 of bedtools. bedtools - a swiss army knife for genome arithmetic
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/)
Repository-Development: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_bedtools_2_22 * [package_squid_1_9g](https://toolshed.g2.bx.psu.edu/view/iuc/package_squid_1_9g): Tool dependency definition that downloads and compiles version 1.9g of the squid library. SQUID is a freely redistributable library of C code functions for sequence analysis. SQUID also includes a number of small utility programs.
- Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md) & Cameron Smith
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/) & Cameron Smith
Repository-Development: https://github.com/bgruening/galaxytools * *From [devteam](https://toolshed.g2.bx.psu.edu/view/devteam):* @@ -576,9 +576,9 @@ In no particular order: # Other News -* An [IPython Notebook that builds Galaxy tool_dependencies.xml file for Perl packages](http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/Perl/perl_package_to_galaxy_tool_dependency.ipynb), from [Björn Grüning](/src/people/bjoern-gruening/index.md) +* An [IPython Notebook that builds Galaxy tool_dependencies.xml file for Perl packages](http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/Perl/perl_package_to_galaxy_tool_dependency.ipynb), from [Björn Grüning](/people/bjoern-gruening/) * [NSF Award CIF21 DIBBS: Tripal Gateway, a Platform for Next-Generation Data Analysis and Sharing](http://nsf.gov/awardsearch/showAward?AWD_ID=1443040). Will integrate [Tripal](http://tripal.info/) and Galaxy, and allow Tripal community databases to create and share workflows. (See also this story in [HPCwire](http://www.hpcwire.com/2015/01/21/nsf-signs-1-4-million-check-advance-community-database/).) -* [Dan Blankenberg](/src/people/dan/index.md) on a [useful way to handle tools with outputs tied to tool version](https://github.com/galaxyproject/tools-iuc/issues/22#issuecomment-69930103) in Galaxy +* [Dan Blankenberg](/people/dan/) on a [useful way to handle tools with outputs tied to tool version](https://github.com/galaxyproject/tools-iuc/issues/22#issuecomment-69930103) in Galaxy * In [galaxy-central](https://bitbucket.org/galaxy/galaxy-central/) now: [tools can explicitly produce collections of datasets](https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset/diff) * [Getting your 23 and Me data into Galaxy](http://genomeintelligence.org/?p=745), at [Genome Intelligence](http://genomeintelligence.org/) * [What are the differences](https://www.biostars.org/p/126034/) between [Biostars - bioinformatics explained](https://www.biostars.org/) and [Biostars - Galaxy explained](https://biostar.usegalaxy.org/)? diff --git a/content/galaxy-updates/2015-03/index.md b/content/galaxy-updates/2015-03/index.md index 509c4067a2..cfdfef96d4 100644 --- a/content/galaxy-updates/2015-03/index.md +++ b/content/galaxy-updates/2015-03/index.md @@ -19,10 +19,10 @@ Welcome to the March 2015 *[Galaxy Update](/src/galaxy-updates/index.md)*, a sum 82 new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in February. Some highlights: * [Multi-omic data analysis using Galaxy](https://doi.org/10.1038/nbt.3134) - Jorrit Boeke, [John M Chilton](/src/people/john-chilton/index.md), Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, *Nature Biotechnology*, Vol. 33, No. 2. (6 February 2015) + Jorrit Boeke, [John M Chilton](/people/john-chilton/), Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, *Nature Biotechnology*, Vol. 33, No. 2. (6 February 2015) * [Online Resources for Genomic Analysis Using High-Throughput Sequencing](https://doi.org/10.1101/pdb.top083667) - [Daniel Blankenberg](/src/people/dan/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 + [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 * [Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud](https://doi.org/10.12694/scpe.v16i1.1058) Philip Church, Andrzej Goscinski, *Scalable Computing: Practice and Experience*, Vol. 16, No. 1. (07 February 2015), doi:10.12694/scpe.v16i1.1058 @@ -31,7 +31,7 @@ Welcome to the March 2015 *[Galaxy Update](/src/galaxy-updates/index.md)*, a sum Yousef Kowsar, Harriet Dashnow, Andrew Lonie, in Utility and Cloud Computing (UCC), 2014 IEEE/ACM 7th International Conference on (December 2014), pp. 696-701, doi:10.1109/ucc.2014.113 * [A Quick Guide for Building a Successful Bioinformatics Community](https://doi.org/10.1371/journal.pcbi.1003972) - Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, [Jeremy Goecks](/src/people/jeremy-goecks/index.md), Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg, *PLoS Computational Biology*, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972 + Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, [Jeremy Goecks](/people/jeremy-goecks/), Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg, *PLoS Computational Biology*, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972 * [Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828](https://peerj.com/preprints/837/) Timothy D Read​, Robert A Petit III, Sandeep J Joseph, Md T Alam, Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S Vuong, Chad P Haase, Harry Webb, Alistair D. M. Dove, *PeerJ PrePrints* 3:e1036 doi:10.7287/peerj.preprints.837v1 @@ -197,17 +197,17 @@ A hands-on, 4 day workshop on *[RNA-Seq and ChIP-Seq Analysis with Galaxy](http: [Video and slides](/src/community/galaxy-admins/meetups/2015-02-19/index.md) from the first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) are now available online. -[Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) also lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/index.md) direction*. +[Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) also lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. Our next meetup will be in April. ### Fall 2014 Questionnaire Summaries -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) was presented by [Dave Clements](/src/people/dave-clements/index.md). A [summary of the admin/devel questionnaire](/src/community/galaxy-admins/surveys/2014/index.md) is now available online. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) was presented by [Dave Clements](/people/dave-clements/index.md). A [summary of the admin/devel questionnaire](/src/community/galaxy-admins/surveys/2014/) is now available online. ### Gravity -[Nate Coraor](/src/people/nate/index.md) introduced [Gravity](/src/community/galaxy-admins/meetups/2015-02-19/index.md#galaxy-project-update-gravity), a process manager (supervisor) for Galaxy servers. +[Nate Coraor](/people/nate/index.md) introduced [Gravity](/src/community/galaxy-admins/meetups/2015-02-19/#galaxy-project-update-gravity), a process manager (supervisor) for Galaxy servers. ## Other Events @@ -239,7 +239,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 4 continents - + diff --git a/content/galaxy-updates/2015-04/index.md b/content/galaxy-updates/2015-04/index.md index 560c7c022f..f259c1996d 100644 --- a/content/galaxy-updates/2015-04/index.md +++ b/content/galaxy-updates/2015-04/index.md @@ -208,7 +208,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents - + @@ -271,7 +271,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents - + @@ -307,7 +307,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents - + @@ -323,7 +323,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents - +
February 16-18 Accessible and Reproducible Large-Scale Analysis with Galaxy Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States James Taylor James Taylor
Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic February 19 February 2015 GalaxyAdmins Web Meetup Online Hans-Rudolf Hotz, Dave Clements Hans-Rudolf Hotz, Dave Clements
March 2-3 Workshop on Bioinformatics Methods in Genomics
Training offered by GTN Member
RBI, Zagreb, Croatia 		Enis Afgan Enis Afgan
March 3-5 April 16 GalaxyAdmins April 2015 Meetup Online Hans-Rudolf Hotz, Dave Clements, Carrie Ganote Hans-Rudolf Hotz, Dave Clements, Carrie Ganote
April 20-21 May 25-29 MIPRO Opatija, Croatia Enis Afgan Enis Afgan
May 26-28 June 22 Introduction to variant calling for pathologists and laboratory managers
Training offered by GTN Member
Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia 		Ross Lazarus, Andrew Lonie Ross Lazarus, Andrew Lonie
July 10-14 Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training ISMB / ECCB 2015, BOSC 2015, Dublin, Ireland Dave Clements Dave Clements
@@ -469,12 +469,12 @@ This is mostly an incremental bug fix release with the following summary of chan * Project source moved to new URL - https://github.com/galaxyproject/bioblend * Huge improvements to automated testing, tests now run against Galaxy release_14.02 and all later versions to ensure backward compatibility (see [travis.yml](https://github.com/galaxyproject/bioblend/blob/master/.travis.yml) for details). -* Many documentation improvements (thanks to [Helena Rasche](/src/people/helena-rasche/index.md)). +* Many documentation improvements (thanks to [Helena Rasche](/people/helena-rasche/)). * Add Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau). * Add method to get the standard error and standard output for the job corresponding to a Galaxy dataset (thanks to Anthony Bretaudeau). * Add `get_state()` method to `JobsClient`. * Add `copy_from_dataset()` method to `LibraryClient`. -* Add `create_repository()` method to `ToolShedClient` (thanks to [Helena Rasche)](/src/people/helena-rasche/index.md). +* Add `create_repository()` method to `ToolShedClient` (thanks to [Helena Rasche)](/people/helena-rasche/). * Fix `DatasetClient.download_dataset()` for certain proxied Galaxy deployments. * Make `LibraryClient._get_root_folder_id()` method safer and faster for Galaxy release_13.06 and later. * Deprecate and ignore invalid deleted parameter to `WorkflowClient.get_workflows()`. @@ -493,7 +493,7 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/src/people/enis-afgan/index.md) & [John](/src/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/index.md) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/index.md) +[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) ## Planemo 0.6.0 @@ -502,7 +502,7 @@ Enjoy and please let us know what you think, * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc… * Fix tool_init to quote file names (thanks to Peter Cock). [Pull Request 98](https://github.com/galaxyproject/planemo/pull/98). -* Allow ignoring file patterns in .shed.yml (thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md)). [Pull Request 99](https://github.com/galaxyproject/planemo/pull/98) +* Allow ignoring file patterns in .shed.yml (thanks to [Björn Grüning](/people/bjoern-gruening/)). [Pull Request 99](https://github.com/galaxyproject/planemo/pull/98) * Add --macros flag to tool_init command to generate a macro file as part of tool generation. [ec6e30f](https://github.com/galaxyproject/planemo/commit/ec6e30f) * Add linting of tag order for tool XML files. [4823c5e](https://github.com/galaxyproject/planemo/commit/4823c5e) * Add linting of stdio tags in tool XML files. [8207026](https://github.com/galaxyproject/planemo/commit/8207026) @@ -518,7 +518,7 @@ New versions [CloudMan](/src/galaxy-updates/2014-09/index.md#august-2014-cloudma # Other News -* From [Björn Grüning](/src/people/bjoern-gruening/index.md): +* From [Björn Grüning](/people/bjoern-gruening/): [New release of our Galaxy Docker container](https://biostar.usegalaxy.org/p/11376/) with a lot of new features * You can browse our tutorials section by visiting this [biostar.usegalaxy.org/t/Tutorial/](https://biostar.usegalaxy.org/t/Tutorial/) (*Note: Deprecated. Now see [training.galaxyproject.org](https://training.galaxyproject.org/)*) * [Should Galaxy use Trello or Github for issue tracking?](http://trello.com/c/iddlQT2p) @@ -580,7 +580,7 @@ Note: Starting with the May news, this list will be placed on a separate page an * *From [bgruening](https://toolshed.g2.bx.psu.edu/view/bgruening):* * [diamond](https://toolshed.g2.bx.psu.edu/view/bgruening/diamond): DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity - Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [text_processing](https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing): High performance text processing tools using the GNU coreutils, sed, awk and friends. That repository contains all kind of different text processing tools. @@ -598,7 +598,7 @@ Note: Starting with the May news, this list will be placed on a separate page an * tail - keep the last X lines in a file. Originally known as "Unix Tools" and developed from Assaf Gordon @ Greg Hannon's lab ( http://hannonlab.cshl.edu ) in Cold Spring Harbor Laboratory, it is now hosted under https://github.com/bgruening/galaxytools/tree/master/unix_tools and open for contributions. It will also replace several smaller sed, sort and uniq wrappers, developed over the time.
- Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [data_manager_diamond_database_builder](https://toolshed.g2.bx.psu.edu/view/bgruening/data_manager_diamond_database_builder): Diamond data manager @@ -607,18 +607,18 @@ Note: Starting with the May news, this list will be placed on a separate page an * [find_subsequences](https://toolshed.g2.bx.psu.edu/view/bgruening/find_subsequences): Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamH1. Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamH1. This tool is based on biopython: 10.1093/bioinformatics/btp163
- Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * *From [iuc](https://toolshed.g2.bx.psu.edu/view/iuc):* * [macs2](https://toolshed.g2.bx.psu.edu/view/iuc/macs2): MACS - Model-based Analysis of ChIP-Seq. With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. - Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/iuc/galaxytools * [seqtk](https://toolshed.g2.bx.psu.edu/view/iuc/seqtk): toolkit for processing FASTA and FASTQ files. Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
https://github.com/lh3/seqtk/
- Repository-Maintainer: [Helena Rasche](/src/people/helena-rasche/index.md)
+ Repository-Maintainer: [Helena Rasche](/people/helena-rasche/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed * *From [hogart](https://toolshed.g2.bx.psu.edu/view/hogart):* @@ -708,7 +708,7 @@ Note: Starting with the May news, this list will be placed on a separate page an * [package_cofold_0_0_1](https://toolshed.g2.bx.psu.edu/view/iuc/package_cofold_0_0_1): Contains a tool dependency definition that downloads and compiles CoFold. A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account. http://www.e-rna.org/cofold/
- Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools/ * [package_samtools_1_2](https://toolshed.g2.bx.psu.edu/view/iuc/package_samtools_1_2): Contains a tool dependency definition that downloads and installs version 1.2 of the SAMTools package. samtools \u2212 Utilities for the Sequence Alignment/Map (SAM) format @@ -718,11 +718,11 @@ Note: Starting with the May news, this list will be placed on a separate page an Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with \u2018ftp://\u2019 or \u2018http://\u2019. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entire alignment file unless it is asked to do so. - Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
* [package_gengetopt_2_22_6](https://toolshed.g2.bx.psu.edu/view/iuc/package_gengetopt_2_22_6): Contains a tool dependency definition that downloads and compiles version 2.22.6 of GNU gengetopt Gengetopt is a tool to write command line option parsing code for C programs. http://www.gnu.org/software/gengetopt/gengetopt.html
- Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/galaxyproject/tools-iuc * [package_rnastructure_5_7](https://toolshed.g2.bx.psu.edu/view/iuc/package_rnastructure_5_7): Contains a tool dependency definition that downloads and compiles version 5.7 of RNAstructure RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. @@ -733,11 +733,11 @@ Note: Starting with the May news, this list will be placed on a separate page an * [package_vienna_rna_2_1](https://toolshed.g2.bx.psu.edu/view/iuc/package_vienna_rna_2_1): Contains a tool dependency definition that downloads and compiles version 2.1 of the Vienna RNA package. The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. http://www.tbi.univie.ac.at/RNA/
- Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [package_diamond_0_6_13](https://toolshed.g2.bx.psu.edu/view/iuc/package_diamond_0_6_13): Contains a tool dependency definition that downloads and compiles version 0.6.13 of DIAMOND DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity - Repository-Maintainer: [Bjoern Gruening](/src/people/bjoern-gruening/index.md)
+ Repository-Maintainer: [Bjoern Gruening](/people/bjoern-gruening/)
Repository-Development: https://github.com/bgruening/galaxytools * [package_stringtie_1_0_1](https://toolshed.g2.bx.psu.edu/view/iuc/package_stringtie_1_0_1): tool dependency definition. Contains a tool dependency definition that downloads and installs version 1.0.1 of the stringtie RNA-seq assembler. StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs. diff --git a/content/galaxy-updates/2015-05/index.md b/content/galaxy-updates/2015-05/index.md index 65aa155bfa..1364ffc382 100644 --- a/content/galaxy-updates/2015-05/index.md +++ b/content/galaxy-updates/2015-05/index.md @@ -28,7 +28,7 @@ Welcome to the May 2015 *[Galactic News](/src/galaxy-updates/index.md)*, a summa Halfdan Rydbeck, Geir Kjetil K. Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig, *PloS one*, Vol. 10, No. 4. (2015) * [StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo](https://doi.org/10.1093/bioinformatics/btv213) - Yin Tang, [Emil Bouvier](/src/people/dave-bouvier/index.md), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/src/people/anton/index.md), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 + Yin Tang, [Emil Bouvier](/people/dave-bouvier/index.md), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/src/people/anton/), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 The new papers were tagged with: @@ -192,7 +192,7 @@ Please let the [organisers](http://gcc2015.tsl.ac.uk/) know if you are intereste
GalaxyAdmins meetup April 16
-[Slides and video](/src/community/galaxy-admins/meetups/2015-04-16/index.md) from the [April GalaxyAdmins online meetup](/src/community/galaxy-admins/meetups/2015-04-16/index.md) are now available. [Carrie Ganote](http://www.researchgate.net/profile/Carrie_Ganote) from the [National Center for Genome Analysis Support (NCGAS)](http://ncgas.org/) and [Pervasive Technology Institute](http://pti.iu.edu/) at [Indiana University](http://iu.edu/) presented her Galaxy work with [Trinity](http://trinityrnaseq.github.io/), IU Galaxy, and the [Open Science Grid](http://www.opensciencegrid.org/). [Sam Guerler](/src/people/guerler/index.md) of the Galaxy Project talked about Galaxy'a new tool form support. +[Slides and video](/src/community/galaxy-admins/meetups/2015-04-16/index.md) from the [April GalaxyAdmins online meetup](/src/community/galaxy-admins/meetups/2015-04-16/index.md) are now available. [Carrie Ganote](http://www.researchgate.net/profile/Carrie_Ganote) from the [National Center for Genome Analysis Support (NCGAS)](http://ncgas.org/) and [Pervasive Technology Institute](http://pti.iu.edu/) at [Indiana University](http://iu.edu/) presented her Galaxy work with [Trinity](http://trinityrnaseq.github.io/), IU Galaxy, and the [Open Science Grid](http://www.opensciencegrid.org/). [Sam Guerler](/people/guerler/) of the Galaxy Project talked about Galaxy'a new tool form support. *Please join us for the [next GalaxyAdmins meetup on June 18](/src/community/galaxy-admins/meetups/2015-06-18/index.md)* when [Peter Briggs](http://galacticengineer.blogspot.co.uk/) of the [University of Manchester](http://www.manchester.ac.uk/) will speak on *Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester*. GalaxyAdmins will also have an in-person meetup at GCC2015. @@ -244,7 +244,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents May 15 RNA-Seq Galaxy Workshop Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko May 22, 29 @@ -256,7 +256,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents May 25-29 MIPRO Opatija, Croatia - Enis Afgan + Enis Afgan May 26-28 @@ -292,25 +292,25 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents June 6-9 WS02: NGS Variant Analysis with Galaxy ESHG 2015, Glasgow, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester June 2015 GalaxyAdmins Web Meetup, Online - Peter Briggs, Hans-Rudolf Hotz + Peter Briggs, Hans-Rudolf Hotz June 22 Introduction to variant calling for pathologists and laboratory managers Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia -
Training offered by GTN Member
Ross Lazarus, Andrew Lonie +
Training offered by GTN Member
Ross Lazarus, Andrew Lonie June 29-30 Introduction to NGS Data Analysis with Galaxy University of Edinburgh, Edinburgh, United Kingdom -
Training offered by GTN Member
Bert Overduin, Dave Clements +
Training offered by GTN Member
Bert Overduin, Dave Clements @@ -356,7 +356,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents July 10-14 Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training ISMB / ECCB 2015, BOSC 2015, Dublin, Ireland - Dave Clements + Dave Clements @@ -447,7 +447,7 @@ And one new Training Resource: * Add pulsar-run script for issues commands against a Pulsar server (experimental). [3cc7f74](https://github.com/galaxyproject/pulsar/commit/3cc7f74) * Changed the name of project to Pulsar, moved to [Github](https://github.com/galaxyproject/pulsar/). * New RESTful web services interface. -* SCP and Rsync file staging options added by [Helena Rasche](/src/people/helena-rasche/index.md). [Pull Request](https://github.com/galaxyproject/pulsar/pull/34) +* SCP and Rsync file staging options added by [Helena Rasche](/people/helena-rasche/). [Pull Request](https://github.com/galaxyproject/pulsar/pull/34) * Allow YAML based configuration. * Support for more traditional pip/setup.py-style installs. diff --git a/content/galaxy-updates/2015-06/index.md b/content/galaxy-updates/2015-06/index.md index 74f4ec16de..e2c1e11821 100644 --- a/content/galaxy-updates/2015-06/index.md +++ b/content/galaxy-updates/2015-06/index.md @@ -242,25 +242,25 @@ There are [upcoming events](/src/events/index.md) in seven countries on three co June 6-9 WS02: NGS Variant Analysis with Galaxy
ESHG 2015, Glasgow, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements June 8-9 Introduction to Galaxy Workshop
Workshop is full, but there is a waiting list
University of Glasgow, Glasgow, United Kingdom -
Training offered by GTN Member
Dave Clements +
Training offered by GTN Member
Dave Clements June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
June 2015 GalaxyAdmins Web Meetup, Online - Peter Briggs, Hans-Rudolf Hotz + Peter Briggs, Hans-Rudolf Hotz June 22 Introduction to variant calling for pathologists and laboratory managers
Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia -
Training offered by GTN Member
Ross Lazarus, Andrew Lonie +
Training offered by GTN Member
Ross Lazarus, Andrew Lonie June 22 diff --git a/content/galaxy-updates/2015-08/index.md b/content/galaxy-updates/2015-08/index.md index 998f731749..d0ff151c78 100644 --- a/content/galaxy-updates/2015-08/index.md +++ b/content/galaxy-updates/2015-08/index.md @@ -212,9 +212,9 @@ There are [upcoming events](/src/events/index.md) in four countries on three con * [Enabling Data-Intensive Biomedical Studies](http://bit.ly/leophd), Simone Leo -* [Enabling cloud bursting for life sciences within Galaxy](http://bit.ly/1TRbuRl), [Afgan](/src/people/enis-afgan/index.md) *et al.* +* [Enabling cloud bursting for life sciences within Galaxy](http://bit.ly/1TRbuRl), [Afgan](/people/enis-afgan/) *et al.* -* [Building and Provisioning Bioinformatics Environments on Public and Private Clouds](http://bit.ly/1gOtVYQ), [Afgan](/src/people/enis-afgan/index.md) *et al.* +* [Building and Provisioning Bioinformatics Environments on Public and Private Clouds](http://bit.ly/1gOtVYQ), [Afgan](/people/enis-afgan/) *et al.* * [LiSIs: An Online Scientific Workflow System for Virtual Screening](https://doi.org/10.2174/1386207318666150305123341), Kannas, *et al.* @@ -407,7 +407,7 @@ Galaxy now has a formal and open policy for managing the project source code - i Three new **[Community Log Board](/src/blog/index.md)** entries were added in July: * **[Moving from MySQL to PostgreSQL](/src/blog/2015-07-mysql-2-postgresql/index.md)** - by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) + by [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) * **[BioJS2Galaxy – A step by step guide](http://www.benjamenwhite.com/2015/07/biojs2galaxy-a-step-by-step-guide/)** by [Benedikt Rauscher](https://twitter.com/bengrauscher) and [Benjamen White](http://www.benjamenwhite.com/2015) @@ -418,10 +418,10 @@ Three new **[Community Log Board](/src/blog/index.md)** entries were added in Ju And the new Galaxy NGS 101 set of exercises, and the [Galaxy Coursera material](https://www.coursera.org/course/gengalaxy) were added to the **Teaching Resources Directory**: * **Galaxy NGS 101** - by [Anton Nekrutenko](/src/people/anton/index.md) + by [Anton Nekrutenko](/people/anton/) * **Genomic Data Science with Galaxy on Coursera** - by [James Taylor](/src/people/james-taylor/index.md) + by [James Taylor](/people/james-taylor/) ---- diff --git a/content/galaxy-updates/2015-09/index.md b/content/galaxy-updates/2015-09/index.md index f382017249..acd3511dd0 100644 --- a/content/galaxy-updates/2015-09/index.md +++ b/content/galaxy-updates/2015-09/index.md @@ -25,7 +25,7 @@ Welcome to the September 2015 *[Galactic News](/src/galaxy-updates/index.md)*, a Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges, Oliver Kohlbacher, *Bioinformatics*, Vol. 31, No. 13. (01 July 2015), pp. 2211-2213, doi:10.1093/bioinformatics/btv116 * [Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq](https://doi.org/10.1186/s12864-015-1767-y) - Anto P. Rajkumar, Per Qvist, [Ross Lazarus](/src/people/fubar/index.md), Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen, *BMC Genomics*, Vol. 16, No. 1. (25 July 2015), 548, doi:10.1186/s12864-015-1767-y + Anto P. Rajkumar, Per Qvist, [Ross Lazarus](/people/fubar/), Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen, *BMC Genomics*, Vol. 16, No. 1. (25 July 2015), 548, doi:10.1186/s12864-015-1767-y * [Galaxy Integrated Omics: Web-based standards-compliant workflows for proteomics informed by transcriptomics](https://doi.org/10.1074/mcp.o115.048777) Jun Fan, Shyamasree Saha, Gary Barker, Kate J. Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant, *Molecular & Cellular Proteomics* (12 August 2015), mcp.O115.048777, doi:10.1074/mcp.o115.048777 @@ -149,7 +149,7 @@ This split allows us to present Galaxy events in a much sparser calendar, that i IRIDA
-The [next GalaxyAdmins meetup on August 20](/src/community/galaxy-admins/meetups/2015-08-20/index.md) was attended by 27 *GalaxyAdmins*. [Aaron Petkau](https://github.com/apetkau) covered *Genomic data management at [Canada's National Microbiology Laboratory](https://www.nml-lnm.gc.ca/index-eng.htm) with [IRIDA](http://www.irida.ca/) and Galaxy* and [Enis Afgan](/src/people/enis-afgan/index.md) presented *Adding transparency and automation into the Galaxy tool installation process*. +The [next GalaxyAdmins meetup on August 20](/src/community/galaxy-admins/meetups/2015-08-20/index.md) was attended by 27 *GalaxyAdmins*. [Aaron Petkau](https://github.com/apetkau) covered *Genomic data management at [Canada's National Microbiology Laboratory](https://www.nml-lnm.gc.ca/index-eng.htm) with [IRIDA](http://www.irida.ca/) and Galaxy* and [Enis Afgan](/people/enis-afgan/) presented *Adding transparency and automation into the Galaxy tool installation process*. In case you missed it, [slides and video are now available online](/src/community/galaxy-admins/meetups/2015-08-20/index.md). @@ -248,7 +248,7 @@ There are [upcoming events](/src/events/index.md) in five countries on three con october 15 October Galaxy Admins Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements October 19 @@ -266,7 +266,7 @@ There are [upcoming events](/src/events/index.md) in five countries on three con October 28 - November 3 Computational & Comparative Genomics Course North America Cold Spring Harbor Laboratory, New York, United States - Training offered by GTN Member James Taylor + Training offered by GTN Member James Taylor diff --git a/content/galaxy-updates/2015-10/index.md b/content/galaxy-updates/2015-10/index.md index c1bbb32c49..72eef5bff8 100644 --- a/content/galaxy-updates/2015-10/index.md +++ b/content/galaxy-updates/2015-10/index.md @@ -158,7 +158,7 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2017! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) ---- @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents October 15 October Galaxy Admins Meetup Around the World Online - David Kovalic, Hans-Rudolf Hotz, Dave Clements + David Kovalic, Hans-Rudolf Hotz, Dave Clements October 28-29 @@ -235,7 +235,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents October 28 - November 3 Computational & Comparative Genomics Course North America Cold Spring Harbor Laboratory, New York, United States - Training offered by GTN Member James Taylor + Training offered by GTN Member James Taylor @@ -245,7 +245,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Anton Nekrutenko, James Taylor + Training offered by GTN Member Anton Nekrutenko, James Taylor Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations Workshop @@ -393,9 +393,9 @@ Thanks to everyone who helped put these together. **[Release Notes v 15.07](http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html)** **Release Highlights ** -* **Interactive Environments** - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by [Helena Rasche](/src/people/helena-rasche/index.md). +* **Interactive Environments** - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by [Helena Rasche](/people/helena-rasche/). * **Workflow Editor Enhancements** - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections. -* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/src/people/bjoern-gruening/index.md), [Nicola Soranzo](/src/people/nicola-soranzo/index.md), and [Helena Rasche](/src/people/helena-rasche/index.md). +* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/people/bjoern-gruening/index.md), [Nicola Soranzo](/people/nicola-soranzo/), and [Helena Rasche](/src/people/helena-rasche/). * And *[much more](http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html)* ## Mid 2015 Galaxy CloudMan Release @@ -486,7 +486,7 @@ See [list of tools contributed in September](/src/toolshed/contributions/2015-09 Center for Open Science gives grant to [Titus Brown](https://twitter.com/ctitusbrown) and team to connect Galaxy Project and the [Open Science Framework](https://osf.io/). See the [full announcement](http://cos.io/pr/2015-09-24/). * From [Globus](https://www.globus.org/genomics): Love (or like!) Globus? Vote for us in the [HPCWire Readers' Choice Awards](http://www.hpcwire.com/2015-hpcwire-readers-choice-awards/) (#16 - Best Data-Intensive System) -* From [Björn Grüning](/src/people/bjoern-gruening/index.md): +* From [Björn Grüning](/people/bjoern-gruening/): Brand new [Galaxy Interactive Environment documentation](/src/admin/gies/index.md): Enterprise Deployments, Docker on a different host... * From [Keywan Hassani-Pak](https://twitter.com/KeywanHP): We encountered [a big problem using bwa-eXpress in Galaxy](https://github.com/Rothamsted/AppliedBioinformatics/wiki/Transcript-abundance-estimation-in-Galaxy) for transcript abundance estimation! @@ -499,7 +499,7 @@ See [list of tools contributed in September](/src/toolshed/contributions/2015-09 [TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis and evaluation](https://usegalaxy.org/u/mwolfien/p/trapline---manual) * From [GigaScience](https://twitter.com/GigaScience) Supporting Galaxy BLAST+ wrappers, archived at the point of publication hosted in GigaDB [dx.doi.org/10.5524/100149](http://gigadb.org/dataset/100149) -* From [Björn Grüning](/src/people/bjoern-gruening/index.md): +* From [Björn Grüning](/people/bjoern-gruening/): [New Galaxy Docker images](https://github.com/bgruening/docker-galaxy-stable)! Enjoy all the new goodies!
diff --git a/content/galaxy-updates/2015-11/index.md b/content/galaxy-updates/2015-11/index.md index 1b7122ed66..9aa651666a 100644 --- a/content/galaxy-updates/2015-11/index.md +++ b/content/galaxy-updates/2015-11/index.md @@ -21,7 +21,7 @@ If you have anything to include in the next News, please send it to [Galaxy Outr **81** new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in October. Highlights include: * **[Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140829)** - [Enis Afgan](/src/people/enis-afgan/index.md), Clare Sloggett, Nuwan Goonasekera, Igor Makunin, Derek Benson, Mark Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie, *PLoS ONE* October 26, 2015 DOI: 10.1371/journal.pone.0140829.
+ [Enis Afgan](/people/enis-afgan/), Clare Sloggett, Nuwan Goonasekera, Igor Makunin, Derek Benson, Mark Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie, *PLoS ONE* October 26, 2015 DOI: 10.1371/journal.pone.0140829.
See also [Australian-made Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud, ...](https://www.vlsci.org.au/news/GVLnews2015). * **[Analyzing HT-SELEX data with the Galaxy Project tools - a web based bioinformatics platform for biomedical research](https://doi.org/10.1016/j.ymeth.2015.10.008)** @@ -205,11 +205,11 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Dan Blankenberg, John Chilton + Training offered by GTN Member Dan Blankenberg, John Chilton Common Workflow Language on Galaxy
Part of Portable Bioinformatics Workshop - John Chilton + John Chilton Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations Workshop @@ -247,7 +247,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online - /src/iuc/index.md, John Chilton + /src/iuc/index.md, John Chilton @@ -277,7 +277,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries January 8 Introduction to Galaxy Workshop North America Arizona State University, Tempe, Arizona, United States - Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko + Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko January 9-13 @@ -287,7 +287,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries Galaxy for SNP and Variant Data Analysis - Dave Clements + Dave Clements January 19 @@ -303,7 +303,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States - Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo + Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo @@ -497,20 +497,20 @@ Ran out of time to compile these. Look for a double batch in December. * Have a [look at a fresh chart of Main's usage](http://pic.twitter.com/G9RxTeXc0x) showing the improvements in Galaxy reports by [Daniel Bouchard](https://twitter.com/D_J_Bouchard). -* From [Björn Grüning](/src/people/bjoern-gruening/index.md): +* From [Björn Grüning](/people/bjoern-gruening/): * 💕 this community! DESeq2 update requested by @mikelove: the [Galaxy wrapper is available](https://github.com/galaxyproject/tools-iuc/pull/294) before BioC version -* From [John Chilton](/src/people/john-chilton/index.md): +* From [John Chilton](/people/john-chilton/): * [Versioned Tap Hackathon Proposal](https://github.com/Homebrew/homebrew-science/issues/2876) * [Galaxy visualizations](https://github.com/galaxyproject/galaxy/pull/378#event-427974576) from [Eteri Sokhoyan](https://github.com/eteriSokhoyan) and powered by [Cytoscape.js](http://js.cytoscape.org/) have been merged. -* [Martin Čech](/src/people/marten/index.md): +* [Martin Čech](/people/marten/): * [A list of tools presented at Genome Informatics 2015](https://github.com/galaxyproject/tools-iuc/issues/361) that might be of interest to the Galaxy community. * From [Oleg Shpynov](https://github.com/olegs) * Published [our first application for the Galaxy Project](https://github.com/JetBrains-Research/galaxy) -* From [Dannon Baker](/src/people/dannon-baker/index.md): +* From [Dannon Baker](/people/dannon-baker/): * [A proposal for bug and issue handling, and roadmap management](https://github.com/galaxyproject/galaxy/pull/902) * [Det'Rprok workflow](http://bit.ly/1aWNeVE) from [this paper](http://www.sciencedirect.com/science/article/pii/S1046202313002041) updated at MyExperiment. @@ -521,6 +521,6 @@ Ran out of time to compile these. Look for a double batch in December. Galaxy codebase -In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/src/people/helena-rasche/index.md) originally submitted by team member [Nate Coraor](/src/people/nate/index.md). +In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/people/helena-rasche/index.md) originally submitted by team member [Nate Coraor](/src/people/nate/). Our thanks go to the community and the team alike. diff --git a/content/galaxy-updates/2015-12/index.md b/content/galaxy-updates/2015-12/index.md index 6ffadd19ac..a5383d4958 100644 --- a/content/galaxy-updates/2015-12/index.md +++ b/content/galaxy-updates/2015-12/index.md @@ -21,7 +21,7 @@ If you have anything to include in the next News, please send it to [Galaxy Outr **81** new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in November. Highlights include: * [Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud](https://doi.org/10.1371/journal.pone.0140829) - by [Enis Afgan](/src/people/enis-afgan/index.md), Clare Sloggett, Nuwan Goonasekera *et al.*, *PloS One*, Vol. 10, No. 10. (2015) + by [Enis Afgan](/people/enis-afgan/), Clare Sloggett, Nuwan Goonasekera *et al.*, *PloS One*, Vol. 10, No. 10. (2015) * [Cost-Aware Cloud Provisioning](https://doi.org/10.1109/escience.2015.67) by Ryan Chard, Kyle Chard, Kris Bubendorfer, Lukasz Lacinski, Ravi Madduri, Ian Foster, In e-Science (e-Science), 2015 IEEE 11th International Conference on (August 2015), pp. 136-144, doi:10.1109/escience.2015.67 @@ -139,7 +139,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online - /src/iuc/index.md, John Chilton + /src/iuc/index.md, John Chilton @@ -169,7 +169,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. January 8 Introduction to Galaxy Workshop North America Arizona State University, Tempe, Arizona, United States - Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko + Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko January 9-13 @@ -203,7 +203,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States - Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo + Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo diff --git a/content/galaxy-updates/2016-01/index.md b/content/galaxy-updates/2016-01/index.md index 03325f99fa..7657d00e67 100644 --- a/content/galaxy-updates/2016-01/index.md +++ b/content/galaxy-updates/2016-01/index.md @@ -159,7 +159,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. January 8 Introduction to Galaxy Workshop North America Arizona State University, Tempe, Arizona, United States - Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko + Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko January 8, 15 @@ -205,7 +205,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States - Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo + Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo diff --git a/content/galaxy-updates/2016-02/index.md b/content/galaxy-updates/2016-02/index.md index 76018ef889..d6b0ec103e 100644 --- a/content/galaxy-updates/2016-02/index.md +++ b/content/galaxy-updates/2016-02/index.md @@ -109,7 +109,7 @@ We continue to seek other sponsors as well and [offer a wide range of sponsorshi Valentina Boeva, (23 Sep 2014) * [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract) - Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/src/people/marten/index.md), and Geir Kjetil Sandve, *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 + Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/people/marten/), and Geir Kjetil Sandve, *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 The new papers were tagged with: @@ -215,13 +215,13 @@ There are [many upcoming events](/src/events/index.md) in the next few months. February 18 GalaxyAdmins Web Meetup Around the World Online - Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements + Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States - Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo + Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo @@ -529,7 +529,7 @@ See [list of tools contributed in January](/src/toolshed/contributions/2016-01/i The app has been in development for over a year at the University of Oslo as part of [Claus Børnich's masters thesis](https://www.duo.uio.no/handle/10852/44701) and is described in - Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/src/people/marten/index.md), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 + Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/people/marten/), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 A [user manual](https://github.com/Tarostar/QMLGalaxyPortal/raw/master/GalaxyPortalUserGuide.pdf), additional information, and the full source are [available on GitHub](https://github.com/Tarostar/QMLGalaxyPortal). diff --git a/content/galaxy-updates/2016-04/index.md b/content/galaxy-updates/2016-04/index.md index 5ae105250b..593c43d33b 100644 --- a/content/galaxy-updates/2016-04/index.md +++ b/content/galaxy-updates/2016-04/index.md @@ -114,7 +114,7 @@ The workshop is intended for Bioinformaticians who want to The workshop will be held at [Heidelberg Center for Human Bioinformatics (HD-HuB)](https://www.denbi.de/index.php/hd-hub-services/15-hd-hub). Location and Accommodation options can be found [here](https://drive.google.com/file/d/0B2xSE9muunQPQ1E1Q3UwMVBTR1k/edit). -Registration is open and their is still space - just send [Björn Grüning](/src/people/bjoern-gruening/index.md) an email. For more information please see the [workshop page](https://goo.gl/8dNSdy). +Registration is open and their is still space - just send [Björn Grüning](/people/bjoern-gruening/) an email. For more information please see the [workshop page](https://goo.gl/8dNSdy).

IFB
@@ -169,13 +169,13 @@ There are [many upcoming events](/src/events/index.md) in the next few months. April 6-7 Galaxy DevOps Workshop - Galaxy and Galaxy tools deployment strategies Europe Galaxy DevOps Workshop 2016, Heidelberg, Germany - Training offered by GTN Member Björn Grüning + Training offered by GTN Member Björn Grüning April 21 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements April 22-26 @@ -193,7 +193,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. April 28 Galaxy Workshop Tokyo 2016 Asia RCAST, The University of Tokyo, Japan - Tazro Ohta, James Taylor + Tazro Ohta, James Taylor @@ -577,7 +577,7 @@ The [IUC](/src/iuc/index.md) is [seeking comments and contributions to this effo * New and recently updated tools are now highlighted on usegalaxy.org. -* From [Bjöern Grüening](/src/people/bjoern-gruening/index.md): +* From [Bjöern Grüening](/people/bjoern-gruening/): * Cheminformatics datatypes were added to Galaxy with [this pull request](https://github.com/galaxyproject/galaxy/pull/1941). Expect new ChemicalToolBox development soon! * [deepTools](https://deeptools.github.io/) visualization, QC, and data normalization tools are now available on [usegalaxy.org](https://usegalaxy.org). Thanks to [Devon Ryan](https://twitter.com/dpryan79) and https://twitter.com/fidel_ramirez|Fidel Ramirez]] * Galaxy Tours, a new interactive way to learn Galaxy, were announced in the [February News](/src/galaxy-updates/2016-02/index.md#new-tutorials--and-tours). We now have an [official repository to collect community tours](https://github.com/galaxyproject/galaxy-tours). diff --git a/content/galaxy-updates/2016-05/index.md b/content/galaxy-updates/2016-05/index.md index 05dc730f73..7c36e88c4a 100644 --- a/content/galaxy-updates/2016-05/index.md +++ b/content/galaxy-updates/2016-05/index.md @@ -262,7 +262,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth June 16 GalaxyAdmins Web Meetup Around the World Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 25-29 @@ -307,7 +307,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth July 13-17 The Allied Genetics Conference 2016 (TAGC) North America Orlando, Florida, United States - Dave Clements + Dave Clements @@ -328,7 +328,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth GalaxyAdmins
-[Slides and video](/src/community/galaxy-admins/meetups/2016-04-21/index.md) from the [April 2016 GalaxyAdmins meetup are now available](/src/community/galaxy-admins/meetups/2016-04-21/index.md). [Ivar Grytten](http://www.mn.uio.no/ifi/english/people/aca/ivargry/) and [Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/) from the [University of Oslo](http://www.uio.no/) discussed [The Galaxy Portal: Accessing Galaxy from Mobile Devices](http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinformatics.btw042.full) ([Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/201604_Admins_Portal.pdf)) and [John Chilton](/src/people/john-chilton/index.md) covered [Tool Development Developments](http://planemo.readthedocs.org/en/latest/galaxy_changelog.html). +[Slides and video](/src/community/galaxy-admins/meetups/2016-04-21/index.md) from the [April 2016 GalaxyAdmins meetup are now available](/src/community/galaxy-admins/meetups/2016-04-21/index.md). [Ivar Grytten](http://www.mn.uio.no/ifi/english/people/aca/ivargry/) and [Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/) from the [University of Oslo](http://www.uio.no/) discussed [The Galaxy Portal: Accessing Galaxy from Mobile Devices](http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinformatics.btw042.full) ([Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/201604_Admins_Portal.pdf)) and [John Chilton](/people/john-chilton/) covered [Tool Development Developments](http://planemo.readthedocs.org/en/latest/galaxy_changelog.html). ## Conda Dependency Codefest Report @@ -456,7 +456,7 @@ The new papers were tagged with:
Diploid variant calling
-There are two new comprehensive online tutorials from [Anton Nekrutenko](/src/people/anton/index.md): +There are two new comprehensive online tutorials from [Anton Nekrutenko](/people/anton/): ## Diploid variant calling @@ -464,11 +464,11 @@ Variant calling is a complex field that was significantly propelled by advances
Reference based RNA seq
-Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/src/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/index.md) ([@davebx](https://github.com/davebx)). +Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Reference based RNA seq -**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/src/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/index.md) ([@davebx](https://github.com/davebx)). +**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Dataset Collections diff --git a/content/galaxy-updates/2016-06/index.md b/content/galaxy-updates/2016-06/index.md index b067fea8c4..ff2ad06293 100644 --- a/content/galaxy-updates/2016-06/index.md +++ b/content/galaxy-updates/2016-06/index.md @@ -175,7 +175,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 20 @@ -226,7 +226,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md July 13-17 An Introduction to Using Galaxy for Genetic Data Analysis North America The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States - Dave Clements + Dave Clements July 15 @@ -238,7 +238,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md July 21 Introduction to Galaxy North America Cornell University, Ithaca, New York, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements @@ -247,7 +247,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop North America ICBO 2016, Corvallis, Oregon, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements August 12 diff --git a/content/galaxy-updates/2016-07/index.md b/content/galaxy-updates/2016-07/index.md index 79635cb3b8..4cfe638cc4 100644 --- a/content/galaxy-updates/2016-07/index.md +++ b/content/galaxy-updates/2016-07/index.md @@ -140,7 +140,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md July 13-17 An Introduction to Using Galaxy for Genetic Data Analysis North America The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States - Dave Clements + Dave Clements July 15 @@ -152,13 +152,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md July 19-20 Introduction to Galaxy North America University of Rochester, Rochester, New York, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements July 21 Introduction to Galaxy North America Cornell University, Ithaca, New York, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements @@ -167,13 +167,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop North America ICBO 2016, Corvallis, Oregon, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements August 9-10 Introduction to Galaxy Workflows Around the World Workflows Workshop, Distributed - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements August 12 @@ -185,7 +185,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -227,13 +227,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-08/index.md b/content/galaxy-updates/2016-08/index.md index e7ad7ba0f7..49b98b6bbe 100644 --- a/content/galaxy-updates/2016-08/index.md +++ b/content/galaxy-updates/2016-08/index.md @@ -68,13 +68,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop North America ICBO 2016, Corvallis, Oregon, United States - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements August 9-10 Introduction to Galaxy Workflows Around the World Workflows Workshop, Distributed - Training offered by GTN Member Dave Clements + Training offered by GTN Member Dave Clements August 12 @@ -92,7 +92,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -152,13 +152,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-09/index.md b/content/galaxy-updates/2016-09/index.md index c4d4d73fc2..064b4c3826 100644 --- a/content/galaxy-updates/2016-09/index.md +++ b/content/galaxy-updates/2016-09/index.md @@ -154,13 +154,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening @@ -181,7 +181,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 8-20 Advanced Sequencing Technologies & Applications
Application deadline is July 15
North America Cold Spring Harbor Laboratory, New York, United States - Training offered by GTN Member Jeremy Goecks + Training offered by GTN Member Jeremy Goecks November 9-11 @@ -266,7 +266,7 @@ Some highlights from last month: Matt Chambers. * **[CloudBridge: a Simple Cross-Cloud Python Library](https://s3.amazonaws.com/cloudbridgelib/CloudBridge.pdf)** - Nuwan Goonasekera, Andrew Lonie, [James Taylor](/src/people/james-taylor/index.md), [Enis Afgan](/src/people/enis-afgan/index.md). XSEDE16. + Nuwan Goonasekera, Andrew Lonie, [James Taylor](/people/james-taylor/index.md), [Enis Afgan](/src/people/enis-afgan/). XSEDE16. * **[DISMISS: detection of stranded methylation in MeDIP-Seq data](http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1158-7)** Umar Niazi, Kathrin K Geyer, Martin J Vickers, Karl F Hoffmann, Martin T Swain. *BMC Bioinformatics*, Vol. 17, No. 1. (2016), pp. 1-12, doi:10.1186/s12859-016-1158-7 @@ -284,7 +284,7 @@ Some highlights from last month: Stephen R. Piccolo, Michael B. Frampton. *GigaScience*, Vol. 5, No. 1. (11 July 2016), doi:10.1186/s13742-016-0135-4 * ** [Streamlined analysis of duplex sequencing data with Du Novo](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1039-4)** - Nicholas Stoler, Barbara Arbeithuber, Wilfried Guiblet, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/index.md). *Genome Biology*, 201617:180 DOI: 10.1186/s13059-016-1039-4 + Nicholas Stoler, Barbara Arbeithuber, Wilfried Guiblet, Kateryna D. Makova, [Anton Nekrutenko](/people/anton/). *Genome Biology*, 201617:180 DOI: 10.1186/s13059-016-1039-4 ## Tagged Publications @@ -559,7 +559,7 @@ Other Galaxy packages that haven't had a release in the past four months can be # Other News -* From [Greg Von Kuster](/src/people/greg_vonkuster/index.md): +* From [Greg Von Kuster](/people/greg_vonkuster/): [Galaxy tools for Constructive Solid Geometry (Galaxy CSG flavor)](https://github.com/gregvonkuster/galaxy-csg/blob/master/README.md) * [How to Build Bioinformatic Pipelines Using Galaxy](http://www.the-scientist.com/?articles.view/articleNo/46670/title/How-to-Build-Bioinformatic-Pipelines-Using-Galaxy), and article by Jeffrey M. Perkel in *The Scientist*. diff --git a/content/galaxy-updates/2016-10/index.md b/content/galaxy-updates/2016-10/index.md index 6a3e298d95..69a32ad1d1 100644 --- a/content/galaxy-updates/2016-10/index.md +++ b/content/galaxy-updates/2016-10/index.md @@ -68,7 +68,7 @@ This will be an online contribution fest and the fun to contribute should be pri Ciao, -[Bérénice](http://bebatut.fr/) and [Bjoern](/src/people/bjoern-gruening/index.md) +[Bérénice](http://bebatut.fr/) and [Bjoern](/people/bjoern-gruening/) ## Galaxy Admin Training, November 7-11, Salt Lake City, Utah @@ -133,7 +133,7 @@ Galaxy and [CloudBridge](http://cloudbridge.readthedocs.io/en/latest/) have join The Galaxy v16.07 release ([see below](/src/galaxy-updates/2016-10/index.md#galaxy-v1607)) included a "Shift of Galaxy tool dependencies to Conda" and that shift is reflected in a whole bunch of activity: -* **[Conda as a new standard for Galaxy tool dependencies](http://blogs.biomedcentral.com/gigablog/2016/09/20/guest-posting-introducing-conda-for-galaxy/)**, a guest blog posting by [Björn Grüning](/src/people/bjoern-gruening/index.md) in *[GigaScience's](http://www.gigasciencejournal.com/)* [GigaBlog](http://blogs.biomedcentral.com/gigablog/). +* **[Conda as a new standard for Galaxy tool dependencies](http://blogs.biomedcentral.com/gigablog/2016/09/20/guest-posting-introducing-conda-for-galaxy/)**, a guest blog posting by [Björn Grüning](/people/bjoern-gruening/) in *[GigaScience's](http://www.gigasciencejournal.com/)* [GigaBlog](http://blogs.biomedcentral.com/gigablog/). * a Galaxy-P Conda contribution fest in September ([see report below](/src/galaxy-updates/2016-10/index.md#galaxy-p-conda-contribution-fest-report)), * enhancements to [Planemo](/src/galaxy-updates/2016-10/index.md#planemo-0332), and * an upcoming **[Bioconda Contribution Fest](https://github.com/bioconda/bioconda-recipes/issues/2277)** on November 2-3. @@ -171,7 +171,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 6-7 Galaxy Training Contribution Fest Around the World Online - Björn Grüning + Björn Grüning October 10 @@ -205,7 +205,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 Genome Program Joint Workshop Asia Kunsan National University, Gunsan, South Korea - Anton Nekrutenko + Anton Nekrutenko October 20-21 @@ -217,19 +217,19 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 24-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy - Dannon Baker, Björn Grüning + Dannon Baker, Björn Grüning @@ -238,7 +238,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 2-3 Bioconda Contribution Fest Around the World Online - Björn Grüning + Björn Grüning November 7-8 @@ -256,7 +256,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 8-20 Advanced Sequencing Technologies & Applications
Application deadline is July 15
North America Cold Spring Harbor Laboratory, New York, United States - Training offered by GTN Member Jeremy Goecks + Training offered by GTN Member Jeremy Goecks November 9-11 @@ -295,7 +295,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md January 14-18 Galaxy Workshop Plant and Animal Genome XXV, San Diego, California, United States - Dave Clements + Dave Clements @@ -361,7 +361,7 @@ Some highlights from last month: Annette McGrath, Steve McMahon, Sean Li, Joel Ludbey, Tim Ho. *Journal of Grid Computing* (2016), pp. 1-11, doi:10.1007/s10723-016-9379-6 **[Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter](http://biorxiv.org/content/early/2016/09/22/075457)** - [Björn Grüning](/src/people/bjoern-gruening/index.md), [Helena Rasche](/src/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/src/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/src/people/john-chilton/index.md), [Nathan Coraor](/src/people/nate/index.md), Rolf Backofen, [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 + [Björn Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 **[Genotyping of evolving prokaryotic populations](https://doi.org/10.7287/peerj.preprints.2449v1)** Markus Zojer, Lisa N. Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei. *PeerJ Preprints* (14 September 2016), doi:10.7287/peerj.preprints.2449v1 @@ -373,7 +373,7 @@ Some highlights from last month: Guillaume Carissimo, Marius van den Beek, Juliana Pegoraro, Kenneth D. Vernick, Christophe Antoniewski. *bioRxiv* (2016), doi:10.1101/048983 **[Cloudflow - A framework for MapReduce pipeline development in Biomedical Research](https://doi.org/10.1109/mipro.2015.7160259)** - Lukas Forer, [Enis Afgan](/src/people/enis-afgan/index.md), Hansi Weißensteiner, Davor Davidović, Günther Specht, Florian Kronenberg, Sebastian Schönherr. 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO) (May 2015), pp. 172-177, doi:10.1109/mipro.2015.7160259 + Lukas Forer, [Enis Afgan](/people/enis-afgan/), Hansi Weißensteiner, Davor Davidović, Günther Specht, Florian Kronenberg, Sebastian Schönherr. 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO) (May 2015), pp. 172-177, doi:10.1109/mipro.2015.7160259 ## Tagged Publications diff --git a/content/galaxy-updates/2016-12/index.md b/content/galaxy-updates/2016-12/index.md index ca5d2390b3..5a7d6b500d 100644 --- a/content/galaxy-updates/2016-12/index.md +++ b/content/galaxy-updates/2016-12/index.md @@ -58,7 +58,7 @@ We are pleased to announce that the keynote speakers for GAMe 2017 will be James **[Dr James Taylor](http://taylorlab.org/)** is the Ralph S. O’Connor Associate Professor of Biology and associate professor of computer science at [Johns Hopkins University](http://jhu.edu/). He is a Galaxy Project PI, and one of the original developers of the Galaxy platform for data analysis. His group works on extending the Galaxy platform, and understanding genomic and epigenomic regulation of gene transcription through integrated analysis of functional genomic data. -**[Dr Björn Grüning](/src/people/bjoern-gruening/index.md)** is with the [Bioinformatics Group](http://www.bioinf.uni-freiburg.de/team.html) at [Albert-Ludwigs-Universität Freiburg](http://www.uni-freiburg.de/), in Freiburg Germany, where he heads the [Freiburg Galaxy Project](http://www.bioinf.uni-freiburg.de/Galaxy/index.html). His [publication list](http://orcid.org/0000-0002-3079-6586) includes several papers that feature Galaxy prominently, including the recent “Enhancing pre-defined workflows with *ad hoc* analytics using Galaxy, Docker and Jupyter” ([Grüning, et al, 2016](http://biorxiv.org/content/early/2016/09/22/075457). He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organize the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at [GCC2016](https://gcc16.sched.org/?s=bj%C3%B6rn). His research interests include data visualisation, computational chemistry, and drug discovery. +**[Dr Björn Grüning](/people/bjoern-gruening/)** is with the [Bioinformatics Group](http://www.bioinf.uni-freiburg.de/team.html) at [Albert-Ludwigs-Universität Freiburg](http://www.uni-freiburg.de/), in Freiburg Germany, where he heads the [Freiburg Galaxy Project](http://www.bioinf.uni-freiburg.de/Galaxy/index.html). His [publication list](http://orcid.org/0000-0002-3079-6586) includes several papers that feature Galaxy prominently, including the recent “Enhancing pre-defined workflows with *ad hoc* analytics using Galaxy, Docker and Jupyter” ([Grüning, et al, 2016](http://biorxiv.org/content/early/2016/09/22/075457). He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organize the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at [GCC2016](https://gcc16.sched.org/?s=bj%C3%B6rn). His research interests include data visualisation, computational chemistry, and drug discovery. ### ORAL Presentation Abstracts Deadline Extended to 14 December @@ -100,13 +100,13 @@ There are [a plenitude of Galaxy related events coming up](/src/events/index.md) December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online - Dannon Baker, Dave Clements + Dannon Baker, Dave Clements December 15 Galaxy Training Materials: Community creation, curation, and use and The new Galaxy Hub: Community creation, curation, and use Online Online - Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements + Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements December 15-16 @@ -180,7 +180,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth Some highlights from last month: -* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/src/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/src/people/dannon-baker/index.md), [John Chilton](/src/people/john-chilton/index.md), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/people/james-taylor/index.md), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) +* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/index.md), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) * [How Are You – and How’s Your Microbiome?](https://theanalyticalscientist.com/issues/1116/how-are-you-and-hows-your-microbiome/), Pratik Jagtap, *The Analytical Scientist*, November 2016 * [Computational workflow for the fine-grained analysis of metagenomic samples](https://doi.org/10.1186/s12864-016-3063-x), Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles, *BMC Genomics*, Vol. 17, No. S8. (25 October 2016), doi:10.1186/s12864-016-3063-x * [Big Data Smart Socket (BDSS): A System that Abstracts Data Transfer Habits from End Users](https://doi.org/10.1093/bioinformatics/btw679), Nick A. Watts, Frank A. Feltus, *Bioinformatics* (26 October 2016), btw679, doi:10.1093/bioinformatics/btw679 @@ -400,7 +400,7 @@ See the [full release notes](https://docs.galaxyproject.org/en/master/releases/1 #### Galaxy Docker Image 16.07 -And, thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md), there is also now [a Docker image for Galaxy 16.07](https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07) as well. +And, thanks to [Björn Grüning](/people/bjoern-gruening/), there is also now [a Docker image for Galaxy 16.07](https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07) as well. ### galaxy-lib 16.10.10 @@ -438,7 +438,7 @@ Didn't get there this month. * Want to use Galaxy on Jetstream? [Learn how to Write a Successful XSEDE Allocation Proposal](https://www.xsede.org/web/xup/course-calendar/-/training-user/class/526/session/1131), December 13 * From [Peter Briggs](http://twitter.com/ironic_cog): * [Nebulizer 0.4.0](https://pypi.python.org/pypi/nebulizer/0.4.0): utilities for managing users, tools and libraries in Galaxy now available from PyPI -* From [Enis Afgan](/src/people/enis-afgan/index.md): +* From [Enis Afgan](/people/enis-afgan/): * [How does Galaxy perform on the AWS cloud: variability across instances, disks and data](http://www.slideshare.net/afgane/galaxy-cloudman-performance-on-aws). * From [Chase Miller](http://marthlab.org/people.html) * [IOBIO Now in Galaxy](http://iobio.io/2016/11/02/galaxy-integration/) diff --git a/content/galaxy-updates/2017-01/index.md b/content/galaxy-updates/2017-01/index.md index 5053153604..303abb1a0c 100644 --- a/content/galaxy-updates/2017-01/index.md +++ b/content/galaxy-updates/2017-01/index.md @@ -33,7 +33,7 @@ We are pleased to announce that the keynote speakers for GAMe 2017 will be James **[Dr James Taylor](http://taylorlab.org/)** is the Ralph S. O’Connor Associate Professor of Biology and associate professor of computer science at [Johns Hopkins University](http://jhu.edu/). He is a Galaxy Project PI, and one of the original developers of the Galaxy platform for data analysis. His group works on extending the Galaxy platform, and understanding genomic and epigenomic regulation of gene transcription through integrated analysis of functional genomic data. -**[Dr Björn Grüning](/src/people/bjoern-gruening/index.md)** is with the [Bioinformatics Group](http://www.bioinf.uni-freiburg.de/team.html) at [Albert-Ludwigs-Universität Freiburg](http://www.uni-freiburg.de/), in Freiburg Germany, where he heads the [Freiburg Galaxy Project](http://www.bioinf.uni-freiburg.de/Galaxy/index.html). His [publication list](http://orcid.org/0000-0002-3079-6586) includes several papers that feature Galaxy prominently, including the recent “Enhancing pre-defined workflows with *ad hoc* analytics using Galaxy, Docker and Jupyter” ([Grüning, et al, 2016](http://biorxiv.org/content/early/2016/09/22/075457). He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organize the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at [GCC2016](https://gcc16.sched.org/?s=bj%C3%B6rn). His research interests include data visualisation, computational chemistry, and drug discovery. +**[Dr Björn Grüning](/people/bjoern-gruening/)** is with the [Bioinformatics Group](http://www.bioinf.uni-freiburg.de/team.html) at [Albert-Ludwigs-Universität Freiburg](http://www.uni-freiburg.de/), in Freiburg Germany, where he heads the [Freiburg Galaxy Project](http://www.bioinf.uni-freiburg.de/Galaxy/index.html). His [publication list](http://orcid.org/0000-0002-3079-6586) includes several papers that feature Galaxy prominently, including the recent “Enhancing pre-defined workflows with *ad hoc* analytics using Galaxy, Docker and Jupyter” ([Grüning, et al, 2016](http://biorxiv.org/content/early/2016/09/22/075457). He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organize the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at [GCC2016](https://gcc16.sched.org/?s=bj%C3%B6rn). His research interests include data visualisation, computational chemistry, and drug discovery. ### Poster abstracts and late oral presentation Abstracts @@ -58,8 +58,8 @@ Screencasts for the [August](/src/community/galaxy-admins/meetups/2016-08-18/ind * *Dynamic Job Expansion: Experiences using [Makeflow](http://ccl.cse.nd.edu/software/makeflow/) in Galaxy*, [Nick Hazekamp](https://engineering.nd.edu/profiles/nhazekamp), [University of Notre Dame](http://www.nd.edu/) * [Video](https://connect.johnshopkins.edu/p9nqie63c7a/) * [December](/src/community/galaxy-admins/meetups/2016-12-15/index.md) - * *Galaxy Training Materials: Community creation, curation, and use*, [Björn Grüning](/src/people/bjoern-gruening/index.md) and Bérénice Batut, University of Freiburg - * *The new Galaxy Hub: Community creation, curation, and use*, [Dannon Baker](/src/people/dannon-baker/index.md), Johns Hopkins University + * *Galaxy Training Materials: Community creation, curation, and use*, [Björn Grüning](/people/bjoern-gruening/) and Bérénice Batut, University of Freiburg + * *The new Galaxy Hub: Community creation, curation, and use*, [Dannon Baker](/people/dannon-baker/), Johns Hopkins University * [Video](https://connect.johnshopkins.edu/p7ek9bf4ez0/) @@ -426,7 +426,7 @@ For full details on all of the enhancements and fixes in this release, please se ### Galaxy Docker Image 16.10 -And, thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md), there is also now [a Docker image for Galaxy 16.10](https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.10) as well. +And, thanks to [Björn Grüning](/people/bjoern-gruening/), there is also now [a Docker image for Galaxy 16.10](https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.10) as well. diff --git a/content/galaxy-updates/2017-03/index.md b/content/galaxy-updates/2017-03/index.md index dee8c0e2d1..7ebafcfca8 100644 --- a/content/galaxy-updates/2017-03/index.md +++ b/content/galaxy-updates/2017-03/index.md @@ -95,7 +95,7 @@ See the [full report](https://www.embl-abr.org.au/game2017report/) for more.
GalaxyAdmins
-A video of the [February 16 GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2017-02-16/index.md) is now available. Nuwan Goonesekera and [Enis Afgan](/src/people/enis-afgan/index.md) presented an all-new version of CloudLaunch, an application for launching Galaxy on the Cloud instances. The [new CloudLaunch](https://beta.launch.usegalaxy.org) allows multiple flavors of Galaxy to be deployed, Docker images or applications other than Galaxy. Each application can have its own custom user interface developed to accommodate the specific application needs. +A video of the [February 16 GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2017-02-16/index.md) is now available. Nuwan Goonesekera and [Enis Afgan](/people/enis-afgan/) presented an all-new version of CloudLaunch, an application for launching Galaxy on the Cloud instances. The [new CloudLaunch](https://beta.launch.usegalaxy.org) allows multiple flavors of Galaxy to be deployed, Docker images or applications other than Galaxy. Each application can have its own custom user interface developed to accommodate the specific application needs. ## All upcoming events @@ -260,7 +260,7 @@ Some highlights from the past two months: Connor Wytko, Brian Soto, Stephen P. Ficklin. *Database*, Vol. 2017 (10 January 2017), baw154, doi:10.1093/database/baw154 * [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://doi.org/10.12688/f1000research.9821.1) - [Nitesh Turaga](/src/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/src/people/dannon-baker/index.md), [John Chilton](/src/people/john-chilton/index.md), [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/james=taylor/index.md). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 + [Nitesh Turaga](/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/index.md), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 * [MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets](https://doi.org/10.1007/s41048-016-0033-4) Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan. *Biophysics Reports* (2017), pp. 1-10, doi:10.1007/s41048-016-0033-4 @@ -452,7 +452,7 @@ For full details on all of the enhancements and fixes in this release, please se ### Galaxy Docker Image 17.01 -And, thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. +And, thanks to [Björn Grüning](/people/bjoern-gruening/), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. diff --git a/content/galaxy-updates/2017-04/index.md b/content/galaxy-updates/2017-04/index.md index 13c6fb6603..035650ae4b 100644 --- a/content/galaxy-updates/2017-04/index.md +++ b/content/galaxy-updates/2017-04/index.md @@ -404,7 +404,7 @@ For full details on all of the enhancements and fixes in this release, please se #### Galaxy Docker Image 17.01 -And, thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. +And, thanks to [Björn Grüning](/people/bjoern-gruening/), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. ### Starforge 0.3 diff --git a/content/galaxy-updates/2017-05/index.md b/content/galaxy-updates/2017-05/index.md index a7598f0d0a..473529c177 100644 --- a/content/galaxy-updates/2017-05/index.md +++ b/content/galaxy-updates/2017-05/index.md @@ -385,7 +385,7 @@ For full details on all of the enhancements and fixes in this release, please se #### Galaxy Docker Image 17.01 -And, thanks to [Björn Grüning](/src/people/bjoern-gruening/index.md), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. +And, thanks to [Björn Grüning](/people/bjoern-gruening/), there is also now [a Docker image for Galaxy 17.01](https://github.com/bgruening/docker-galaxy-stable/releases/tag/17.01) as well. ### CloudLaunch ## @@ -452,7 +452,7 @@ Other Galaxy packages that haven't had a release in the past four months can be * [Guardians of the Galaxy Workflow](http://gigasciencejournal.com/blog/guardians-of-the-galaxy-workflow/) * A nice writeup from [Scott Edmunds](http://gigasciencejournal.com/blog/author/scottedmunds/) about the [*GigaScience* Galaxy Series](https://academic.oup.com/gigascience/pages/galaxy_series_data_intensive_reproducible_research) (now on it's 12th paper) and GCC2017. *[GigaScience](https://academic.oup.com/gigascience)* is a returning GCC sponsor this year and submissions relating to talks and posters at GCC2017 will be eligible for a continuing 15% discount. -* From [Björn Grüning](/src/people/bjoern-gruening/index.md) +* From [Björn Grüning](/people/bjoern-gruening/) * Are you interested in #RNA #Bioinformatics? Try our new community maintained [RNA Workbench](http://bgruening.github.io/galaxy-rna-workbench/) * From [Peter Briggs](https://twitter.com/ironic_cog): * [Galactic Engineer: Securing Galaxy with HTTPS running with Nginx using Let’s Encrypt](http://galacticengineer.blogspot.co.uk/2017/04/securing-galaxy-with-https-running-with.html) diff --git a/content/galaxy-updates/2017-06/index.md b/content/galaxy-updates/2017-06/index.md index 209686bf50..bf829d87c5 100644 --- a/content/galaxy-updates/2017-06/index.md +++ b/content/galaxy-updates/2017-06/index.md @@ -31,7 +31,7 @@ If you missed the May 31 regular registration deadline then don't worry because **The Galaxy Project: from the Planck epoch to Montpellier** -[Dr. Anton Nekrutenko](/src/people/anton/index.md) and [Dr. James Taylor](/src/people/james-taylor/index.md) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. +[Dr. Anton Nekrutenko](/people/anton/index.md) and [Dr. James Taylor](/src/people/james-taylor/) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. If you are reading this, you probably already know who they are. If not, see their [bios here](https://gcc2017.sciencesconf.org/). @@ -211,7 +211,7 @@ Some highlights from the papers added last month: *Nucleic Acids Research* (02 May 2017), doi:10.1093/nar/gkx315 * [Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](https://doi.org/10.1371/journal.pcbi.1005425) - [Björn A. Grüning](/src/people/bjoern-gruening/index.md), [Helena Rasche](/src/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/src/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/src/people/john-chilton/index.md), [Nate Coraor](/src/people/nate/index.md), Rolf Backofen, [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 + [Björn A. Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 * [MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization](https://doi.org/10.1093/bioinformatics/btx320) Katherine M. McCoy, Margaret L. Antonio, Tim van Opijnen. *Bioinformatics* (11 May 2017), doi:10.1093/bioinformatics/btx320 @@ -382,8 +382,8 @@ The [Galaxy Docker project has seen a new release](https://github.com/bgruening/ And * The [Galaxy Docker Project](https://github.com/bgruening/docker-galaxy-stable) has reached more than 23k downloads on [Dockerhub](https://hub.docker.com/r/bgruening/galaxy-stable/) - not counting quay.io and all flavors -* From [John Chilton](/src/people/john-chilton/index.md): - * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/src/people/bjoern-gruening/index.md): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) +* From [John Chilton](/people/john-chilton/): + * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/people/bjoern-gruening/): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) ## Parsec 1.0.0 - 1.0.2 @@ -439,12 +439,12 @@ Other Galaxy packages that haven't had a release in the past four months can be * From [Paul Gordon](https://www.blogger.com/profile/02637194860456629067) * [The ungoogleable: Authenticating a Galaxy Portal with Active Directory ](http://achri.blogspot.ca/2017/05/the-final-frontier-authenticating.html) -* From [Björn Grüning](/src/people/bjoern-gruening/index.md) +* From [Björn Grüning](/people/bjoern-gruening/) * There is a new [HiCExplorer Galaxy Docker version](https://github.com/maxplanck-ie/docker-galaxy-hicexplorer), based on Galaxy 17.05, made possible by [Fidel Ramírez](https://twitter.com/fidel_ramirez) and friends. -* From [Mo Heydarian](/src/people/mo-heydarian/index.md) +* From [Mo Heydarian](/people/mo-heydarian/) * Creating Galaxy workflows [is easier than you think](https://depot.galaxyproject.org/hub/attachments/documents/videos/2017-05-workflow-example.gif). If you like reproducibility, you'll like workflows! * New video on [Creating collections by uploading from SRA](https://vimeo.com/217216264). -* From [Nate Coraor](/src/people/nate/index.md) +* From [Nate Coraor](/people/nate/) * Heads up: Galaxy roles published on galaxy.ansible.com have changed namespaces from `galaxyprojectdotorg` to just `galaxyproject` diff --git a/content/galaxy-updates/2017-08/index.md b/content/galaxy-updates/2017-08/index.md index 0fc8072057..8936bd94de 100644 --- a/content/galaxy-updates/2017-08/index.md +++ b/content/galaxy-updates/2017-08/index.md @@ -380,8 +380,8 @@ The [Galaxy Docker project has seen a new release](https://github.com/bgruening/ And * The [Galaxy Docker Project](https://github.com/bgruening/docker-galaxy-stable) has reached more than 23k downloads on [Dockerhub](https://hub.docker.com/r/bgruening/galaxy-stable/) - not counting quay.io and all flavors -* From [John Chilton](/src/people/john-chilton/index.md): - * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/src/people/bjoern-gruening/index.md): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) +* From [John Chilton](/people/john-chilton/): + * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/people/bjoern-gruening/): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) ### Parsec 1.0.0 - 1.0.2 @@ -425,7 +425,7 @@ Other Galaxy packages that haven't had a release in the past four months can be * [Five years of Galaxy-P!](https://twitter.com/usegalaxyp/status/888157211612110849) * A [plugin framework for Galaxy tool error handling](https://github.com/galaxyproject/galaxy/pull/4305) (work-in-progress) by [Helena Rasche](https://github.com/hexylena). * [A Galaxy docker container with R markdown based Galaxy tools installed](https://github.com/statonlab/docker-GRReport). This Docker image is used as a demonstration to show how to use R markdown as a unified framework for Galaxy tool development. -* From [John Chilton](/src/people/john-chilton/index.md): A cool outcome from our GCC hackathon - [support for Galaxy tool localization](https://github.com/galaxyproject/galaxy/pull/4251) (work in progress). +* From [John Chilton](/people/john-chilton/): A cool outcome from our GCC hackathon - [support for Galaxy tool localization](https://github.com/galaxyproject/galaxy/pull/4251) (work in progress). * From Mallory Freeberg: [Differential abundance testing of small RNAs](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html) tutorial -* From [Enis Afgan](/src/people/enis-afgan/index.md): [First launch of #usegalaxy on Microsoft #Azure!](https://twitter.com/enisafgan/status/880796649160880128) A huge thanks to RC Carter and Elizabeth Bruce for setting the wheels in motion.) A huge thanks to RC Carter and Elizabeth Bruce for setting the wheels in motion. +* From [Enis Afgan](/people/enis-afgan/): [First launch of #usegalaxy on Microsoft #Azure!](https://twitter.com/enisafgan/status/880796649160880128) A huge thanks to RC Carter and Elizabeth Bruce for setting the wheels in motion.) A huge thanks to RC Carter and Elizabeth Bruce for setting the wheels in motion. diff --git a/content/galaxy-updates/2017-09/index.md b/content/galaxy-updates/2017-09/index.md index ecfb3fd571..6ebd80c28d 100644 --- a/content/galaxy-updates/2017-09/index.md +++ b/content/galaxy-updates/2017-09/index.md @@ -17,16 +17,16 @@ Welcome to the September 2017 *[Galactic News](/src/galaxy-updates/index.md)*, a Some highlights from the recently added pubs: * [2017 Galaxy community update](https://doi.org/10.7490/f1000research.1114388.1) - [Dan Blankenberg](/src/people/dan/index.md), [Jeremy Goecks](/src/people/jeremy-goecks/index.md). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 + [Dan Blankenberg](/people/dan/index.md), [Jeremy Goecks](/src/people/jeremy-goecks/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 * [Approaches for small RNA-seq in Galaxy](https://doi.org/10.7490/f1000research.1114423.1) - Mallory Freeberg, [James Taylor](/src/people/james-taylor/index.md). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114423.1 + Mallory Freeberg, [James Taylor](/people/james-taylor/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114423.1 * [Bio-Docklets: virtualization containers for single-step execution of NGS pipelines](https://doi.org/10.1093/gigascience/gix048) Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis. *GigaScience*, Vol. 6, No. 8. (August 2017), pp. 1-7, doi:10.1093/gigascience/gix048 * [Building an open, collaborative, online infrastructure for bioinformatics training](https://doi.org/10.7490/f1000research.1114447.1) - Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/src/people/dave-clements/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 + Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/people/dave-clements/index.md), [Björn Grüning](/src/people/bjoern-gruening/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 * [Galaxy-compatible Tool for Rapid Aptamer Clustering and HT-SELEX Data Analysis](https://doi.org/10.22377/ajp.v11i02.1265) Nikita A. Skrylnik, *Asian Journal of Pharmaceutics (AJP)*, Vol. 11, No. 02. (2017), doi:10.22377/ajp.v11i02.1265 @@ -50,13 +50,13 @@ Some highlights from the recently added pubs: Jeffrey Miller, Brenna Miller. *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114436.1 * [Recent object formation in the core of Galaxy](https://doi.org/10.7490/f1000research.1114483.1) - [Martin Čech](/src/people/marten/index.md), et. al. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114483.1 + [Martin Čech](/people/marten/), et. al. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114483.1 * [Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data](https://doi.org/10.12688/f1000research.12168.1) Chao Zhang, Jochem Bijlard, Christine Staiger, et al. *F1000Research*, Vol. 6 (16 August 2017), 1488, doi:10.12688/f1000research.12168.1 * [The backbone of research reproducibility-sustainable and flexible tool deployment](https://doi.org/10.7490/f1000research.1114482.1) - [Björn Grüning](/src/people/bjoern-gruening/index.md), [John Chilton](/src/people/john-chilton/index.md), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 + [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/src/people/john-chilton/), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 * [ToolDog-generating tool descriptors from the ELIXIR tool registry](https://doi.org/10.7490/f1000research.1114473.1) Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison, Hervé Ménager. *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114473.1 @@ -290,8 +290,8 @@ The [Galaxy Docker project has seen a new release](https://github.com/bgruening/ And * The [Galaxy Docker Project](https://github.com/bgruening/docker-galaxy-stable) has reached more than 23k downloads on [Dockerhub](https://hub.docker.com/r/bgruening/galaxy-stable/) - not counting quay.io and all flavors -* From [John Chilton](/src/people/john-chilton/index.md): - * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/src/people/bjoern-gruening/index.md): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) +* From [John Chilton](/people/john-chilton/): + * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/people/bjoern-gruening/): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) ### Parsec 1.0.0 diff --git a/content/galaxy-updates/2017-10/index.md b/content/galaxy-updates/2017-10/index.md index bfb96d912b..b740ebdfde 100644 --- a/content/galaxy-updates/2017-10/index.md +++ b/content/galaxy-updates/2017-10/index.md @@ -190,7 +190,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth The Galaxy is expanding! Please help it grow. -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States * [Implémentation d’outils d’analyse et de visualisation de variations structurales et génomes mosaïques](https://www.sfbi.fr/content/impl%C3%A9mentation-d%E2%80%99outils-d%E2%80%99analyse-et-de-visualisation-de-variations-structurales-et-g%C3%A9nomes-), IRD (Institut de Recherche pour le Développement), Montpellier, France * [Metabarcoding, analyses écologiques et statistiques de paleocommunautés de protistes de l’écosystème côtier](https://www.sfbi.fr/content/metabarcoding-analyses-%C3%A9cologiques-et-statistiques-de-paleocommunaut%C3%A9s-de-protistes-de-l%E2%80%99%C3%A9co), IFREMER DYNECO/Pelagos, Brest, France @@ -337,8 +337,8 @@ The [Galaxy Docker project has seen a new release](https://github.com/bgruening/ And * The [Galaxy Docker Project](https://github.com/bgruening/docker-galaxy-stable) has reached more than 23k downloads on [Dockerhub](https://hub.docker.com/r/bgruening/galaxy-stable/) - not counting quay.io and all flavors -* From [John Chilton](/src/people/john-chilton/index.md): - * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/src/people/bjoern-gruening/index.md): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) +* From [John Chilton](/people/john-chilton/): + * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/people/bjoern-gruening/): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) ### Galaxy CloudMan 17.05 on AWS diff --git a/content/galaxy-updates/2017-11/index.md b/content/galaxy-updates/2017-11/index.md index 364457a1a6..06eba3ccbe 100644 --- a/content/galaxy-updates/2017-11/index.md +++ b/content/galaxy-updates/2017-11/index.md @@ -15,11 +15,11 @@ The new *[Galactic Blog](/src/blog/index.md)* was launched in October. The *Gal The blog is off to a running start with these posts in October: -* [ELIXIR Galaxy Community](/src/blog/2017-10-05-elixir-galaxy-community/index.md), by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/src/people/bjoern-gruening/index.md) -* [Public Galaxy Server Dashboard](/src/blog/2017-10-public-galaxy-dashboard/index.md), by [Helena Rasche](/src/people/helena-rasche/index.md) -* [SciPy and scikit-learn integration into Galaxy](/src/blog/2017-10-10-scipy-galaxy/index.md), by [Björn Grüning](/src/people/bjoern-gruening/index.md) -* [Small genome assembly in Galaxy](/src/blog/2017-10-16-UnicyclerTutorial/index.md), by [Anton Nekrutenko](/src/people/anton/index.md) -* [Galaxy: the first 5,000 pubs](/src/blog/2017-10-5000-pubs/index.md), by [Dave Clements](/src/people/dave-clements/index.md) +* [ELIXIR Galaxy Community](/src/blog/2017-10-05-elixir-galaxy-community/index.md), by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/people/bjoern-gruening/) +* [Public Galaxy Server Dashboard](/src/blog/2017-10-public-galaxy-dashboard/index.md), by [Helena Rasche](/people/helena-rasche/) +* [SciPy and scikit-learn integration into Galaxy](/src/blog/2017-10-10-scipy-galaxy/index.md), by [Björn Grüning](/people/bjoern-gruening/) +* [Small genome assembly in Galaxy](/src/blog/2017-10-16-UnicyclerTutorial/index.md), by [Anton Nekrutenko](/people/anton/) +* [Galaxy: the first 5,000 pubs](/src/blog/2017-10-5000-pubs/index.md), by [Dave Clements](/people/dave-clements/) ## The Galactic Blog needs you! @@ -43,7 +43,7 @@ microbial genomic epidemiology](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC562 * [An Arranged Marriage: Integrating DKPro Core in the Language Analysis Portal](https://www.clarin.eu/sites/default/files/Kouylekov-CLARIN2017_paper_37.pdf), Milen Kouylekov, Emanuele Lapponi, Stephan Oepen, and Richard Eckart de Castilho. [CLARIN2017 Book of Abstracts](https://www.clarin.eu/content/abstracts-overview-clarin-annual-conference-2017) * [An Architecture for Genomics Analysis in a Clinical Setting Using Galaxy and Docker](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/gix099/4557139), W. Digan, H. Countouris, M. Barritault, D. Baudoin, P. Laurent-Puig, H. Blons, A. Burgun, B. Rance. *GigaScience*, gix099, doi: 10.1093/gigascience/gix099 Published: 18 October 2017 -* [Bioconda: A sustainable and comprehensive software distribution for the life sciences](https://doi.org/10.1101/207092), [Björn Grüning](/src/people/bjoern-gruening/index.md), Ryan Dale, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, The Bioconda Team, Johannes Köster, *bioRxiv* 207092, doi: https://doi.org/10.1101/207092 +* [Bioconda: A sustainable and comprehensive software distribution for the life sciences](https://doi.org/10.1101/207092), [Björn Grüning](/people/bjoern-gruening/), Ryan Dale, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, The Bioconda Team, Johannes Köster, *bioRxiv* 207092, doi: https://doi.org/10.1101/207092 * [Cloud Computing for Science and Engineering](https://mitpress.mit.edu/books/cloud-computing-science-and-engineering), Ian Foster and Dennis B. Gannon. . MIT Press; 2017 Sep 22 ## Publication Topics @@ -203,7 +203,7 @@ The Galaxy is expanding! Please help it grow. * [Développeur d’outils MS/MS pour le projet Workflow4Metabolomics sous Galaxy](https://www.sfbi.fr/content/d%C3%A9veloppeur-d%E2%80%99outils-msms-pour-le-projet-workflow4metabolomics-sous-galaxy-0), Station Biologique de Roscoff, France * [Bioinformaticien Gustave Roussy](https://www.sfbi.fr/content/bioinformaticien-gustave-roussy), Villejuif, France -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States * [Implémentation d’outils d’analyse et de visualisation de variations structurales et génomes mosaïques](https://www.sfbi.fr/content/impl%C3%A9mentation-d%E2%80%99outils-d%E2%80%99analyse-et-de-visualisation-de-variations-structurales-et-g%C3%A9nomes-), IRD (Institut de Recherche pour le Développement), Montpellier, France * [Bioinformatics Research Associate](https://academicpositions.harvard.edu/postings/7556), Huttenhower Lab, Harvard School of Public Health, Boston, Massachusetts, United States @@ -357,8 +357,8 @@ The [Galaxy Docker project has seen a new release](https://github.com/bgruening/ And * The [Galaxy Docker Project](https://github.com/bgruening/docker-galaxy-stable) has reached more than 23k downloads on [Dockerhub](https://hub.docker.com/r/bgruening/galaxy-stable/) - not counting quay.io and all flavors -* From [John Chilton](/src/people/john-chilton/index.md): - * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/src/people/bjoern-gruening/index.md): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) +* From [John Chilton](/people/john-chilton/): + * Awesome new mode for docker-galaxy-stable by [Björn Grüning](/people/bjoern-gruening/): [container scheduling with Condor](https://github.com/bgruening/docker-galaxy-stable/pull/323) ## And the rest ... diff --git a/content/galaxy-updates/2017-12/index.md b/content/galaxy-updates/2017-12/index.md index a0be16ef2f..faaff26b7a 100644 --- a/content/galaxy-updates/2017-12/index.md +++ b/content/galaxy-updates/2017-12/index.md @@ -174,7 +174,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth We've got two new *[Galactic Blog](/src/blog/index.md)* entries: * [Setup your own instance of the Galaxy Bioinformatics platform on DigitalOcean](https://vimal.io/setup-your-own-galaxy-bioinformatics-instance-on-digitalocean/), by [Vimalkumar Velayudhan](https://vimal.io/) -* [Galaxy Docker 17.09](/src/blog/2017-11-galaxy-docker-17.09/index.md), by [Björn Grüning](/src/people/bjoern-gruening/index.md) +* [Galaxy Docker 17.09](/src/blog/2017-11-galaxy-docker-17.09/index.md), by [Björn Grüning](/people/bjoern-gruening/) The *Galactic Blog* is a place for longer-form posts that are relevant to Galaxy. (See [Galaxy News](/src/news/index.md) for shorter-form items.) @@ -194,11 +194,11 @@ Questions? [Ask us](mailto:outreach@galaxyproject.org). The *Galactic* and *Stellar* publications added in October were: -* [Using bio.tools to generate and annotate workbench tool descriptions](https://f1000research.com/articles/6-2074/v1), Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, [Helena Rasche](/src/people/helena-rasche/index.md), Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager. *F1000Research* 2017, 6(ELIXIR):2074 (doi: 10.12688/f1000research.12974.1) +* [Using bio.tools to generate and annotate workbench tool descriptions](https://f1000research.com/articles/6-2074/v1), Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, [Helena Rasche](/people/helena-rasche/), Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager. *F1000Research* 2017, 6(ELIXIR):2074 (doi: 10.12688/f1000research.12974.1) * [Galaksio, a user friendly workflow-centric front end for Galaxy](http://journal.embnet.org/index.php/embnetjournal/article/view/897), Tomas Klingström, Rafael Hernández-de-Diego, Théo Collard, Erik Bongcam-Rudloff. *EMBnet.journal*, [S.l.], v. 23, p. e897, nov. 2017. ISSN 2226-6089. * [Data integration and handling](https://pub.epsilon.slu.se/14669/), Klingström, Tomas. Doctoral thesis, Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2017:99, ISBN 978-91-7760-088-6, eISBN 978-91-7760-089-3 * [TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application](https://peerj.com/preprints/3385/), Ali T, Kim B, Lijeron C, Ogunwobi OO, Mazumder R, Krampis K. (2017). *PeerJ Preprints* 5:e3385v1 https://doi.org/10.7287/peerj.preprints.3385v1 -* [An Accessible Proteogenomics Informatics Resource for Cancer Researchers](http://cancerres.aacrjournals.org/content/77/21/e43), Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, [Björn Grüning](/src/people/bjoern-gruening/index.md), Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. +* [An Accessible Proteogenomics Informatics Resource for Cancer Researchers](http://cancerres.aacrjournals.org/content/77/21/e43), Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, [Björn Grüning](/people/bjoern-gruening/), Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. *Cancer Research,* DOI: 10.1158/0008-5472.CAN-17-0331 Published November 2017 * [A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data](http://cancerres.aacrjournals.org/content/77/21/e23.article-info), Bradley M. Broom, Michael C. Ryan, Robert E. Brown, Futa Ikeda, Mark Stucky, David W. Kane, James Melott, Chris Wakefield, Tod D. Casasent, Rehan Akbani and John N. Weinstein. *Cancer Research,* DOI: 10.1158/0008-5472.CAN-17-0318 Published November 2017 @@ -222,7 +222,7 @@ The Galaxy is expanding! Please help it grow. * [Classification des micropolluants dans l'environnement : amélioration de l'algorithme online TyPol](https://www.sfbi.fr/content/classification-des-micropolluants-dans-lenvironnement-am%C3%A9lioration-de-lalgorithme-online-typ), INRA-LBE, Narbonne, France * [Bioinformaticien immunologie](https://www.sfbi.fr/content/bioinformaticien-immunologie), Gustave Roussy Institute, Villejuif, France * [Bioinformaticien Gustave Roussy](https://www.sfbi.fr/content/bioinformaticien-gustave-roussy), Villejuif, France -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-01/index.md b/content/galaxy-updates/2018-01/index.md index 6b0eff5246..d65ef85fb3 100644 --- a/content/galaxy-updates/2018-01/index.md +++ b/content/galaxy-updates/2018-01/index.md @@ -267,7 +267,7 @@ The Galaxy is expanding! Please help it grow. * [Responsable Opérationnel de la Plateforme de Bioinformatique ARTbio](https://www.sfbi.fr/content/responsable-op%C3%A9rationnel-de-la-plateforme-de-bioinformatique-artbio), ARTbio, Institut de Biologie Paris Seine, France * [Classification des micropolluants dans l'environnement : amélioration de l'algorithme online TyPol](https://www.sfbi.fr/content/classification-des-micropolluants-dans-lenvironnement-am%C3%A9lioration-de-lalgorithme-online-typ), INRA-LBE, Narbonne, France -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -461,10 +461,10 @@ Other Galaxy packages that haven't had a release in the past four months can be # Other News * Would you like to learn some Python or JavaScript and improve Galaxy at the same time? Check out our collection of very friendly issues tagged [help wanted](https://github.com/galaxyproject/galaxy/issues?q=label%3A%22help+wanted%22+is%3Aissue+is%3Aopen). Please feel free to ask, comment, and request guidance. -* From [Björn Grüning](/src/people/bjoern-gruening/index.md) +* From [Björn Grüning](/people/bjoern-gruening/) * `shed-tools update` will now update all Galaxy tools in your Galaxy instance. What a wonderful [contribution](https://github.com/galaxyproject/ephemeris/pull/64) from [Ruben Vorderman](https://github.com/rhpvorderman)! - * Our community maintained [CVFMS](http://cernvm.cern.ch/) based reference data storage has now a European mirror. Thanks to [JRC / EU Science Hub](https://ec.europa.eu/jrc/en), the [European Commission](http://ec.europa.eu/), [Nate Coraor](/src/people/nate/index.md) and [Guy Van den Eede](https://twitter.com/guyvandeneede). This is now also available in the [Galaxy Docker project](https://github.com/bgruening/docker-galaxy-stable)! Enjoy! -* From [John Chilton](/src/people/john-chilton/index.md) + * Our community maintained [CVFMS](http://cernvm.cern.ch/) based reference data storage has now a European mirror. Thanks to [JRC / EU Science Hub](https://ec.europa.eu/jrc/en), the [European Commission](http://ec.europa.eu/), [Nate Coraor](/people/nate/) and [Guy Van den Eede](https://twitter.com/guyvandeneede). This is now also available in the [Galaxy Docker project](https://github.com/bgruening/docker-galaxy-stable)! Enjoy! +* From [John Chilton](/people/john-chilton/) * WIP: [API to build hierarchical data in Galaxy](https://github.com/galaxyproject/galaxy/pull/5220) (libraries & collections) from zip files, YAML descriptions, BagIt archives, etc... * [Allow Galaxy tools to detect out of memory errors and job runners to resubmit to other resources](https://github.com/galaxyproject/galaxy/pull/5196) based on this and other tool detected errors. * Galaxy [no longer depends on having samtools on its PATH](https://github.com/galaxyproject/galaxy/pull/5037). Another huge deployability step forward from [Marius van den Beek](https://github.com/mvdbeek)! diff --git a/content/galaxy-updates/2018-02/index.md b/content/galaxy-updates/2018-02/index.md index 38af394329..381685f5f5 100644 --- a/content/galaxy-updates/2018-02/index.md +++ b/content/galaxy-updates/2018-02/index.md @@ -88,9 +88,9 @@ morning session will include presentations on genomic and metagenomic data analy [Galaxy Administrators Course](https://github.com/galaxyproject/dagobah-training)
-A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/src/people/bjoern-gruening/index.md) and [Enis Afgan](/src/people/enis-afgan/index.md) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. +A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/people/bjoern-gruening/index.md) and [Enis Afgan](/src/people/enis-afgan/) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. -Plenty of materials for Galaxy administration are now [up to date and available online](https://github.com/galaxyproject/dagobah-training). The workshop included a sneak [preview of what's coming in the 18.01 release](https://galaxyproject.github.io/dagobah-training/2018-oslo/whatsnew/18.01.html#1) from [Nate Coraor](/src/people/nate/index.md). +Plenty of materials for Galaxy administration are now [up to date and available online](https://github.com/galaxyproject/dagobah-training). The workshop included a sneak [preview of what's coming in the 18.01 release](https://galaxyproject.github.io/dagobah-training/2018-oslo/whatsnew/18.01.html#1) from [Nate Coraor](/people/nate/). # Select Upcoming events @@ -272,7 +272,7 @@ The *Galactic* and *Stellar* publications added in January were: The Galaxy is expanding! Please help it grow. * The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/galaxy-freiburg/people/) is [looking for 2 Postdoctoral researchers](https://usegalaxy-eu.github.io/galaxy-freiburg/2018/01/18/openpositions.html) -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -428,5 +428,5 @@ Other Galaxy packages that haven't had a release in the past four months can be # Other News * The semi-annual update of the project statistics page is done. [See what's new](/src/galaxy-project/statistics/index.md). -* From [John Chilton](/src/people/john-chilton/index.md): +* From [John Chilton](/people/john-chilton/): * Galaxy can now [by-pass re-running jobs with duplicate parameters/inputs](https://github.com/galaxyproject/galaxy/pull/4690) thanks to the brilliant [Marius Van Den Beek](https://twitter.com/mariusvdbeek/) diff --git a/content/galaxy-updates/2018-03/index.md b/content/galaxy-updates/2018-03/index.md index 9e4fc6d2e5..40a435466f 100644 --- a/content/galaxy-updates/2018-03/index.md +++ b/content/galaxy-updates/2018-03/index.md @@ -261,7 +261,7 @@ February had one new *[Galactic Blog](/src/blog/index.md)* entry: The *Galactic* and *Stellar* publications added in February were: * [GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees](https://doi.org/10.1093/gigascience/giy005), Anil S Thanki, Nicola Soranzo, Wilfried Haerty, Robert P Davey. *GigaScience*, giy005, doi: 10.1093/gigascience/giy005 -* [Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework](https://doi.org/10.3390/proteomes6010007), Clemens Blank, Caleb Easterly, [Bjoern Gruening](/src/people/bjoern-gruening/index.md), James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. *Proteomes* 2018, 6(1), 7; doi:10.3390/proteomes6010007 +* [Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework](https://doi.org/10.3390/proteomes6010007), Clemens Blank, Caleb Easterly, [Bjoern Gruening](/people/bjoern-gruening/), James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. *Proteomes* 2018, 6(1), 7; doi:10.3390/proteomes6010007 * [Mind your gaps: Overlooking assembly gaps confounds statistical testing in genome analysis](https://doi.org/10.1101/252973), Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve. *bioRxiv* 252973; doi: 10.1101/252973 * [MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data](https://doi.org/10.1093/bioinformatics/btx565), Christopher J Green, Matthew R Gazzara, Yoseph Barash. *Bioinformatics*, Volume 34, Issue 2, 15 January 2018, Pages 300–302, doi: 10.1093/bioinformatics/btx565 * [Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and *Apodemus* B chromosomes](https://link.springer.com/article/10.1007/s00412-018-0662-0), Makunin, A.I., Rajičić, M., Karamysheva, T.V. et al. *Chromosoma* (2018). doi: 10.1007/s00412-018-0662-0 @@ -286,7 +286,7 @@ The Galaxy is expanding! Please help it grow. * [Développement d'outils bioinformatiques et statistiques pour l'analyse de l'air expiré en médecine par spectrométrie de masse en temps-réel](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA Saclay, France * [Ingénieur en développement de composants Galaxy pour la protéomique](https://www.sfbi.fr/content/ing%C3%A9nieur-en-d%C3%A9veloppement-de-composants-galaxy-pour-la-prot%C3%A9omique-0), MaIAGE , INRA, Jouy-en-Josas, France * The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/galaxy-freiburg/people/) is [looking for 2 Postdoctoral researchers](https://usegalaxy-eu.github.io/galaxy-freiburg/2018/01/18/openpositions.html) -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -423,4 +423,4 @@ Other Galaxy packages that haven't had a release in the past four months can be * From Björn Grüning * New Galaxy tutorial by Simon Gladman and Torsten Seeman about [Microbial Variant Calling using snippy](https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html). - * This is big: [Aysam Guerler](/src/people/guerler/index.md) has reworked the Galaxy visualization plugin architecture. + * This is big: [Aysam Guerler](/people/guerler/) has reworked the Galaxy visualization plugin architecture. diff --git a/content/galaxy-updates/2018-04/index.md b/content/galaxy-updates/2018-04/index.md index b5481307ca..892780f283 100644 --- a/content/galaxy-updates/2018-04/index.md +++ b/content/galaxy-updates/2018-04/index.md @@ -315,7 +315,7 @@ The Galaxy is expanding! Please help it grow. * [Post-Doc / IR analyse de données miRNA](https://www.sfbi.fr/content/post-doc-ir-analyse-de-donn%C3%A9es-mirna), Unité de Nutrition Humaine, Clermont-Fd, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany * [Development of innovative algorithms to process real-time mass spectrometry data for the clinical analysis of exhaled breath](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA, Saclay, France -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-05/index.md b/content/galaxy-updates/2018-05/index.md index 833617f81c..e50ef30c55 100644 --- a/content/galaxy-updates/2018-05/index.md +++ b/content/galaxy-updates/2018-05/index.md @@ -278,7 +278,7 @@ The Galaxy is expanding! Please help it grow. * [Post-Doc / IR analyse de données miRNA](https://www.sfbi.fr/content/post-doc-ir-analyse-de-donn%C3%A9es-mirna), Unité de Nutrition Humaine, Clermont-Fd, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany * [Development of innovative algorithms to process real-time mass spectrometry data for the clinical analysis of exhaled breath](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA, Saclay, France -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-08/index.md b/content/galaxy-updates/2018-08/index.md index 9e527895aa..fa9a4876a0 100644 --- a/content/galaxy-updates/2018-08/index.md +++ b/content/galaxy-updates/2018-08/index.md @@ -300,23 +300,23 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t This included a new paper to reference [whenever using, extending, or referencing Galaxy](/src/citing-galaxy/index.md#primary-publication): -* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Vahid Jalili](/src/people/vahid-jalili/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Daniel Blankenberg](/src/people/dan/index.md). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 A new paper to reference [when discussing Galaxy in the context of reproducibility](/src/citing-galaxy/index.md#reproducibility): -* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/src/people/bjoern-gruening/index.md), [John Chilton](/src/people/john-chilton/index.md), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/index.md), [James Taylor](/src/people/james-taylor/index.md). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 +* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/people/john-chilton/index.md), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 And a new paper to reference [when discussing Galaxy training](/src/citing-galaxy/index.md#training): -* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/src/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/index.md), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 And a new paper to cite [when discussing Galaxy in a cloud context](/src/citing-galaxy/index.md#cloud): -* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/src/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/index.md), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 +* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 Other highlighted papers include: -* [**Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization**](https://academic.oup.com/nar/article/46/W1/W11/5036837), Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, [Björn Grüning](/src/people/bjoern-gruening/index.md). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi:10.1093/nar/gky504 +* [**Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization**](https://academic.oup.com/nar/article/46/W1/W11/5036837), Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, [Björn Grüning](/people/bjoern-gruening/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi:10.1093/nar/gky504 * [**ASaiM: a Galaxy-based framework to analyze microbiota data**](https://doi.org/10.1093/gigascience/giy057), [Bérénice Batut](http://bebatut.fr/), Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret. *GigaScience*, Volume 7, Issue 6, 1 June 2018, giy057, doi:10.1093/gigascience/giy057 * [**Selection of computational environments for PSP processing on scientific gateways**](https://doi.org//10.1016/j.heliyon.2018.e00690) Edvard Martins de Oliveira, Júlio Cézar Estrella, Alexandre Cláudio Botazzo Delbem, Luiz Henrique Nunes, Henrique Yoshikazu Shishido, Stephan Reiff-Marganiec. *Heliyon* 4 (2018) e00690 @@ -351,7 +351,7 @@ Edvard Martins de Oliveira, Júlio Cézar Estrella, Alexandre Cláudio Botazzo D The Galaxy is expanding! Please help it grow. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -422,8 +422,8 @@ We tag papers that use, mention, implement or extend public Galaxy Servers. Her # Hub and Doc Updates * Semi-annual [project statistics update](/src/galaxy-project/statistics/index.md) is *mostly* done. -* New [Cloud Storage API page](/src/cloud/storage/index.md) from [Vahid Jalili](/src/people/vahid-jalili/index.md). -* A general update by [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md) to several support pages: +* New [Cloud Storage API page](/src/cloud/storage/index.md) from [Vahid Jalili](/people/vahid-jalili/). +* A general update by [Jennifer Hillman-Jackson](/people/jennifer-jackson/) to several support pages: * [Issues](/src/issues/index.md) * [Support](/src/support/index.md) * [Tool Errors](/src/support/tool-error/index.md) diff --git a/content/news/2012-02-galaxy-update/index.md b/content/news/2012-02-galaxy-update/index.md index 5d2abd279d..934af0e9b4 100644 --- a/content/news/2012-02-galaxy-update/index.md +++ b/content/news/2012-02-galaxy-update/index.md @@ -17,4 +17,4 @@ The [inaugural edition](/src/galaxy-updates/2012-02/index.md) of *[Galaxy Update If you have anything you would like to see in the March *Galaxy Update*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-03-galaxy-update/index.md b/content/news/2012-03-galaxy-update/index.md index a2b43e2737..722fa9b376 100644 --- a/content/news/2012-03-galaxy-update/index.md +++ b/content/news/2012-03-galaxy-update/index.md @@ -18,4 +18,4 @@ The [March 2012 Galaxy Update](/src/galaxy-updates/2012-03/index.md) is now avai If you have anything you would like to see in the April *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-04-galaxy-update/index.md b/content/news/2012-04-galaxy-update/index.md index e2fdea9177..4c27513882 100644 --- a/content/news/2012-04-galaxy-update/index.md +++ b/content/news/2012-04-galaxy-update/index.md @@ -16,4 +16,4 @@ The [April 2012 Galaxy Update](/src/galaxy-updates/2012-04/index.md) is now avai If you have anything you would like to see in the May *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-05-galaxy-update/index.md b/content/news/2012-05-galaxy-update/index.md index 028f31c3e1..41ead83a30 100644 --- a/content/news/2012-05-galaxy-update/index.md +++ b/content/news/2012-05-galaxy-update/index.md @@ -19,4 +19,4 @@ The [May 2012 Galaxy Update](/src/galaxy-updates/2012-05/index.md) is now availa If you have anything you would like to see in the June *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-06-galaxy-update/index.md b/content/news/2012-06-galaxy-update/index.md index 4541c04f0a..07063b0b1c 100644 --- a/content/news/2012-06-galaxy-update/index.md +++ b/content/news/2012-06-galaxy-update/index.md @@ -21,4 +21,4 @@ The [June 2012 Galaxy Update](/src/galaxy-updates/2012-06/index.md) is now avail If you have anything you would like to see in the July *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-07-galaxy-update/index.md b/content/news/2012-07-galaxy-update/index.md index 15528d2490..1e1a9dc251 100644 --- a/content/news/2012-07-galaxy-update/index.md +++ b/content/news/2012-07-galaxy-update/index.md @@ -25,4 +25,4 @@ The [July 2012 Galaxy Update is now available](/src/galaxy-updates/2012-07/index If you have anything you would like to see in the August *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-08-galaxy-update/index.md b/content/news/2012-08-galaxy-update/index.md index 7782dc2636..a76636525b 100644 --- a/content/news/2012-08-galaxy-update/index.md +++ b/content/news/2012-08-galaxy-update/index.md @@ -19,4 +19,4 @@ The [August 2012 Galaxy Update is now available](/src/galaxy-updates/2012-08/ind If you have anything you would like to see in the September *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-09-20-distribution-news-brief/index.md b/content/news/2012-09-20-distribution-news-brief/index.md index 0bc8469a69..08a7b17b3c 100644 --- a/content/news/2012-09-20-distribution-news-brief/index.md +++ b/content/news/2012-09-20-distribution-news-brief/index.md @@ -21,4 +21,4 @@ upgrade: $ hg pull -u -r da9d740fce31 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/index.md) +[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-09-galaxy-update/index.md b/content/news/2012-09-galaxy-update/index.md index 8d2c3e4573..ea6dd59966 100644 --- a/content/news/2012-09-galaxy-update/index.md +++ b/content/news/2012-09-galaxy-update/index.md @@ -19,4 +19,4 @@ The [September 2012 Galaxy Update is now available](/src/galaxy-updates/2012-09/ If you have anything you would like to see in the October *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-10-05-distribution-news-brief/index.md b/content/news/2012-10-05-distribution-news-brief/index.md index cf8071c3e7..814bd30f25 100644 --- a/content/news/2012-10-05-distribution-news-brief/index.md +++ b/content/news/2012-10-05-distribution-news-brief/index.md @@ -22,4 +22,4 @@ upgrade: $ hg pull -u -r b5bda7a5c345 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/index.md) +[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-10-23-distribution-news-brief/index.md b/content/news/2012-10-23-distribution-news-brief/index.md index 0319438963..3d8e2b1a94 100644 --- a/content/news/2012-10-23-distribution-news-brief/index.md +++ b/content/news/2012-10-23-distribution-news-brief/index.md @@ -23,4 +23,4 @@ upgrade: $ hg pull -u -r 12fcd068b12e **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/index.md) +[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-10-galaxy-update/index.md b/content/news/2012-10-galaxy-update/index.md index cfa1726508..fedb1b57c3 100644 --- a/content/news/2012-10-galaxy-update/index.md +++ b/content/news/2012-10-galaxy-update/index.md @@ -18,4 +18,4 @@ The [October 2012 Galaxy Update is now available](/src/galaxy-updates/2012-10/in If you have anything you would like to see in the November *[Galaxy Update](/src/galaxy-updates/index.md)*, please let me know. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2012-11-galaxy-update/index.md b/content/news/2012-11-galaxy-update/index.md index c4812509a9..ca1e43b7fb 100644 --- a/content/news/2012-11-galaxy-update/index.md +++ b/content/news/2012-11-galaxy-update/index.md @@ -18,4 +18,4 @@ The [November 2012 Galaxy Update is now available](/src/galaxy-updates/2012-11/i If you have anything you would like to see in the December *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-12-galaxy-update/index.md b/content/news/2012-12-galaxy-update/index.md index 53da366bd0..d12a8d578e 100644 --- a/content/news/2012-12-galaxy-update/index.md +++ b/content/news/2012-12-galaxy-update/index.md @@ -20,4 +20,4 @@ The [December 2012 Galaxy Update is now available](/src/galaxy-updates/2012-12/i If you have anything you would like to see in the January *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-01-galaxy-update/index.md b/content/news/2013-01-galaxy-update/index.md index 3a91928436..50911c9a18 100644 --- a/content/news/2013-01-galaxy-update/index.md +++ b/content/news/2013-01-galaxy-update/index.md @@ -19,4 +19,4 @@ The [January 2013 Galaxy Update is now available](/src/galaxy-updates/2013-01/in If you have anything you would like to see in the Febrarury *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-02-galaxy-update/index.md b/content/news/2013-02-galaxy-update/index.md index b3be97e7e6..5074f85fff 100644 --- a/content/news/2013-02-galaxy-update/index.md +++ b/content/news/2013-02-galaxy-update/index.md @@ -20,4 +20,4 @@ The [February 2013 Galaxy Update is now available](/src/galaxy-updates/2013-02/i If you have anything you would like to see in the March *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-03-galaxy-admins/index.md b/content/news/2013-03-galaxy-admins/index.md index 7f3023f766..63c4a10e12 100644 --- a/content/news/2013-03-galaxy-admins/index.md +++ b/content/news/2013-03-galaxy-admins/index.md @@ -23,7 +23,7 @@ The [next meeting](/src/community/galaxy-admins/meetups/2013-03-20/index.md) of Presenters - Hailiang "Leon" Mei
There will also be a Galaxy Project Update from Dan Blankenberg of the Galaxy Team + Hailiang "Leon" Mei
There will also be a Galaxy Project Update from Dan Blankenberg of the Galaxy Team Links diff --git a/content/news/2013-03-galaxy-update/index.md b/content/news/2013-03-galaxy-update/index.md index 4cdc102ee1..aaca2429d8 100644 --- a/content/news/2013-03-galaxy-update/index.md +++ b/content/news/2013-03-galaxy-update/index.md @@ -19,4 +19,4 @@ The [March 2013 Galaxy Update is now available](/src/galaxy-updates/2013-03/inde If you have anything you would like to see in the April *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-04-galaxy-update/index.md b/content/news/2013-04-galaxy-update/index.md index 6135fa5546..673271ed0d 100644 --- a/content/news/2013-04-galaxy-update/index.md +++ b/content/news/2013-04-galaxy-update/index.md @@ -20,4 +20,4 @@ The [April 2013 Galaxy Update is now available](/src/galaxy-updates/2013-04/inde If you have anything you would like to see in the May *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-05-galaxy-admins/index.md b/content/news/2013-05-galaxy-admins/index.md index df10d582fb..7cdaa30d6c 100644 --- a/content/news/2013-05-galaxy-admins/index.md +++ b/content/news/2013-05-galaxy-admins/index.md @@ -10,7 +10,7 @@ The [next meeting](/src/community/galaxy-admins/meetups/2013-05-15/index.md) of Andrew Warren of the [Cyberinfrastructure Division](http://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division) of the [Virginia Bioinformatics Institute](https://www.vbi.vt.edu/) at Virginia Tech will talk about their [Galaxy deployment](http://rnaseq.pathogenportal.org/) at [Pathogen Portal](http://pathogenportal.org), a highly customized Galaxy installation, and also about the group's objectives and future plans. -[Dannon Baker](/src/people/dannon-baker/index.md) will bring the group up to speed on what's happening in the Galaxy project. +[Dannon Baker](/people/dannon-baker/) will bring the group up to speed on what's happening in the Galaxy project. @@ -23,7 +23,7 @@ Andrew Warren of the [Cyberinfrastructure Division](http://www.vbi.vt.edu/facult - + @@ -38,4 +38,4 @@ We use the [Blackboard Collaborate Web Conferencing system](/src/community/galax [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a discussion group for Galaxy community members who are responsible for large Galaxy installations. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2013-05-galaxy-update/index.md b/content/news/2013-05-galaxy-update/index.md index 37ddbfc2fe..de966ccf74 100644 --- a/content/news/2013-05-galaxy-update/index.md +++ b/content/news/2013-05-galaxy-update/index.md @@ -17,4 +17,4 @@ The [May 2013 Galaxy Update is now available](/src/galaxy-updates/2013-05/index. If you have anything you would like to see in the June *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-06-galaxy-update/index.md b/content/news/2013-06-galaxy-update/index.md index 60ba10057f..5dbc138024 100644 --- a/content/news/2013-06-galaxy-update/index.md +++ b/content/news/2013-06-galaxy-update/index.md @@ -18,4 +18,4 @@ The [June 2013 Galaxy Update is now available](/src/galaxy-updates/2013-06/index If you have anything you would like to see in the July *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-07-galaxy-update/index.md b/content/news/2013-07-galaxy-update/index.md index 27bac6ee13..b470adaad2 100644 --- a/content/news/2013-07-galaxy-update/index.md +++ b/content/news/2013-07-galaxy-update/index.md @@ -19,4 +19,4 @@ The [July 2013 Galaxy Update is now available](/src/galaxy-updates/2013-07/index If you have anything you would like to see in the August *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-08-galaxy-update/index.md b/content/news/2013-08-galaxy-update/index.md index cba99d0fef..4aa5c697a8 100644 --- a/content/news/2013-08-galaxy-update/index.md +++ b/content/news/2013-08-galaxy-update/index.md @@ -21,4 +21,4 @@ The [August 2013 Galaxy Update is now available](/src/galaxy-updates/2013-08/ind If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-09-galaxy-update/index.md b/content/news/2013-09-galaxy-update/index.md index 001a7de6b8..b36c4b0fb9 100644 --- a/content/news/2013-09-galaxy-update/index.md +++ b/content/news/2013-09-galaxy-update/index.md @@ -18,4 +18,4 @@ The [September 2013 Galaxy Update is hot off the press](/src/galaxy-updates/2013 If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-10-galaxy-update/index.md b/content/news/2013-10-galaxy-update/index.md index 0b29b998c3..a1fd4f8bdb 100644 --- a/content/news/2013-10-galaxy-update/index.md +++ b/content/news/2013-10-galaxy-update/index.md @@ -16,4 +16,4 @@ The [October 2013 Galaxy Update is out](/src/galaxy-updates/2013-10/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-11-galaxy-update/index.md b/content/news/2013-11-galaxy-update/index.md index 7adf5c499f..094ca6a88a 100644 --- a/content/news/2013-11-galaxy-update/index.md +++ b/content/news/2013-11-galaxy-update/index.md @@ -19,4 +19,4 @@ The [November 2013 Galaxy Update is out](/src/galaxy-updates/2013-11/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-12-galaxy-update/index.md b/content/news/2013-12-galaxy-update/index.md index 27bc77a6d8..cf2cb6dfd4 100644 --- a/content/news/2013-12-galaxy-update/index.md +++ b/content/news/2013-12-galaxy-update/index.md @@ -20,4 +20,4 @@ The [December 2013 Galaxy Update is out](/src/galaxy-updates/2013-12/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-01-galaxy-update/index.md b/content/news/2014-01-galaxy-update/index.md index 1dc6409904..de896c76a3 100644 --- a/content/news/2014-01-galaxy-update/index.md +++ b/content/news/2014-01-galaxy-update/index.md @@ -32,4 +32,4 @@ If you have anything you would like to see in the next *[Galaxy Update](/src/gal Best wishes to you and yours for a happy and spectacular 2014, -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-02-galaxy-update/index.md b/content/news/2014-02-galaxy-update/index.md index 3ceb273d4c..dbaa4bf102 100644 --- a/content/news/2014-02-galaxy-update/index.md +++ b/content/news/2014-02-galaxy-update/index.md @@ -25,4 +25,4 @@ The [25th Edition of Galaxy Update is out](/src/galaxy-updates/2014-02/index.md) If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-03-galaxy-update/index.md b/content/news/2014-03-galaxy-update/index.md index de2d41a907..92b9df3569 100644 --- a/content/news/2014-03-galaxy-update/index.md +++ b/content/news/2014-03-galaxy-update/index.md @@ -24,4 +24,4 @@ Find out [what's happening in the Galaxy](/src/galaxy-updates/2014-03/index.md). If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-04-galaxy-update/index.md b/content/news/2014-04-galaxy-update/index.md index 7eba3c1794..89a4ce1970 100644 --- a/content/news/2014-04-galaxy-update/index.md +++ b/content/news/2014-04-galaxy-update/index.md @@ -24,4 +24,4 @@ And as always, there are [new ToolShed contributions](/src/galaxy-updates/2014-0 If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-05-galaxy-update/index.md b/content/news/2014-05-galaxy-update/index.md index 5fc465cf5c..a43bcf8e6d 100644 --- a/content/news/2014-05-galaxy-update/index.md +++ b/content/news/2014-05-galaxy-update/index.md @@ -19,4 +19,4 @@ There's also a [Galaxy UK Tour](/src/galaxy-updates/2014-05/index.md#uk-may-2014 As always, there are [new papers](/src/galaxy-updates/2014-05/index.md#new-papers) (47 of them, including four we highlighted), [new public Galaxy Servers](/src/galaxy-updates/2014-05/index.md#new-public-servers) ([Globus Genomics Proteomics](/src/galaxy-updates/2014-05/index.md#globus-genomics-proteomics) and [SunLab Galaxy](/src/galaxy-updates/2014-05/index.md#sunlab)), [new jobs](/src/galaxy-updates/2014-05/index.md#whos-hiring) (7 postings in 6 countries), [new tools in the project ToolShed](/src/galaxy-updates/2014-05/index.md#galaxy-project-toolshed-new-repositories) (um, *lots*), and a [new public ToolShed](/src/galaxy-updates/2014-05/index.md#new-public-toolsheds) (at the [Dutch Techcentre for Life Sciences (DTL)](http://www.dtls.nl/dtl/). -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-06-galaxy-update/index.md b/content/news/2014-06-galaxy-update/index.md index 4df8a98c13..098466ef35 100644 --- a/content/news/2014-06-galaxy-update/index.md +++ b/content/news/2014-06-galaxy-update/index.md @@ -24,4 +24,4 @@ And, in the past month there were: * [One new Galaxy deployment description (deepTools)](/src/galaxy-updates/2014-06/index.md#galaxy-community-hubs) * and [a stunning number of ToolShed contributions](/src/galaxy-updates/2014-06/index.md#toolshed-contributions) -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-07-galaxy-update/index.md b/content/news/2014-07-galaxy-update/index.md index a70e06c644..2bf45ba1ac 100644 --- a/content/news/2014-07-galaxy-update/index.md +++ b/content/news/2014-07-galaxy-update/index.md @@ -18,4 +18,4 @@ The [July 2014 Galaxy Update Newsletter](/src/galaxy-updates/2014-07/index.md) i * [One new Galaxy Log Board entry](/src/galaxy-updates/2014-07/index.md#galaxy-community-hubs) * and [a stunning number of ToolShed contributions](/src/galaxy-updates/2014-07/index.md#toolshed-contributions) once again. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-08-galaxy-update/index.md b/content/news/2014-08-galaxy-update/index.md index 5e0b1a3644..fb9bbf2f42 100644 --- a/content/news/2014-08-galaxy-update/index.md +++ b/content/news/2014-08-galaxy-update/index.md @@ -15,4 +15,4 @@ The [August 2014 Galaxy Update Newsletter](/src/galaxy-updates/2014-08/index.md) * [One new public server (IM-PET)](/src/galaxy-updates/2014-08/index.md#new-public-servers) * [Who's hiring?](/src/galaxy-updates/2014-08/index.md#whos-hiring) It turns out that lots of places are. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-09-galaxy-update/index.md b/content/news/2014-09-galaxy-update/index.md index eb62a76603..1f4b405897 100644 --- a/content/news/2014-09-galaxy-update/index.md +++ b/content/news/2014-09-galaxy-update/index.md @@ -24,4 +24,4 @@ And, as always, there are [new papers](/src/galaxy-updates/2014-09/index.md#new- Happy September, -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-10-galaxy-update/index.md b/content/news/2014-10-galaxy-update/index.md index eed8b004c6..488876669b 100644 --- a/content/news/2014-10-galaxy-update/index.md +++ b/content/news/2014-10-galaxy-update/index.md @@ -20,4 +20,4 @@ A lot is happening in in the Galaxy in October, and a lot of good stuff happened Happy October! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-11-galaxy-update/index.md b/content/news/2014-11-galaxy-update/index.md index 74e158f662..65138cab97 100644 --- a/content/news/2014-11-galaxy-update/index.md +++ b/content/news/2014-11-galaxy-update/index.md @@ -20,4 +20,4 @@ A lot is happening in in the Galaxy in November, and a lot of good stuff happene * [35 new ToolShed repos](/src/galaxy-updates/2014-11/index.md#toolshed-contributions) * And a [smattering of other news](/src/galaxy-updates/2014-11/index.md#other-news) too -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-12-galaxy-update/index.md b/content/news/2014-12-galaxy-update/index.md index 7226d71800..cc37e6b3cd 100644 --- a/content/news/2014-12-galaxy-update/index.md +++ b/content/news/2014-12-galaxy-update/index.md @@ -18,4 +18,4 @@ As always there's a lot going on in the Galaxy this month. "Like what?" you say * [15 new ToolShed repositories from 10 contributors](/src/galaxy-updates/2014-12/index.md#toolshed-contributions) * And, [10 other juicy](/src/galaxy-updates/2014-12/index.md#other-news) (well maybe not *juicy*, but certainly not *crunchy*) [bits of news](/src/galaxy-updates/2014-12/index.md#other-news) -[Dave Clements](/src/people/dave-clements/index.md) and the *crisp* [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the *crisp* [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-galaxy-training-survey/index.md b/content/news/2014-galaxy-training-survey/index.md index 14c0131058..7ae50657e0 100644 --- a/content/news/2014-galaxy-training-survey/index.md +++ b/content/news/2014-galaxy-training-survey/index.md @@ -8,5 +8,5 @@ Help guide Galaxy's 2014 training efforts by taking the [Galaxy Training Survey] Thanks, -[Dave Clements](/src/people/dave-clements/index.md)
+[Dave Clements](/people/dave-clements/)
Galaxy Training and Outreach diff --git a/content/news/2015-01-galaxy-update/index.md b/content/news/2015-01-galaxy-update/index.md index f9d18d97a9..4179b19d46 100644 --- a/content/news/2015-01-galaxy-update/index.md +++ b/content/news/2015-01-galaxy-update/index.md @@ -21,4 +21,4 @@ Happy New Year from the Galaxy Project! * [Over 30 new and updated ToolShed repositories from 12 contributors](/src/galaxy-updates/2014-12/index.md#toolshed-contributions) * And, [other news](/src/galaxy-updates/2014-12/index.md#other-news) too. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-02-galaxy-update/index.md b/content/news/2015-02-galaxy-update/index.md index c7ef87d520..f4d870875f 100644 --- a/content/news/2015-02-galaxy-update/index.md +++ b/content/news/2015-02-galaxy-update/index.md @@ -31,4 +31,4 @@ and *Community News* too: * [Ruđer Bošković Institute joins GTN](/src/galaxy-updates/2015-02/index.md#new-gtn-member-ruđer-bošković-institute) * And, [other news](/src/galaxy-updates/2015-02/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-03-galaxy-update/index.md b/content/news/2015-03-galaxy-update/index.md index 5ff368cd04..46fb8ef1a3 100644 --- a/content/news/2015-03-galaxy-update/index.md +++ b/content/news/2015-03-galaxy-update/index.md @@ -50,4 +50,4 @@ In addition, there is news on: * **[Galaxy on GitHub!](/src/galaxy-updates/2015-03/index.md#galaxy-github)** Come and join us in developing Galaxy! * And, [other news](/src/galaxy-updates/2015-03/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-04-galaxy-update/index.md b/content/news/2015-04-galaxy-update/index.md index 4b2bc892da..ab3faac231 100644 --- a/content/news/2015-04-galaxy-update/index.md +++ b/content/news/2015-04-galaxy-update/index.md @@ -31,4 +31,4 @@ In addition, there is news on: * [One new Community Log Board entry](/src/galaxy-updates/2015-04/index.md#galaxy-community-hubs) * And, [other news](/src/galaxy-updates/2015-04/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-05-galaxy-update/index.md b/content/news/2015-05-galaxy-update/index.md index 8e0f3131e9..b0127169f1 100644 --- a/content/news/2015-05-galaxy-update/index.md +++ b/content/news/2015-05-galaxy-update/index.md @@ -25,4 +25,4 @@ The **[May Galactic News](/src/galaxy-updates/2015-05/index.md)** brings lots of And, [other news](/src/galaxy-updates/2015-05/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-06-galaxy-update/index.md b/content/news/2015-06-galaxy-update/index.md index 7b21944ffb..df2c4450c4 100644 --- a/content/news/2015-06-galaxy-update/index.md +++ b/content/news/2015-06-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[June Galactic News](/src/galaxy-updates/2015-06/index.md)** brings this * And, [other news](/src/galaxy-updates/2015-06/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-08-galaxy-update/index.md b/content/news/2015-08-galaxy-update/index.md index 524732957a..e2f7c58f81 100644 --- a/content/news/2015-08-galaxy-update/index.md +++ b/content/news/2015-08-galaxy-update/index.md @@ -25,7 +25,7 @@ The **[August Galactic News](/src/galaxy-updates/2015-08/index.md)** is out. It * [76 Tool Shed updates and additions from 20+ contributors](/src/toolshed/contributions/2015-07/index.md) * And, of course [other news](/src/galaxy-updates/2015-08/index.md#other-news) as well. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/)
diff --git a/content/news/2015-09-galaxy-update/index.md b/content/news/2015-09-galaxy-update/index.md index 6147b940c4..93da3d3434 100644 --- a/content/news/2015-09-galaxy-update/index.md +++ b/content/news/2015-09-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[September Galactic News](/src/galaxy-updates/2015-09/index.md)** is hot o * [Workflow4Metabolomics](/src/galaxy-updates/2015-09/index.md#workflow4metabolomics) and [EpiToolKit](/src/galaxy-updates/2015-09/index.md#epitoolkit) * [Three security advisories](/src/galaxy-updates/2015-09/index.md#security-advisories), [Recent Releases](/src/galaxy-updates/2015-09/index.md#other-releases), and [ToolShed Contributions](/src/galaxy-updates/2015-09/index.md#toolshed-contributions) -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-10-galaxy-update/index.md b/content/news/2015-10-galaxy-update/index.md index 72c66f59b7..46eb24495f 100644 --- a/content/news/2015-10-galaxy-update/index.md +++ b/content/news/2015-10-galaxy-update/index.md @@ -28,4 +28,4 @@ The **[October Galactic News](/src/galaxy-updates/2015-10/index.md)** is hot off * [Lots of Tool Shed contributions](/src/toolshed/contributions/2015-09/index.md). * and [lots of other news too](/src/galaxy-updates/2015-10/index.md#other-news), [including a birthday](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) (OK, maybe we are chronologically challenged, but we're young!) -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-11-galaxy-update/index.md b/content/news/2015-11-galaxy-update/index.md index fd0c84f5e1..58eff7d52e 100644 --- a/content/news/2015-11-galaxy-update/index.md +++ b/content/news/2015-11-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[November Galactic News](/src/galaxy-updates/2015-11/index.md)** is hot of * [Planemo 0.15.0 - 0.18.1](/src/galaxy-updates/2015-11/index.md#planemo-0150---0181) * and [lots of other news too](/src/galaxy-updates/2015-11/index.md#other-news). -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-12-galaxy-update/index.md b/content/news/2015-12-galaxy-update/index.md index 1e002180bb..bb38d1aefd 100644 --- a/content/news/2015-12-galaxy-update/index.md +++ b/content/news/2015-12-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[December Galactic News](/src/galaxy-updates/2015-12/index.md)** is hot of * [ToolShed Contributions in October and November](/src/galaxy-updates/2015-12/index.md#toolshed-contributions) * and [lots of other news too](/src/galaxy-updates/2015-12/index.md#other-news). -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/201502-galaxy-admins/index.md b/content/news/201502-galaxy-admins/index.md index 420ca94ad9..8fd23b35f4 100644 --- a/content/news/201502-galaxy-admins/index.md +++ b/content/news/201502-galaxy-admins/index.md @@ -6,10 +6,10 @@ date: "2015-01-28" The first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) will happen online [on Thursday, 19 February](http://bit.ly/1yZJSkN). [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/src/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) will lead a short discussion on *GalaxyAdmins direction*. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) will lead a short discussion on *GalaxyAdmins direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. We are looking forward to starting this group again, -[Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/index.md) +[Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/) diff --git a/content/news/2016-01-galaxy-update/index.md b/content/news/2016-01-galaxy-update/index.md index 071d82237e..eb037dc294 100644 --- a/content/news/2016-01-galaxy-update/index.md +++ b/content/news/2016-01-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[January 2016 Galactic News](/src/galaxy-updates/2016-01/index.md)** is ho * [ToolShed Contributions](/src/galaxy-updates/2016-01/index.md#toolshed-contributions) from December * and [some other news too](/src/galaxy-updates/2016-01/index.md#other-news). -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-02-galaxy-update/index.md b/content/news/2016-02-galaxy-update/index.md index 9120a86bbc..bc32e6eaea 100644 --- a/content/news/2016-02-galaxy-update/index.md +++ b/content/news/2016-02-galaxy-update/index.md @@ -30,4 +30,4 @@ The **[February 2016 Galactic News](/src/galaxy-updates/2016-02/index.md)** is h Happy February! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-03-galaxy-update/index.md b/content/news/2016-03-galaxy-update/index.md index 7bd49a76dc..7d61c9a307 100644 --- a/content/news/2016-03-galaxy-update/index.md +++ b/content/news/2016-03-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[March 2016 Galactic News](/src/galaxy-updates/2016-03/index.md)** is hot * [Three new Galaxy servers](/src/galaxy-updates/2016-03/index.md#new-public-galaxy-servers) * [New ToolShed Contributions](/src/galaxy-updates/2016-03/index.md#toolshed-contributions) -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-04-galaxy-update/index.md b/content/news/2016-04-galaxy-update/index.md index 5483eea1c7..aafd803f9b 100644 --- a/content/news/2016-04-galaxy-update/index.md +++ b/content/news/2016-04-galaxy-update/index.md @@ -42,4 +42,4 @@ And some [other news](/src/galaxy-updates/2016-04/index.md#other-news) too. Happy April, -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-05-galaxy-update/index.md b/content/news/2016-05-galaxy-update/index.md index faa7c3a7e8..6249a3934a 100644 --- a/content/news/2016-05-galaxy-update/index.md +++ b/content/news/2016-05-galaxy-update/index.md @@ -30,4 +30,4 @@ Some highlights from the **[May Galaxy News](/src/galaxy-updates/2016-05/index.m Don't miss those deadlines, and [see you in June](https://web.archive.org/web/http://gcc2016.iu.edu/), -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-06-galaxy-update/index.md b/content/news/2016-06-galaxy-update/index.md index 8a48ec61af..752bf39d07 100644 --- a/content/news/2016-06-galaxy-update/index.md +++ b/content/news/2016-06-galaxy-update/index.md @@ -28,4 +28,4 @@ Some highlights from the **[June Galaxy News](/src/galaxy-updates/2016-06/index. Hope to [see you in Bloomington](https://web.archive.org/web/http://gcc2016.iu.edu/), -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-07-galaxy-update/index.md b/content/news/2016-07-galaxy-update/index.md index 429ae49e62..767334483b 100644 --- a/content/news/2016-07-galaxy-update/index.md +++ b/content/news/2016-07-galaxy-update/index.md @@ -30,4 +30,4 @@ Some highlights from the **[July Galaxy News](/src/galaxy-updates/2016-07/index. Hope to [see you in Montpellier](/src/galaxy-updates/2016-07/index.md#gcc2017-26-30-june-2017-montpellier-france)! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-08-galaxy-update/index.md b/content/news/2016-08-galaxy-update/index.md index 7c142ad0a0..19c2624637 100644 --- a/content/news/2016-08-galaxy-update/index.md +++ b/content/news/2016-08-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[August Galaxy News](/src/galaxy-updates/2016-08/index.md) is out:** * [TooShed Contributions](/src/galaxy-updates/2016-08/index.md#toolshed-contributions) * And [other news](/src/galaxy-updates/2016-08/index.md#other-news) too. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-09-galaxy-update/index.md b/content/news/2016-09-galaxy-update/index.md index 73799d845f..8f1698a05d 100644 --- a/content/news/2016-09-galaxy-update/index.md +++ b/content/news/2016-09-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[September Galaxy News](/src/galaxy-updates/2016-09/index.md) is out:** * [TooShed Contributions](/src/galaxy-updates/2016-09/index.md#toolshed-contributions) * And [other news](/src/galaxy-updates/2016-09/index.md#other-news) too. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-10-galaxy-update/index.md b/content/news/2016-10-galaxy-update/index.md index 9e3120b093..f0019a9c13 100644 --- a/content/news/2016-10-galaxy-update/index.md +++ b/content/news/2016-10-galaxy-update/index.md @@ -25,4 +25,4 @@ There are also [117 new publications](/src/galaxy-updates/2016-10/index.md#new-p We hope to see you in Freiburg, Salt Lake, Melbourne, online, and around the world, -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2017-09-hiring-at-cc/index.md b/content/news/2017-09-hiring-at-cc/index.md index de0b8c9284..21df987ebc 100644 --- a/content/news/2017-09-hiring-at-cc/index.md +++ b/content/news/2017-09-hiring-at-cc/index.md @@ -7,6 +7,6 @@ date: "2017-09-13" [Cleveland Clinic Lerner Research Institute](https://www.postdocjobs.com/posting/7048061/)
-The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) has several [Postdoctoral Fellowships](http://www.lerner.ccf.org/jobs/postdoctoral/#760) available. We utilize high-throughput omics technologies, such as next generation sequencing, and data-intensive computing to explore biomedical research questions. +The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) has several [Postdoctoral Fellowships](http://www.lerner.ccf.org/jobs/postdoctoral/#760) available. We utilize high-throughput omics technologies, such as next generation sequencing, and data-intensive computing to explore biomedical research questions. Interested? See the [Galaxy is Hiring](/src/galaxy-is-hiring/index.md) page for the full posting (and for other openings too). diff --git a/content/news/2017-09-publication-lib-on-zotero/index.md b/content/news/2017-09-publication-lib-on-zotero/index.md index 66b3d0a3b4..dcf7be683d 100644 --- a/content/news/2017-09-publication-lib-on-zotero/index.md +++ b/content/news/2017-09-publication-lib-on-zotero/index.md @@ -34,4 +34,4 @@ Finally, Zotero is a community platform. If you are interested in helping to ca Thanks for using (and [mentioning and referencing](/src/citing-galaxy/index.md) :-) Galaxy, -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2017-11-oslo-admin-reg/index.md b/content/news/2017-11-oslo-admin-reg/index.md index 398e131bb1..6c6256c993 100644 --- a/content/news/2017-11-oslo-admin-reg/index.md +++ b/content/news/2017-11-oslo-admin-reg/index.md @@ -24,5 +24,5 @@ Instructors * [Björn Grüning](https://github.com/bgruening) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Elixir Germany](https://www.elixir-europe.org/about-us/who-we-are/nodes/germany), [University of Freiburg](https://www.uni-freiburg.de/?set_language=en)) * [Marius van den Beek](https://github.com/mvdbeek) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Institute Curie](https://science.institut-curie.org/), France) * [Nicola Soranzo](http://www.earlham.ac.uk/nicola-soranzo) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Earlham Institute](http://www.earlham.ac.uk/), UK) -* [Enis Afgan](/src/people/enis-afgan/index.md) ([Galaxy Project](/src/index.md), [Johns Hopkins University](https://jhu.edu/), USA) +* [Enis Afgan](/people/enis-afgan/index.md) ([Galaxy Project](/src/), [Johns Hopkins University](https://jhu.edu/), USA) * [Abdulrahman Azab](http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html) ([Elixir Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway), [USIT](http://www.usit.uio.no/), [University of Oslo](http://www.uio.no/), Norway) diff --git a/content/news/2018-05-gccbosc-childcare/index.md b/content/news/2018-05-gccbosc-childcare/index.md index 9d3c87c368..badebf716c 100644 --- a/content/news/2018-05-gccbosc-childcare/index.md +++ b/content/news/2018-05-gccbosc-childcare/index.md @@ -21,4 +21,4 @@ Childcare can be booked in half-day increments and **rates work out to $5.50/hou We hope to see you, and your kids, in Portland, -[Dave Clements](/src/people/dave-clements/index.md) on behalf of the [GCCBOSC 2018 Organizers](/src/events/gccbosc2018/organizers/index.md) +[Dave Clements](/people/dave-clements/index.md) on behalf of the [GCCBOSC 2018 Organizers](/src/events/gccbosc2018/organizers/) diff --git a/content/news/2018-09-galaxy-update/index.md b/content/news/2018-09-galaxy-update/index.md index 98875f226f..cafa7a9cf9 100644 --- a/content/news/2018-09-galaxy-update/index.md +++ b/content/news/2018-09-galaxy-update/index.md @@ -202,7 +202,7 @@ Four *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* * [次世代シーケンサーデータの解析手法 第 11 回 統合データ解析環境 Galaxy](http://www.iu.a.u-tokyo.ac.jp/~kadota/JSLAB_11_kadota.pdf), by , 大田 達郎, 寺田 朋子, 清水 謙多郎 , 門田 幸二, *Japanese Journal of Lactic Acid Bacteria* * [The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty655/5058096), by Jonathan Laperle, Simon Hébert-Deschamps, Joanny Raby, David Anderson de Lima Morais, Michel Barrette, David Bujold, Charlotte Bastin, Marc-Antoine Robert, Jean-François Nadeau, Marie Harel, Alexei Nordell-Markovits, Alain Veilleux, Guillaume Bourque, Pierre-Étienne Jacques, *Bioinformatics*, bty655, doi:10.1093/bioinformatics/bty655 -* [Bioconda: sustainable and comprehensive software distribution for the life sciences](https://www.nature.com/articles/s41592-018-0046-7), by [Björn Grüning](/src/people/bjoern-gruening/index.md), Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster & The Bioconda Team +* [Bioconda: sustainable and comprehensive software distribution for the life sciences](https://www.nature.com/articles/s41592-018-0046-7), by [Björn Grüning](/people/bjoern-gruening/), Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster & The Bioconda Team ## Publication Topics @@ -224,7 +224,7 @@ The Galaxy is expanding! Please help it grow. * [Bioinformaticien/biostatisticien biologiste](http://www.sfbi.fr/content/offre-de-poste-de-bioinformaticienbiostatisticien-biologiste-soci%C3%A9t%C3%A9-phylogene), Phylogene S.A, Bernis, France * [M2 : Diversité bactérienne associée aux microalgues toxiques (metabarcoding)](http://www.sfbi.fr/content/m2-diversit%C3%A9-bact%C3%A9rienne-associ%C3%A9e-aux-microalgues-toxiques-metabarcoding), IFREMER Centre Bretagne, Plouzané, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -277,10 +277,10 @@ We tag papers that use, mention, implement or extend public Galaxy Servers. Her # Hub and Doc Updates -* The [Galaxy publication library](/src/publication-library/index.md) is now integrated into the [Pan-Galactic search page](/src/search/index.md), thanks to [Dannon Baker](/src/people/dannon-baker/index.md). Search for something and click on the pub library tab. +* The [Galaxy publication library](/src/publication-library/index.md) is now integrated into the [Pan-Galactic search page](/src/search/index.md), thanks to [Dannon Baker](/people/dannon-baker/). Search for something and click on the pub library tab. * [Data Manager XML syntax description](/src/admin/tools/data-managers/data-manager-xml-syntax/index.md) updated by [Peter van Heusden](https://github.com/pvanheus) -* [Hub Editing Guidelines](https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md) updated by [Mo Heydarian](/src/people/mo-heydarian/index.md) -* There was a massive Hub infrastructure update by [Dannon Baker](/src/people/dannon-baker/index.md), but it's one of those you won't even notice. +* [Hub Editing Guidelines](https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md) updated by [Mo Heydarian](/people/mo-heydarian/) +* There was a massive Hub infrastructure update by [Dannon Baker](/people/dannon-baker/), but it's one of those you won't even notice. ---- diff --git a/content/news/2018-09-upcoming-events/index.md b/content/news/2018-09-upcoming-events/index.md index feacbc391a..99da5979f8 100644 --- a/content/news/2018-09-upcoming-events/index.md +++ b/content/news/2018-09-upcoming-events/index.md @@ -52,4 +52,4 @@ In addition to these events, there are many others offered this year, and around We hope to see you somewhere! -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/2018-10-galaxy-update/index.md b/content/news/2018-10-galaxy-update/index.md index 0a5d4c2126..b000388e57 100644 --- a/content/news/2018-10-galaxy-update/index.md +++ b/content/news/2018-10-galaxy-update/index.md @@ -281,7 +281,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2018-11-galaxy-update/index.md b/content/news/2018-11-galaxy-update/index.md index 3344dab537..3965ed897b 100644 --- a/content/news/2018-11-galaxy-update/index.md +++ b/content/news/2018-11-galaxy-update/index.md @@ -267,7 +267,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -285,7 +285,7 @@ There was a mind-boggling amount of activity in the [Galaxy Training Materials]( [Galaxy Training Materials](https://galaxyproject.github.io/training-material/) * New [Deploying a compute cluster in OpenStack via Terraform hands-on tutorial](https://galaxyproject.github.io/training-material/topics/admin/tutorials/terraform/tutorial.html) and [Slides](https://galaxyproject.github.io/training-material/topics/admin/tutorials/terraform/slides.html), by [Helena Rasche](https://github.com/hexylena) -* New [Ansible hands-on tutoral](https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/tutorial.html) and [Slides](https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/slides.html), by [Helena Rasche](/src/people/helena-rasche/index.md) +* New [Ansible hands-on tutoral](https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/tutorial.html) and [Slides](https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/slides.html), by [Helena Rasche](/people/helena-rasche/) * New [Network analysis with Heinz slides](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/slides.html) and an updated [tutorial](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html) from [Cico Zhang](https://github.com/CicoZhang) and [Saskia Hiltemann](https://github.com/shiltemann) * A general update to the [Contributing to the Galaxy Training Material](https://galaxyproject.github.io/training-material/topics/contributing/) materials from Saskia Hiltemann * Update to [Genome annotation with Prokka](https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html) tutorial from [Bérénice Batut](https://github.com/bebatut) and [Ekaterina Polkh](https://github.com/polkhe) @@ -303,7 +303,7 @@ And we would especially like to welcome new contributors [Matthias313](https://g ## Hub -* [Sorting Your Inputs](/src/support/sort-your-inputs/index.md), a how-to page by [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md) +* [Sorting Your Inputs](/src/support/sort-your-inputs/index.md), a how-to page by [Jennifer Hillman-Jackson](/people/jennifer-jackson/) * And the Hub now supports [DataTables](https://datatables.net/) (in a limited fashion, look for more in the future) and [Font Awesome 5](https://fontawesome.com/) (look for more spiffy icons). --- diff --git a/content/news/2018-12-galaxy-admins/index.md b/content/news/2018-12-galaxy-admins/index.md index f23da7a73b..abeab5a29f 100644 --- a/content/news/2018-12-galaxy-admins/index.md +++ b/content/news/2018-12-galaxy-admins/index.md @@ -13,14 +13,14 @@ Got some ideas? **[Nominate them](https://docs.google.com/forms/d/e/1FAIpQLSfv25 We hope to see you in February, -[Helena Rasche](/src/people/helena-rasche/index.md) and [Dave Clements](/src/people/dave-clements/index.md) +[Helena Rasche](/people/helena-rasche/index.md) and [Dave Clements](/src/people/dave-clements/)
Q: Why did the bimonthly meetups go away for *two years?*

-A: In early 2017, [Hans-Rudolf](/src/people/hansrudolf-hotz/index.md) stepped down after several years of leading the group. [Dave C](/src/people/dave-clements/index.md) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/src/people/helena-rasche/index.md) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.* +A: In early 2017, [Hans-Rudolf](/people/hansrudolf-hotz/index.md) stepped down after several years of leading the group. [Dave C](/people/dave-clements/) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/src/people/helena-rasche/) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.*

diff --git a/content/news/2018-12-galaxy-update/index.md b/content/news/2018-12-galaxy-update/index.md index adab13e3d0..65d91aee5a 100644 --- a/content/news/2018-12-galaxy-update/index.md +++ b/content/news/2018-12-galaxy-update/index.md @@ -287,7 +287,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md): distributed computing engineer and a full stack developer; see [this for more details on the positions](https://jobs.jhu.edu/job/Baltimore-Software-Engineer-MD-21218/442289500/, Baltimore, Maryland, United States). Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -330,7 +330,7 @@ And we would especially like to welcome new contributors [Anup Kumar](https://gi ## Hub -* [Galaxy Federation](/src/federation/index.md), by [Enis Afgan](/src/people/enis-afgan/index.md) +* [Galaxy Federation](/src/federation/index.md), by [Enis Afgan](/people/enis-afgan/) --- diff --git a/content/news/2019-01-galaxy-update/index.md b/content/news/2019-01-galaxy-update/index.md index fb998acd23..327f2c4b96 100644 --- a/content/news/2019-01-galaxy-update/index.md +++ b/content/news/2019-01-galaxy-update/index.md @@ -212,11 +212,11 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications from December: -* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/src/people/enis-afgan/index.md), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/src/people/bjoern-gruening/index.md), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; +* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/index.md), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/src/people/bjoern-gruening/), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; doi: 10.1101/488643 * **[PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud](https://doi.org/10.1093/gigascience/giy149)**, Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Steffen Neumann, Jon Ander Novella, Claire O'Donovan, Jake T M Pearce, Alina Peluso, Marco Enrico Piras, Luca Pireddu, Michelle A C Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R Viant, Ralf J M Weber, Gianluigi Zanetti, Christoph Steinbeck, *GigaScience*, giy149, doi: 10.1093/gigascience/giy149 -* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/src/people/vahid-jalili/index.md), [Enis Afgan](/src/people/enis-afgan/index.md), [James Taylor](/src/people/james-taylor/index.md), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), *bioRxiv* 506238, doi: 10.1101/506238 +* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/people/vahid-jalili/index.md), [Enis Afgan](/people/enis-afgan/index.md), [James Taylor](/src/people/james-taylor/), [Jeremy Goecks](/src/people/jeremy-goecks/), *bioRxiv* 506238, doi: 10.1101/506238 * **[SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data](https://doi.org/10.1093/bioinformatics/bty947 )**, Jamie Soul, Tim E Hardingham, Ray P Boot-Handford, Jean-Marc Schwartz, *Bioinformatics*, bty947, doi: 10.1093/bioinformatics/bty947 @@ -292,7 +292,7 @@ There is one new *[Galactic Blog](/src/blog/index.md)* entry: * **[Contributor of the Month: Simon Gladman](/src/blog/2018-12-cotm-simon-gladman/index.md):** * 'firefighter, cheesemaker, pillar of the [Galaxy Australia](https://usegalaxy.org.au/), and an overall jolly good fellow' - * by [Martin Čech](/src/people/marten/index.md) + * by [Martin Čech](/people/marten/) ---- @@ -316,7 +316,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Bioinformatics Scientist](https://www.indeed.com/viewjob?jk=5288546935e35605), ResearchDx, Irvine, California, United States * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States). Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -339,8 +339,8 @@ Here some significant activity from the [Galaxy Training Materials](https://gala ## Hub -* [Cloud Storage API](https://galaxyproject.org/cloud/storage/), by [Vahid Jalili](/src/people/vahid-jalili/index.md) -* [Securely Authorize Galaxy to Access Protected Data on Cloud](/src/authnz/cloud/index.md), by [Vahid Jalili](/src/people/vahid-jalili/index.md) +* [Cloud Storage API](https://galaxyproject.org/cloud/storage/), by [Vahid Jalili](/people/vahid-jalili/) +* [Securely Authorize Galaxy to Access Protected Data on Cloud](/src/authnz/cloud/index.md), by [Vahid Jalili](/people/vahid-jalili/) ## Other Training Materials and Doc diff --git a/content/news/2019-02-galaxy-update/index.md b/content/news/2019-02-galaxy-update/index.md index 0e508303f5..699fb307b9 100644 --- a/content/news/2019-02-galaxy-update/index.md +++ b/content/news/2019-02-galaxy-update/index.md @@ -150,7 +150,7 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications from January: -* **[G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation](https://doi.org/10.1101/499558)**, Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, [Jeremy Goecks](/src/people/jeremy-goecks/index.md). *bioRxiv* 499558; doi: https://doi.org/10.1101/499558 +* **[G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation](https://doi.org/10.1101/499558)**, Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, [Jeremy Goecks](/people/jeremy-goecks/). *bioRxiv* 499558; doi: https://doi.org/10.1101/499558 * **[Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur](https://doi.org/10.1093/gigascience/giy166)**, Saskia D Hiltemann, Stefan A Boers, Peter J van der Spek, Ruud Jansen, John P Hays, Andrew P Stubbs. *GigaScience*, giy166, doi:10.1093/gigascience/giy166 * **[MEGARes: an antimicrobial resistance database for high throughput sequencing](https://doi.org/10.1093/nar/gkw1009)**, Steven M. Lakin, Chris Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher. *Nucleic Acids Research*, Volume 45, Issue D1, 4 January 2017, Pages D574–D580, doi: 10.1093/nar/gkw1009 * **[Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes](https://doi.org/10.1186/s12864-019-5431-9)**, Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin and Charles Pineau. *BMC Genomics* 201920:56 doi:10.1186/s12864-019-5431-9 @@ -160,7 +160,7 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t * **[VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes](https://doi.org/10.1101/492074)**, Sara Silva Pereira, John Heap, Andrew R Jones, Andrew P. Jackson. *bioRxiv* 492074; doi: 10.1101/492074 * **[PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting](https://doi.org/10.1101/522458)**, Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau. *bioRxiv* 522458; doi: 10.1101/522458 * **[Enhancing Access to Digital Media: The Language Application Grid in the HTRC Data Capsule](https://doi.org/10.1145/3093338.3104171)**, James Pustejovsky, Marc Verhagen, Keongmin Rim, Yu Ma, Liang Ran, Samitha Liyanage, Jaimie Murdock, Robert H. McDonald, Beth Plale. In PEARC17 Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, Article No. 60. doi: 10.1145/3093338.3104171 -* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/src/people/nate/index.md), [Anton Nekrutenko](/src/people/anton/index.md). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 +* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/people/nate/index.md), [Anton Nekrutenko](/src/people/anton/). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 * **[Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis](https://link.springer.com/protocol/10.1007%2F978-1-4939-8982-9_8)**, Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer. In: Lai X., Gupta S., Vera J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY * **[QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics](https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727)**, Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda J. Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian A. Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy J. Griffin , and Pratik D. Jagtap. *Journal of Proteome Research*, Article ASAP DOI: 10.1021/acs.jproteome.8b00727 @@ -230,7 +230,7 @@ G-OnRamp is supported by [Washington University in St. Louis](https://wustl.edu/ ## AmrPlusPlus -[AmrPlusPlus](http://megares.meglab.org/amrplusplus/latest/html/) is a Docker container with a Galaxy-based metagenomics pipeline that is intuitive and easy to use. AmrPlusPlus takes advantage of current and new tools to help identify and characterize resistance genes within metagenomic sequence data. The pipeline can be used under a local instance of Galaxy and installed via Galaxy's Main Tool Shed. It is also available as a Galaxy-based Docker Image, using base images developed by [Björn Grüning](/src/people/bjoern-gruening/index.md) at the University of Freiburg. It has [Documentation](http://megares.meglab.org/amrplusplus/latest/html/) and [Email support](http://megares.meglab.org/amrplusplus/latest/html/contact.html). AmrPlusPlus is supported by [Colorado State University](https://www.colostate.edu/). +[AmrPlusPlus](http://megares.meglab.org/amrplusplus/latest/html/) is a Docker container with a Galaxy-based metagenomics pipeline that is intuitive and easy to use. AmrPlusPlus takes advantage of current and new tools to help identify and characterize resistance genes within metagenomic sequence data. The pipeline can be used under a local instance of Galaxy and installed via Galaxy's Main Tool Shed. It is also available as a Galaxy-based Docker Image, using base images developed by [Björn Grüning](/people/bjoern-gruening/) at the University of Freiburg. It has [Documentation](http://megares.meglab.org/amrplusplus/latest/html/) and [Email support](http://megares.meglab.org/amrplusplus/latest/html/contact.html). AmrPlusPlus is supported by [Colorado State University](https://www.colostate.edu/). ## Lifeportal @@ -309,7 +309,7 @@ The *dark energy* of irreproducible research is threatening the science universe * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * The [The European Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2019/01/10/openpositions/), Freiburg, Germany * Software engineer, system analysts/administrators, data analyst, and a comunnity and/or research manager -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States. Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). @@ -331,7 +331,7 @@ Updates from the [Galaxy Training Materials](https://galaxyproject.github.io/tra ## Hub -* [Configure Cloud Authorizatoin for Azure](/src/authnz/cloud/azure/index.md), by [Vahid Jalili](/src/people/vahid-jalili/index.md) +* [Configure Cloud Authorizatoin for Azure](/src/authnz/cloud/azure/index.md), by [Vahid Jalili](/people/vahid-jalili/) --- @@ -364,7 +364,7 @@ See [GitHub for details](https://github.com/galaxyproject/planemo/blob/master/HI # Other News * The [Galaxy statistics page](/src/galaxy-project/statistics/index.md) has received it's semi-annual update. -* From [James Taylor](/src/people/james-taylor/index.md): +* From [James Taylor](/people/james-taylor/): * [Visualizing scRNA-Seq data](https://twitter.com/jxtx/status/1088580033512390657/video/1) using [cellxgene](https://github.com/chanzuckerberg/cellxgene/blob/master/README.md) inside Galaxy. ## PAG 2019 Presentations and Posters are Available diff --git a/content/news/2019-03-galaxy-update/index.md b/content/news/2019-03-galaxy-update/index.md index fbf93ed264..60dfaf3694 100644 --- a/content/news/2019-03-galaxy-update/index.md +++ b/content/news/2019-03-galaxy-update/index.md @@ -13,7 +13,7 @@ The *March 2019 Galactic News* is here! This is a summary of what is going on i * **[The GalaxyAdmins](/src/news/2019-03-galaxy-update/index.md#galaxyadmins)** meetup is back March 21! * [184 new publications](/src/news/2019-03-galaxy-update/index.md#publications), great resources lead to great insight. * Some most excellent [Galaxy Platform News](/src/news/2019-03-galaxy-update/index.md#galaxy-platforms-news), including metagenomics, predictive model building, epigenome-wide association studies, immunogenomics, DNA methylation analysis, and more! -* An interview on [The Galactic Blog](/src/news/2019-03-galaxy-update/index.md#new-galactic-blog-post) with [Nate Coraor](/src/people/nate/index.md) about CVMFS & Galaxy. +* An interview on [The Galactic Blog](/src/news/2019-03-galaxy-update/index.md#new-galactic-blog-post) with [Nate Coraor](/people/nate/) about CVMFS & Galaxy. * At least [15 Open positions](/src/news/2019-03-galaxy-update/index.md#whos-hiring) in five countries on two continents. * [A burst of Training Updates](/src/news/2019-03-galaxy-update/index.md#doc-hub-and-training-updates). * [ToolShed contributions](/src/news/2019-03-galaxy-update/index.md#toolshed-contributions). @@ -184,12 +184,12 @@ These and [other Galaxy related events](/src/events/index.md) are coming up: * **[Développement d’outils et de méthodes pour l’analyse de données épigénomiques](https://savoirs.usherbrooke.ca/handle/11143/14918?show=full)**, Jonathan Laperle, M. Sc thesis, Université de Sherbrooke, 2019 * **[GCAC: galaxy workflow system for predictive model building for virtual screening](https://doi.org/10.1186/s12859-018-2492-8)**, Deepak R. Bharti, Anmol J. Hemrom and Andrew M. Lynn. *BMC Bioinformatics* 2019 19 (Suppl 13) :550 doi:10.1186/s12859-018-2492-8 -* **[EWAS-Galaxy: a tools suite for population epigeneticsintegrated into Galaxy](https://doi.org/10.1101/553784 )**, Katarzyna Murat, [Björn Grüning](/src/people/bjoern-gruening/index.md), Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J Tobin, *Krzysztof Poterlowicz. *bioRxiv* 553784; doi:doi.org/10.1101/553784 " +* **[EWAS-Galaxy: a tools suite for population epigeneticsintegrated into Galaxy](https://doi.org/10.1101/553784 )**, Katarzyna Murat, [Björn Grüning](/people/bjoern-gruening/), Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J Tobin, *Krzysztof Poterlowicz. *bioRxiv* 553784; doi:doi.org/10.1101/553784 " * **[Statistical Mitogenome Assembly with Repeats](https://dna.engr.uconn.edu/bibtexmngr/upload/AM18.pdf)**, Fahad Alqahtani and Ion I. Mandoiu. 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) * **[SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis](https://academic.oup.com/gigascience/article/8/2/giy167/5304063)**, Samuel Blanck and Guillemette Marot. *GigaScience*, Volume 8, Issue 2, 1 February 2019, giy167, doi:10.1093/gigascience/giy167 * **[Enrichment of phosphate solubilizing bacteria during late developmental stages of eggplant (*Solanum melongena* L.)](https://academic.oup.com/femsec/advance-article/doi/10.1093/femsec/fiz023/5319216)**, Huixiu Li, Xiaoyan Ding, Chen Chen, Xiangnan Zheng, Hui Han, Chennan Li, Jingyang Gong, Ting Xu, Qing X Li, Guo-chun Ding, Ji Li. *FEMS Microbiology Ecology*, fiz023, doi:10.1093/femsec/fiz023 * **[Optimized Storing of Workflow Outputs through Mining Association Rules](https://doi.org/10.1109/BigData.2018.8622351)**, Debasish Chakroborti, Manishankar Mondal, Banani Roy, Chanchal K. Roy, Kevin A. Schneider. 2018 IEEE International Conference on Big Data (Big Data), doi:10.1109/BigData.2018.8622351 -* **[Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE)](https://doi.org/10.1093/bioinformatics/btz107)**, Tharindu Senapathi, Simon Bray, Christopher B. Barnett, [Björn Grüning](/src/people/bjoern-gruening/index.md), Kevin J Naidoo. *Bioinformatics*, btz107, doi:10.1093/bioinformatics/btz107 +* **[Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE)](https://doi.org/10.1093/bioinformatics/btz107)**, Tharindu Senapathi, Simon Bray, Christopher B. Barnett, [Björn Grüning](/people/bjoern-gruening/), Kevin J Naidoo. *Bioinformatics*, btz107, doi:10.1093/bioinformatics/btz107 Five of the eight highlighted publications are open access. @@ -291,7 +291,7 @@ The *dark energy* of irreproducible research is threatening the science universe * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * The [The European Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2019/01/10/openpositions/), Freiburg, Germany * Software engineer, system analysts/administrators, data analyst, and a comunnity and/or research manager -* The [Blankenberg](/src/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/index.md). +* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States. Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2019-04-galaxy-update/index.md b/content/news/2019-04-galaxy-update/index.md index af4ab2361d..b5623b2523 100644 --- a/content/news/2019-04-galaxy-update/index.md +++ b/content/news/2019-04-galaxy-update/index.md @@ -164,7 +164,7 @@ These and [other Galaxy related events](/src/events/index.md) are coming up: Recently added *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications: -* **[GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering](https://doi.org/10.1101/550335)**, Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, [Björn Grüning](/src/people/bjoern-gruening/index.md), Rolf Backofen. *bioRxiv* 550335; doi: 10.1101/550335 +* **[GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering](https://doi.org/10.1101/550335)**, Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, [Björn Grüning](/people/bjoern-gruening/), Rolf Backofen. *bioRxiv* 550335; doi: 10.1101/550335 * **[CAFU: a Galaxy framework for exploring unmapped RNA-Seq data](https://doi.org/10.1093/bib/bbz018)**, Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jiantao Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma. *Briefings in Bioinformatics*, bbz018,doi:10.1093/bib/bbz018. 28 February 2019 * **[Visualization to Support Advanced Analysis of Genomic Data](http://urn.nb.no/URN:NBN:no-69721)**, Kumar Aman. Master Thesis, University of Oslo * **[Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework](https://doi.org/10.1007/978-1-4939-9164-8_18)**, Nguyen L., Brun V., Combes F., Loux V., Vandenbrouck Y. (2019) diff --git a/content/news/2019-04-gcc-extension/index.md b/content/news/2019-04-gcc-extension/index.md index 54c0df6d44..3e27a3e28f 100644 --- a/content/news/2019-04-gcc-extension/index.md +++ b/content/news/2019-04-gcc-extension/index.md @@ -19,7 +19,7 @@ I am now keenly aware of that second fact as we have heard from many folks that With apologies for the original date, -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) ---- diff --git a/content/news/2019-06-galaxy-update/index.md b/content/news/2019-06-galaxy-update/index.md index ca6e3fa167..2495ea4f30 100644 --- a/content/news/2019-06-galaxy-update/index.md +++ b/content/news/2019-06-galaxy-update/index.md @@ -172,12 +172,12 @@ These and [other Galaxy related events](/src/events/index.md) are coming up: There were 10 *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications added, and 9 of those are open access: * **[Accessible and reproducible mass spectrometry imaging data analysis in Galaxy]( https://doi.org/10.1101/628719)**, Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling. *bioRxiv* 628719; doi: 10.1101/628719 -* **[G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes](https://doi.org/10.1093/bioinformatics/btz309)**, Yating Liu, Luke Sargent, Wilson Leung, Sarah C. R. Elgin and [Jeremy Goecks](/src/people/jeremy-goecks/index.md). *Bioinformatics*, btz309, doi: 10.1093/bioinformatics/btz309 +* **[G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes](https://doi.org/10.1093/bioinformatics/btz309)**, Yating Liu, Luke Sargent, Wilson Leung, Sarah C. R. Elgin and [Jeremy Goecks](/people/jeremy-goecks/). *Bioinformatics*, btz309, doi: 10.1093/bioinformatics/btz309 * **[MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data](https://f1000research.com/articles/8-726)**, Mike W.C. Thang, Xin-Yi Chua, Gareth Price, Dominique Gorse, Matt A. Field. *F1000Research* 2019, 8:726, doi: 10.12688/f1000research.18866.1) * **[NGPhylogeny.fr: new generation phylogenetic services for non-specialists](https://doi.org/10.1093/nar/gkz303)**, Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier Gascuel. *Nucleic Acids Research*, gkz303, doi: 10.1093/nar/gkz303 * **[Rice Galaxy: an open resource for plant science](https://academic.oup.com/gigascience/article/8/5/giz028/5492234)**, Venice Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay Triplett, Jillian Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar and Ramil P. Mauleon. *GigaScience*, 8, 2019, 1–14, doi: 10.1093/gigascience/giz028 * **[The RNA workbench 2.0: next generation RNA data analysis](https://doi.org/10.1093/nar/gkz353)**, Jorg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen and [Björn Grüning](https://github.com/bgruening). *Nucleic Acids Research*, gkz353, doi: 10.1093/nar/gkz353 -* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/src/people/dan/index.md), [John Chilton](/src/people/john-chilton/index.md), and [Nate Coraor](/src/people/nate/index.md). *bioRxiv* 642280; doi: 10.1101/642280 +* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). *bioRxiv* 642280; doi: 10.1101/642280 * **[Prediction and Characterization of miRNA/Target Pairs in Non‐Model Plants Using RNA‐seq](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cppb.20090)**, Kira C. M. Neller, Alexander Klenov, Katalin A. Hudak. *Current Protocols in Plant Biology*, e20090. doi: 10.1002/cppb.20090 * **[The Repetitive DNA Composition in the Natural Pesticide Producer *Tanacetum cinerariifolium:* Interindividual Variation of Subtelomeric Tandem Repeats](https://doi.org/10.3389/fpls.2019.00613)**, Jelena Mlinarec, Ana Skuhala, Adela Jurković, Nenad Malenica, Jamie McCann, Hanna Weiss-Schneeweiss, Borut Bohanec and Višnja Besendorfer. *Frontiers in Plant Science*, 16 May 2019, doi: 10.3389/fpls.2019.00613 @@ -263,7 +263,7 @@ For the second month in a row we have a new *[Galactic Blog](/src/blog/index.md) The *dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy push it back! * [Bioinformaticien h/f - INNOLEA](https://www.sfbi.fr/node/11698), Mondonville, France. "Le développement d'outils pour l'analyse de données génétiques, génomiques et la mise en œuvre dans une plateforme Galaxy" -* [Postdoctoral Fellows](https://www.postdocjobs.com/posting/7057197), [Blankenberg Lab](/src/people/dan/index.md), Cleveland Clinic, Cleveland, Ohio, United States. +* [Postdoctoral Fellows](https://www.postdocjobs.com/posting/7057197), [Blankenberg Lab](/people/dan/), Cleveland Clinic, Cleveland, Ohio, United States. * [Scientist - Molecular R&D](https://jobs.vibrantm.com/emd/job/Rockville-Scientist-Molecular-R&D-MD-20850-3304/518778201/), MilliporeSigma, Rockville, Maryland, United States * ELIXIR Belgium has **three Galaxy-related openings** in Ghent: * [ELIXIR Open Science Community Manager](https://vibvzw.jobsoid.com/j/17164/elixir-open-science-community-manager), VIB-UGent Center for Plant Systems Biology @@ -289,7 +289,7 @@ Updates from the [Galaxy Training Materials](https://training.galaxyproject.org/ Hub updates: -* [Data Privacy in Galaxy](/src/learn/privacy-features/index.md): A new page describing how to use Galaxy's data privacy features; from [Martin Cech](/src/people/marten/index.md) +* [Data Privacy in Galaxy](/src/learn/privacy-features/index.md): A new page describing how to use Galaxy's data privacy features; from [Martin Cech](/people/marten/) --- @@ -344,7 +344,7 @@ Automated status tracking of our most important services is available at [statu ## data.galaxyproject.org directory view. -From [Enis Afgan](/src/people/enis-afgan/index.md): +From [Enis Afgan](/people/enis-afgan/): * If you ever wondered what reference data is available on the Galaxy Project CVMFS at data.galaxyproject.org, here's a snapshot [file system directory view](https://gist.github.com/afgane/b527eb857244f43a680c9654b30deb1f), and here's the [equivalent navigable view](http://datacache.galaxyproject.org/). diff --git a/content/news/2019-07-biohackathon/index.md b/content/news/2019-07-biohackathon/index.md index 0578c97d57..a5f5d9a7a8 100644 --- a/content/news/2019-07-biohackathon/index.md +++ b/content/news/2019-07-biohackathon/index.md @@ -22,13 +22,13 @@ date: "2019-07-16" Galaxy will be featured at [BioHackathon-Europe 2019](https://www.biohackathon-europe.org/index.html) as a prominent part of many of [this year's selected projects](https://www.biohackathon-europe.org/projects): * **[Interoperable Workflows for Communities](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/1)** - * Organizers: Frederik Coppens, [Björn Grüning](/src/people/bjoern-gruening/index.md), Marek Suchánek, Rob Hooft + * Organizers: Frederik Coppens, [Björn Grüning](/people/bjoern-gruening/), Marek Suchánek, Rob Hooft * **[Improve the support of Common Workflow Language in Galaxy](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/3)** - * Organizers: Hervé Ménager, [John Chilton](/src/people/john-chilton/index.md), Michael Crusoe + * Organizers: Hervé Ménager, [John Chilton](/people/john-chilton/), Michael Crusoe * **[Towards seamless Galaxy and InterMine integration: Enhanced region analysis](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/7)** * Organizers: Yo Yehudi * **[Scalable delivery of FAIR training in Life Sciences using Galaxy and the Carpentries training material](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/8)** - * Organizers: [Helena Rasche](/src/people/helena-rasche/index.md), Saskia Hiltemann, Bérénice Batut + * Organizers: [Helena Rasche](/people/helena-rasche/), Saskia Hiltemann, Bérénice Batut * **Gallantries Project: Galaxy + Carpentries for Scalable Training** * Organizers: Helena Rasche, Saskia Hiltemann, Bérénice Batut * **[Development of a Pulsar toolkit](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/17)** @@ -38,7 +38,7 @@ Galaxy will be featured at [BioHackathon-Europe 2019](https://www.biohackathon-e * **[A graph database of Galaxy tool interoperability](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/30)** * Organizers: Wolfgang Maier, Jon Ison * **[Bioconda and Biocontainers helpdesk](https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/31)** - * Organizers: [Björn Grüning](/src/people/bjoern-gruening/index.md), Devon Ryan + * Organizers: [Björn Grüning](/people/bjoern-gruening/), Devon Ryan Join us to learn from and work with experts of the Open Source Life Science community, and discuss the future of the [ELIXIR Galaxy community](https://elixir-europe.org/communities/galaxy) and enjoy the great food and venue. diff --git a/content/news/2019-07-galaxy-update/index.md b/content/news/2019-07-galaxy-update/index.md index 02bb33d048..09910bc0c4 100644 --- a/content/news/2019-07-galaxy-update/index.md +++ b/content/news/2019-07-galaxy-update/index.md @@ -233,7 +233,7 @@ Platforms that were referenced at least twice in the past month's publications: The *dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy push it back! * [Bioinformaticien h/f - INNOLEA](https://www.sfbi.fr/node/11698), Mondonville, France. "Le développement d'outils pour l'analyse de données génétiques, génomiques et la mise en œuvre dans une plateforme Galaxy" -* [Postdoctoral Fellows](https://www.postdocjobs.com/posting/7057197), [Blankenberg Lab](/src/people/dan/index.md), Cleveland Clinic, Cleveland, Ohio, United States. +* [Postdoctoral Fellows](https://www.postdocjobs.com/posting/7057197), [Blankenberg Lab](/people/dan/), Cleveland Clinic, Cleveland, Ohio, United States. * ELIXIR Belgium has **three Galaxy-related openings** in Ghent: * [ELIXIR Open Science Community Manager](https://vibvzw.jobsoid.com/j/17164/elixir-open-science-community-manager), VIB-UGent Center for Plant Systems Biology * [ELIXIR Software developer data management tools](https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/17168/software-developer-data-management-tools), VIB-UGent Center for Plant Systems Biology diff --git a/content/news/2019-08-galaxy-update/index.md b/content/news/2019-08-galaxy-update/index.md index 6fa269e9b6..f6f2477efe 100644 --- a/content/news/2019-08-galaxy-update/index.md +++ b/content/news/2019-08-galaxy-update/index.md @@ -349,7 +349,7 @@ Wageningen University & Research is hiring.
[Postdoctoral Fellows](https://www.postdocjobs.com/posting/7057197)
-In the [Blankenberg Lab](/src/people/dan/index.md) at the Cleveland Clinic, Cleveland, Ohio, United States. +In the [Blankenberg Lab](/people/dan/) at the Cleveland Clinic, Cleveland, Ohio, United States. Cleveland Clinic
diff --git a/content/news/2019-08-incob-building/index.md b/content/news/2019-08-incob-building/index.md index e6ef6643ad..8f3323bae2 100644 --- a/content/news/2019-08-incob-building/index.md +++ b/content/news/2019-08-incob-building/index.md @@ -16,4 +16,4 @@ Several regional communities and resources already exist in the Galaxy ecosystem Galaxy is a widely used and deployed open-source platform that integrates thousands of analysis tools, and supports data integration and analysis, workflow creation, data visualization, and sharing and publishing your analyses and pipelines. Galaxy is also *a global community* of researchers, programmers, trainers, and users all doing and supporting data intensive research. Interested? Then we hope to see you at INCOB.
-[Dave Clements](/src/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/index.md) +[Dave Clements](/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) diff --git a/content/news/2019-09-galaxy-update/index.md b/content/news/2019-09-galaxy-update/index.md index dad343e50d..b8422cab8e 100644 --- a/content/news/2019-09-galaxy-update/index.md +++ b/content/news/2019-09-galaxy-update/index.md @@ -295,7 +295,7 @@ By [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-
[Help for Differential Expression Analysis](/src/support/diff-expression/index.md)

-By [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md)

+By [Jennifer Hillman-Jackson](/people/jennifer-jackson/)

A new support page for one of Galaxy's most popular applications: differential gene expression analysis.

@@ -306,7 +306,7 @@ A new support page for one of Galaxy's most popular applications: differential g
[Displaying Datasets at External Display Applications / Websites using GEDAs](/src/admin/tools/external-display-applications-tutorial/index.md)
GEDA example config

-By [Dan Blankenberg](/src/people/dan/index.md)

+By [Dan Blankenberg](/people/dan/)

How to add a new external display application (UCSC genome browser, GeneTrack, JBrowse, etc. to Galaxy.


diff --git a/content/news/2019-10-galaxy-update/index.md b/content/news/2019-10-galaxy-update/index.md index 3df6ef1b55..c60710e629 100644 --- a/content/news/2019-10-galaxy-update/index.md +++ b/content/news/2019-10-galaxy-update/index.md @@ -132,7 +132,7 @@ Ellrott, Kyle, Alex Buchanan, et al. *Genome Biology* 20 (1): 195. doi: 10.1186/
[You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda](http://doi.acm.org/10.1145/3307339.3343178)
-[Daniel Blankenberg](/src/people/dan/index.md), [Martin Cech](/src/people/marten/index.md). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178 +[Daniel Blankenberg](/people/dan/index.md), [Martin Cech](/src/people/marten/). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178
diff --git a/content/news/2019-10-hacktoberfest/index.md b/content/news/2019-10-hacktoberfest/index.md index e5d0811188..6cf9218ab0 100644 --- a/content/news/2019-10-hacktoberfest/index.md +++ b/content/news/2019-10-hacktoberfest/index.md @@ -15,4 +15,4 @@ Not sure what to contribute? Here are a few suggestions to get you started: * Get your hands dirty with some DevOps topics, check out Galaxy’s incubator project: [CloudVE](https://github.com//cloudve) See you online,
-[Alex Ostrovsky](/src/people/alex-ostrovsky/index.md) and [Enis Afgan](/src/people/enis-afgan/index.md) +[Alex Ostrovsky](/people/alex-ostrovsky/index.md) and [Enis Afgan](/src/people/enis-afgan/) diff --git a/content/news/2019-10-pag/index.md b/content/news/2019-10-pag/index.md index b105bf2664..ea76ab6a07 100644 --- a/content/news/2019-10-pag/index.md +++ b/content/news/2019-10-pag/index.md @@ -37,4 +37,4 @@ Interested? [Apply now](https://support.nlm.nih.gov/Pan_Meta_Scopeathon/).
Hope to see you in San Diego,
-[Dave Clements](/src/people/dave-clements/index.md) and [Mo Heydarian](/src/people/mo-heydarian) +[Dave Clements](/people/dave-clements/) and [Mo Heydarian](/src/people/mo-heydarian) diff --git a/content/news/2019-11-abrf/index.md b/content/news/2019-11-abrf/index.md index 372fd53c2d..17ced0a73a 100644 --- a/content/news/2019-11-abrf/index.md +++ b/content/news/2019-11-abrf/index.md @@ -23,4 +23,4 @@ The [Association of Biomolecular Resource Facilities 2020 Conference (ABRF 2020) We hope to see you Palm Springs, -[Pratik](https://www.researchgate.net/profile/Pratik_Jagtap2), [Saskia](https://www.researchgate.net/profile/Saskia_Hiltemann), [Subina](https://www.researchgate.net/profile/Subina_Mehta), [Mehmet](https://www.researchgate.net/profile/Mehmet_Tekman), and [Dave C](/src/people/dave-clements/index.md) +[Pratik](https://www.researchgate.net/profile/Pratik_Jagtap2), [Saskia](https://www.researchgate.net/profile/Saskia_Hiltemann), [Subina](https://www.researchgate.net/profile/Subina_Mehta), [Mehmet](https://www.researchgate.net/profile/Mehmet_Tekman), and [Dave C](/people/dave-clements/) diff --git a/content/news/2019-11-galaxy-update/index.md b/content/news/2019-11-galaxy-update/index.md index ecd08e5b5a..8449eefeb3 100644 --- a/content/news/2019-11-galaxy-update/index.md +++ b/content/news/2019-11-galaxy-update/index.md @@ -106,7 +106,7 @@ Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T.,
[A high resolution view of adaptive event dynamics in a plasmid](https://doi.org/10.1093/gbe/evz197)
-Mei, H., Arbeithuber, B., Cremona, M. A., DeGiorgio, M., & [Nekrutenko, A](/src/people/anton/index.md). (2019). Genome Biology and Evolution. doi: 10.1093/gbe/evz197 +Mei, H., Arbeithuber, B., Cremona, M. A., DeGiorgio, M., & [Nekrutenko, A](/people/anton/). (2019). Genome Biology and Evolution. doi: 10.1093/gbe/evz197
diff --git a/content/news/2019-12-aus/index.md b/content/news/2019-12-aus/index.md index be791b1f0e..d7ed460e6a 100644 --- a/content/news/2019-12-aus/index.md +++ b/content/news/2019-12-aus/index.md @@ -7,11 +7,11 @@ date: "2019-12-19" [](https://mailchi.mp/melbournebioinformatics/2019wrap) -Following [Galaxy Australia](https://usegalaxy.org.au/)’s very successful representation at Jakarta for the [INCOB 2019 meeting](/src/events/2019-09-incob/index.md), [Dave Clements](/src/people/dave-clements/index.md) of the Galaxy project asked our resident Galaxy guru Simon Gladman to represent the Galaxy community at the [Galaxy Africa](https://www.iscb.org/iscbafrica2019-ps/iscbafrica2019-worktut#galaxy) and [ISCB-Africa ASBCB Conference on Bioinformatics](https://www.iscb.org/iscbafrica2019) being held in Ghana in November 2019. +Following [Galaxy Australia](https://usegalaxy.org.au/)’s very successful representation at Jakarta for the [INCOB 2019 meeting](/src/events/2019-09-incob/index.md), [Dave Clements](/people/dave-clements/) of the Galaxy project asked our resident Galaxy guru Simon Gladman to represent the Galaxy community at the [Galaxy Africa](https://www.iscb.org/iscbafrica2019-ps/iscbafrica2019-worktut#galaxy) and [ISCB-Africa ASBCB Conference on Bioinformatics](https://www.iscb.org/iscbafrica2019) being held in Ghana in November 2019. Galaxy Africa is developing into a strong community and this was an opportunity to welcome them into the broader Galaxy community. Over two days prior to the ISCB conference, a series of talks and training sessions were held. Simon ran the Galaxy administrators’ workshop and assisted at others. Attendees came from over twelve states in Africa. The meetings also presented an opportunity for Simon to talk about how Galaxy Australia is structured and to discuss mutual problem solving efforts. The Galaxy community in Africa is building up capacity and outreach, seeking ways to operate systems administration for large scale Galaxy servers. Once operational, they hope to join the global “usegalaxy.*” network. -Our thanks to Simon’s generous hosts at this terrific community building event: Galaxy Project Team (Dave Clements, Jennifer Vessio, [Marten Čech](/src/people/marten/index.md), KNUST University, Kumasi (Pandam Salifu, Michael Thompson, SANBI (Peter van Heusden, Thoba Lose, Alan Christoffels), ISCB – ASBCB (Bel Hanson, Amel Ghouila). +Our thanks to Simon’s generous hosts at this terrific community building event: Galaxy Project Team (Dave Clements, Jennifer Vessio, [Marten Čech](/people/marten/), KNUST University, Kumasi (Pandam Salifu, Michael Thompson, SANBI (Peter van Heusden, Thoba Lose, Alan Christoffels), ISCB – ASBCB (Bel Hanson, Amel Ghouila). --- diff --git a/content/news/2019-12-galaxy-update/index.md b/content/news/2019-12-galaxy-update/index.md index 7eb07cbfdf..3b59797dda 100644 --- a/content/news/2019-12-galaxy-update/index.md +++ b/content/news/2019-12-galaxy-update/index.md @@ -97,13 +97,13 @@ There are
[Tool recommender system in Galaxy using deep learning](https://doi.org/10.1101/838599)
-Kumar, A., [Grüning, B.](/src/people/bjoern-gruening/index.md), & Backofen, R. (2019). *BioRxiv*, 838599. doi: 10.1101/838599 +Kumar, A., [Grüning, B.](/people/bjoern-gruening/), & Backofen, R. (2019). *BioRxiv*, 838599. doi: 10.1101/838599
[The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR](https://doi.org/10.12688/f1000research.20244.1)
-Wibberg, D., Batut, B., Belmann, P., Blom, J., Glöckner, F. O., [Grüning, B.](/src/people/bjoern-gruening/index.md), … Kohlbacher, O. (2019). *F1000Research*, 8, 1877. doi: 10.12688/f1000research.20244.1 +Wibberg, D., Batut, B., Belmann, P., Blom, J., Glöckner, F. O., [Grüning, B.](/people/bjoern-gruening/), … Kohlbacher, O. (2019). *F1000Research*, 8, 1877. doi: 10.12688/f1000research.20244.1
@@ -260,7 +260,7 @@ New comprehensive documentation by [@selten](https://github.com/selten) on [how
Cite GTN Tutorials
-Thanks to [Helena Rasche](/src/people/helena-rasche/index.md), every [GTN Tutorial](https://training.galaxyproject.org/) now includes a *Citing this Tutorial* section, including a BibTex citation for the tutorial. +Thanks to [Helena Rasche](/people/helena-rasche/), every [GTN Tutorial](https://training.galaxyproject.org/) now includes a *Citing this Tutorial* section, including a BibTex citation for the tutorial. Cite tutorials
@@ -276,7 +276,7 @@ The documentation on [how to run Galaxy on Windows](/src/admin/config/windows/in
Account Creation Help
-The account creation documentation was expanded by [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md) to cover additional situations and help resources. +The account creation documentation was expanded by [Jennifer Hillman-Jackson](/people/jennifer-jackson/) to cover additional situations and help resources. Accounts help
diff --git a/content/news/2020-06-galaxy-update/index.md b/content/news/2020-06-galaxy-update/index.md index 2f67f869af..457dace02b 100644 --- a/content/news/2020-06-galaxy-update/index.md +++ b/content/news/2020-06-galaxy-update/index.md @@ -174,7 +174,7 @@ June is an active month for the Scientific Gateways Community Institute: [This workshop](https://galaxyproject.eu/event/2020-05-27-Machine-Learning-Elixir/) will be held online 22-26 June. **Registration deadline is 16 June!** -*The organizers are seeking French-speaking Teaching Assistants for this workshop. If you can help (Tues + Thurs only) please contact [Björn Grüning](/src/people/bjoern-gruening/index.md).* +*The organizers are seeking French-speaking Teaching Assistants for this workshop. If you can help (Tues + Thurs only) please contact [Björn Grüning](/people/bjoern-gruening/).*
diff --git a/content/news/2020-07-galaxy-update/index.md b/content/news/2020-07-galaxy-update/index.md index 8384ec9816..bf4e8d6363 100644 --- a/content/news/2020-07-galaxy-update/index.md +++ b/content/news/2020-07-galaxy-update/index.md @@ -354,7 +354,7 @@ The GVL Beta 3 release features complete analysis on one platform, including tra By [Emily Lescak](https://eventfund.codeforscience.org/author/emily/) of [Code for Science & Society](https://codeforscience.org/) -A conversation with [Dave Clements](/src/people/dave-clements/index.md) about moving BCC2020 from an in-person to a virtual event, and the opportunities that move enabled. +A conversation with [Dave Clements](/people/dave-clements/) about moving BCC2020 from an in-person to a virtual event, and the opportunities that move enabled. Code for Science & Society
diff --git a/content/news/2020-10-galaxy-update/index.md b/content/news/2020-10-galaxy-update/index.md index c817464524..363f5927aa 100644 --- a/content/news/2020-10-galaxy-update/index.md +++ b/content/news/2020-10-galaxy-update/index.md @@ -226,7 +226,7 @@ Two funding opportunities are now open within the EU project [EOSC-Life](https:/
[refgenie for Local Instances](/src/admin/refgenie/index.md)
-By [Dan Blankenberg](/src/people/dan/index.md). +By [Dan Blankenberg](/people/dan/). How to use **[refgenie](http://refgenie.databio.org/)** with your local instance of Galaxy. refgenie diff --git a/content/news/2021-03-gsoc/index.md b/content/news/2021-03-gsoc/index.md index 02c769b0c2..b36398e7dc 100644 --- a/content/news/2021-03-gsoc/index.md +++ b/content/news/2021-03-gsoc/index.md @@ -15,7 +15,7 @@ And we need your help, of course. ## Galaxy Community, before March 29 -*Give some thought to what would make a good GSoC project and then propose them.* Good ideas are both tractable and impactful. Also, consider if you have the time and expertise to server as a mentor. If you don't then can you identify who does? GSoc has [extensive documentation describing best practices for both mentors and students](https://google.github.io/gsocguides/). When you are ready, add your idea to the list of possible projects [by adding it here](http://gmod.org/wiki/GSOC_Project_Ideas_2021) or by sending your idea to [Dave Clements](/src/people/dave-clements/index.md). +*Give some thought to what would make a good GSoC project and then propose them.* Good ideas are both tractable and impactful. Also, consider if you have the time and expertise to server as a mentor. If you don't then can you identify who does? GSoc has [extensive documentation describing best practices for both mentors and students](https://google.github.io/gsocguides/). When you are ready, add your idea to the list of possible projects [by adding it here](http://gmod.org/wiki/GSOC_Project_Ideas_2021) or by sending your idea to [Dave Clements](/people/dave-clements/). ## Students, March 29 through April 12 diff --git a/content/news/an-update-to-galaxy-cloudman/index.md b/content/news/an-update-to-galaxy-cloudman/index.md index 96a1443bad..1ab438db3a 100644 --- a/content/news/an-update-to-galaxy-cloudman/index.md +++ b/content/news/an-update-to-galaxy-cloudman/index.md @@ -12,4 +12,4 @@ The new version brings the following updates/features: * `post_start_service` now runs if the script exists in the cluster bucket even if no URL was provided as part of current user data * Fix recognition of existing and attached file system volumes on instance reboot -[EnisAfgan](/src/people/enis-afgan/index.md) +[EnisAfgan](/people/enis-afgan/) diff --git a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md index eba185fa99..4332b6bc67 100644 --- a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md +++ b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md @@ -4,4 +4,4 @@ date: "2011-09-01" ---
Concurrency and Computation: Practice & Experience
-A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. +A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. diff --git a/content/news/aug2011-distribution-news-brief/index.md b/content/news/aug2011-distribution-news-brief/index.md index 888b0473cd..8264a98dfb 100644 --- a/content/news/aug2011-distribution-news-brief/index.md +++ b/content/news/aug2011-distribution-news-brief/index.md @@ -22,6 +22,6 @@ upgrade: % hg pull -u -r 949e4f5fa03a **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/baltimore-meetup201501/index.md b/content/news/baltimore-meetup201501/index.md index 545aed1084..adff5edd6d 100644 --- a/content/news/baltimore-meetup201501/index.md +++ b/content/news/baltimore-meetup201501/index.md @@ -16,4 +16,4 @@ We are hoping this will be the first of many meetups, both in the Baltimore area Thanks, -[Enis Afgan](/src/people/enis-afgan/index.md) and [Nitesh Turaga](/src/people/nitesh-turaga/index.md), of the [Galaxy Team](/src/galaxy-team/index.md) +[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/), of the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/bio-blend-paper/index.md b/content/news/bio-blend-paper/index.md index 816ed1924e..1e6d722111 100644 --- a/content/news/bio-blend-paper/index.md +++ b/content/news/bio-blend-paper/index.md @@ -4,7 +4,7 @@ date: "2013-05-02" ---
Bioinformatics
-A new paper, "[BioBlend: automating pipeline analyses within Galaxy and CloudMan](http://bit.ly/11AuV4O)," by Clare Sloggett, Nuwan Goonasekera and [Enis Afgan](/src/people/enis-afgan/index.md) has just been published in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. BioBlend is +A new paper, "[BioBlend: automating pipeline analyses within Galaxy and CloudMan](http://bit.ly/11AuV4O)," by Clare Sloggett, Nuwan Goonasekera and [Enis Afgan](/people/enis-afgan/) has just been published in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. BioBlend is
a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large-data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provision the required infrastructure, and automate complex analyses over large data sets within the familiar Galaxy environment. @@ -13,4 +13,4 @@ a unified API in a high-level language (python) that wraps the functionality of Documentation is [available at ReadTheDocs](http://bioblend.readthedocs.org/). BioBlend can be installed with [PyPI](https://pypi.python.org/pypi), and the source code is at [GitHub](https://github.com/afgane/bioblend). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/bio-blend-v0.5.2/index.md b/content/news/bio-blend-v0.5.2/index.md index 547044cde7..5da3f5c52e 100644 --- a/content/news/bio-blend-v0.5.2/index.md +++ b/content/news/bio-blend-v0.5.2/index.md @@ -22,4 +22,4 @@ See the [commit messages](https://github.com/afgane/bioblend/compare/d8925715a5a Enjoy and please let us know what you think, -[Enis](/src/people/enis-afgan/index.md) & [John](/src/people/john-chilton/index.md) & Simone Leo & Nicola Soranzo & [The Galaxy Team](/src/galaxy-team/index.md) +[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/) & Simone Leo & Nicola Soranzo & [The Galaxy Team](/src/galaxy-team/) diff --git a/content/news/bio-blend-v0.5.3/index.md b/content/news/bio-blend-v0.5.3/index.md index 48ba1a73fa..61f7aac55f 100644 --- a/content/news/bio-blend-v0.5.3/index.md +++ b/content/news/bio-blend-v0.5.3/index.md @@ -10,12 +10,12 @@ This is mostly an incremental bug fix release with the following summary of chan * Project source moved to new URL - https://github.com/galaxyproject/bioblend * Huge improvements to automated testing, tests now run against Galaxy release_14.02 and all later versions to ensure backward compatibility (see [travis.yml](https://github.com/galaxyproject/bioblend/blob/master/.travis.yml) for details). -* Many documentation improvements (thanks to [Helena Rasche](/src/people/helena-rasche/index.md)). +* Many documentation improvements (thanks to [Helena Rasche](/people/helena-rasche/)). * Add Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau). * Add method to get the standard error and standard output for the job corresponding to a Galaxy dataset (thanks to Anthony Bretaudeau). * Add `get_state()` method to `JobsClient`. * Add `copy_from_dataset()` method to `LibraryClient`. -* Add `create_repository()` method to `ToolShedClient` (thanks to [Helena Rasche)](/src/people/helena-rasche/index.md). +* Add `create_repository()` method to `ToolShedClient` (thanks to [Helena Rasche)](/people/helena-rasche/). * Fix `DatasetClient.download_dataset()` for certain proxied Galaxy deployments. * Make `LibraryClient._get_root_folder_id()` method safer and faster for Galaxy release_13.06 and later. * Deprecate and ignore invalid deleted parameter to `WorkflowClient.get_workflows()`. @@ -34,4 +34,4 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/src/people/enis-afgan/index.md) & [John](/src/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/index.md) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/index.md) +[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) diff --git a/content/news/bioinformatician-freiburg2014/index.md b/content/news/bioinformatician-freiburg2014/index.md index 3b25219790..db6c6c8d27 100644 --- a/content/news/bioinformatician-freiburg2014/index.md +++ b/content/news/bioinformatician-freiburg2014/index.md @@ -46,4 +46,4 @@ Our lab is located in Freiburg, a beautiful university city in the south west of Germany with the Black Forest, France and Switzerland just around the corner and excellent research facilities all over the city. -Please contact [Bjoern Gruening](/src/people/bjoern-gruening/index.md) for further details. +Please contact [Bjoern Gruening](/people/bjoern-gruening/) for further details. diff --git a/content/news/cloud-map/index.md b/content/news/cloud-map/index.md index 68b5fe6f1e..083cd7c8c6 100644 --- a/content/news/cloud-map/index.md +++ b/content/news/cloud-map/index.md @@ -7,7 +7,7 @@ date: "2012-10-15" [CloudMap](http://www.genetics.org/content/early/2012/10/11/genetics.112.144204.1.abstract) is a Galaxy-based pipeline that greatly simplifies the analysis of mutant genome sequences from raw FASTQ reads all the way to mapping plots and short lists of candidate mutations. We demonstrate the utility of CloudMap for WGS analysis of *C. elegans* and *Arabidopsis* genomes and describe how other organisms (e.g. Zebrafish, *Drosophila*) can easily be accommodated. [Automated workflows and extensive video user guides are available](http://usegalaxy.org/cloudmap) to detail the individual analysis steps performed. For details, see -* Gregory Minevich, Danny S. Park, [Daniel Blankenberg](/src/people/dan/index.md), Richard J. Poole and Oliver Hobert1, "[CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences](http://www.genetics.org/content/early/2012/10/11/genetics.112.144204.1)." *[Genetics](http://www.genetics.org/)*. 2012 Oct 11; and +* Gregory Minevich, Danny S. Park, [Daniel Blankenberg](/people/dan/), Richard J. Poole and Oliver Hobert1, "[CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences](http://www.genetics.org/content/early/2012/10/11/genetics.112.144204.1)." *[Genetics](http://www.genetics.org/)*. 2012 Oct 11; and * the [CloudMap Galaxy Page](http://usegalaxy.org/cloudmap) -Greg Minevich and [Dan Blankenberg](/src/people/dan/index.md) +Greg Minevich and [Dan Blankenberg](/people/dan/) diff --git a/content/news/cloudman-release/index.md b/content/news/cloudman-release/index.md index ed3e95cbe2..baa815aa2f 100644 --- a/content/news/cloudman-release/index.md +++ b/content/news/cloudman-release/index.md @@ -23,4 +23,4 @@ For more details on the new features, see the the [CHANGELOG](https://bitbucket. Enjoy and please let us know what you think, -[Enis Afgan](/src/people/enis-afgan/index.md) +[Enis Afgan](/people/enis-afgan/) diff --git a/content/news/cloudman-release201401/index.md b/content/news/cloudman-release201401/index.md index e5a0c33769..ade419305e 100644 --- a/content/news/cloudman-release201401/index.md +++ b/content/news/cloudman-release201401/index.md @@ -32,4 +32,4 @@ For more details on the new features, see the the [CHANGELOG](https://bitbucket. Enjoy and please let us know what you think, -[Enis Afgan](/src/people/enis-afgan/index.md) and [Dannon Baker](/src/people/dannon-baker/index.md) +[Enis Afgan](/people/enis-afgan/index.md) and [Dannon Baker](/src/people/dannon-baker/) diff --git a/content/news/cloudman-release201408/index.md b/content/news/cloudman-release201408/index.md index 1243816454..df0020de6e 100644 --- a/content/news/cloudman-release201408/index.md +++ b/content/news/cloudman-release201408/index.md @@ -26,4 +26,4 @@ For complete details on implemented changes, please see the [source code commits Enjoy and please let us know what you think, -[Enis](/src/people/enis-afgan/index.md) & [Dannon](/src/people/dannon-baker/index.md) & [The Galaxy Team](/src/galaxy-team/index.md) +[Enis](/people/enis-afgan/index.md) & [Dannon](/people/dannon-baker/) & [The Galaxy Team](/src/galaxy-team/) diff --git a/content/news/community-log-board/index.md b/content/news/community-log-board/index.md index 43ec6a8838..e4838152d8 100644 --- a/content/news/community-log-board/index.md +++ b/content/news/community-log-board/index.md @@ -20,4 +20,4 @@ The *[Galaxy Community Log Board](/src/blog/index.md)* is a place to share how y The [Galaxy Community Log Board](/src/blog/index.md) describes how things can be done, and it complements the (also [recently announced](/src/news/galaxy-deployment-catalog/index.md)) *Galaxy Deployments Catalog*, which describes different Galaxy installations. Both the [Log Board](/src/blog/index.md) and the Deployments Catalog came out of discussions at the [GCC2013 GalaxyAdmins Birds-of-a-Feather gathering](/src/events/gcc2013/bof/galaxy-admins/index.md). Thanks to everyone who attended that BoF. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/conda-dependency-codefest-report/index.md b/content/news/conda-dependency-codefest-report/index.md index c9b1230c71..556477a102 100644 --- a/content/news/conda-dependency-codefest-report/index.md +++ b/content/news/conda-dependency-codefest-report/index.md @@ -4,7 +4,7 @@ date: "2016-04-07" --- The [codefest](https://github.com/galaxyproject/tools-iuc/issues/700) started via hangouts at 10am EDT on Monday April 4, with around 8 participants. It was designed to be beginner friendly, which increased contribution from the community. 4 members of the galaxy community were [added as contributors](https://github.com/bioconda/bioconda-recipes/issues/1#issuecomment-205241333) to the [bioconda-recipe repository](https://github.com/bioconda/bioconda-recipes) as a result of this hackathon. -The codefest started with [Björn Grüning](/src/people/bjoern-gruening/index.md) giving a small introduction to [Conda](http://conda.pydata.org/docs/) and its channel [Bioconda](https://bioconda.github.io/). Followed by how to create a new Conda recipe and the scripts involved in it. Members of the hack started by then picking up a simple tool and creating a Pull request against both the [Tools-IUC](https://github.com/galaxyproject/tools-iuc) and [bioconda-recipes](https://github.com/bioconda/bioconda-recipes) repositories on GitHub. +The codefest started with [Björn Grüning](/people/bjoern-gruening/) giving a small introduction to [Conda](http://conda.pydata.org/docs/) and its channel [Bioconda](https://bioconda.github.io/). Followed by how to create a new Conda recipe and the scripts involved in it. Members of the hack started by then picking up a simple tool and creating a Pull request against both the [Tools-IUC](https://github.com/galaxyproject/tools-iuc) and [bioconda-recipes](https://github.com/bioconda/bioconda-recipes) repositories on GitHub. The main aim of the codefest was to get community members familiar with the Conda-Galaxy integration, and to remove tools from testing blacklist (shown below). @@ -38,4 +38,4 @@ Infrastructure: Thanks to everyone who participated! -[Rémi Marenco](/src/people/remi-marenco/index.md). [Nitesh Turaga](/src/people/nitesh-turaga/index.md), and [Björn Grüning](/src/people/bjoern-gruening/index.md) +[Rémi Marenco](/people/remi-marenco/index.md). [Nitesh Turaga](/people/nitesh-turaga/), and [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/news/custom-galaxy-search/index.md b/content/news/custom-galaxy-search/index.md index 85f2e28dbb..b8ae6db2bb 100644 --- a/content/news/custom-galaxy-search/index.md +++ b/content/news/custom-galaxy-search/index.md @@ -21,4 +21,4 @@ We strongly encourage you to give these try. Please send feedback and suggestio Thanks, -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/dev-ops-heidelberg/index.md b/content/news/dev-ops-heidelberg/index.md index 68fe296ae4..108d93c2cf 100644 --- a/content/news/dev-ops-heidelberg/index.md +++ b/content/news/dev-ops-heidelberg/index.md @@ -22,4 +22,4 @@ The workshop is intended for Bioinformaticians who want to For more information please see the [workshop page](https://goo.gl/8dNSdy). -[Björn Grüning](/src/people/bjoern-gruening/index.md) +[Björn Grüning](/people/bjoern-gruening/) diff --git a/content/news/developer-workshop-january23/index.md b/content/news/developer-workshop-january23/index.md index f3d8694c66..55663e2a72 100644 --- a/content/news/developer-workshop-january23/index.md +++ b/content/news/developer-workshop-january23/index.md @@ -17,4 +17,4 @@ This workshop also includes contributed talks from participants. If you have a *15 December is the preferred registration deadline.* However, later registration will certainly be accepted dependent on availability. The registration fee is $200 USD (payment terms provided upon acceptance). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/first2500-papers/index.md b/content/news/first2500-papers/index.md index ea179ed242..c9e48bde38 100644 --- a/content/news/first2500-papers/index.md +++ b/content/news/first2500-papers/index.md @@ -379,4 +379,4 @@ We will continue to report new papers in the [monthly Galaxy newsletters](/src/g In the meantime, I expect the next 2500 papers will be published in considerably less than time than the first 2500. I'm looking forward to all that research -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/g-so-c2014-call/index.md b/content/news/g-so-c2014-call/index.md index 38aa4c42c2..28f436b134 100644 --- a/content/news/g-so-c2014-call/index.md +++ b/content/news/g-so-c2014-call/index.md @@ -13,4 +13,4 @@ The Genome Informatics Group is organizing the joint efforts of Galaxy, [http:// If your interests lean more towards toolkits, I would like to point out that the [Open Bioinformatics Foundation (OBF)](http://open-bio.org), the group behind the *Bio** toolkits (including [BioPython](http://biopython.org/)) and the [BOSC](http://www.open-bio.org/wiki/BOSC_2014) conferences, is also [looking for people to coordinate their proposal](http://lists.open-bio.org/pipermail/open-bio-l/2014-January/000922.html). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-admins-future/index.md b/content/news/galaxy-admins-future/index.md index 2b5eb1ce12..addd3df5cd 100644 --- a/content/news/galaxy-admins-future/index.md +++ b/content/news/galaxy-admins-future/index.md @@ -12,4 +12,4 @@ The [GalaxyAdmins group](/src/community/galaxy-admins/index.md) is coming up on These topics are currently being discussed in email thread. Whatever consensus and plan we reach will be posted to the [wiki page](/src/community/galaxy-admins/future/index.md). Ideally we should have a plan of action in place before [GCC2103](/src/events/gcc2013/index.md) at the end of June. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-at-asms2013/index.md b/content/news/galaxy-at-asms2013/index.md index 799f06e474..73cdf3585f 100644 --- a/content/news/galaxy-at-asms2013/index.md +++ b/content/news/galaxy-at-asms2013/index.md @@ -8,4 +8,4 @@ Galaxy will have a significant presence at the [61st ASMS Conference on Mass Spe If you do research in proteomics than please consider attending. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-at-pag2012/index.md b/content/news/galaxy-at-pag2012/index.md index 3c84deabde..1f74e56b81 100644 --- a/content/news/galaxy-at-pag2012/index.md +++ b/content/news/galaxy-at-pag2012/index.md @@ -6,9 +6,9 @@ date: "2012-01-06" [Plant and Animal Genome XX (PAG2012)](/src/events/pag2012/index.md) starts in San Diego on January 14. If you are attending PAG then you will have (at least) [a half-dozen opportunities](/src/events/pag2012/index.md) to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the [Galaxy @ PAG2012 page](/src/events/pag2012/index.md) and the [conference website](http://www.intlpag.org/) for more information. -Dannon Baker and [Dave Clements](/src/people/dave-clements/index.md) from the [/Galaxy Team](/Galaxy Team) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. +Dannon Baker and [Dave Clements](/people/dave-clements/) from the [/Galaxy Team](/Galaxy Team) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, -[Dave Clements](/src/people/dave-clements/index.md) and Dannon Baker
+[Dave Clements](/people/dave-clements/) and Dannon Baker
[/Galaxy Team](/Galaxy Team) diff --git a/content/news/galaxy-cite-u-like-paper1000/index.md b/content/news/galaxy-cite-u-like-paper1000/index.md index 865f694cb7..02222e1e4c 100644 --- a/content/news/galaxy-cite-u-like-paper1000/index.md +++ b/content/news/galaxy-cite-u-like-paper1000/index.md @@ -80,6 +80,6 @@ Each paper in the group is tagged to indicate how it is related to Galaxy. The The Galaxy CiteULike group was launched 18 months ago. It continues to grow *rapidly.* -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) * These tags were added in 2013 and very few papers before 2013 have been back-curated with them. All the tags are explained on the [CiteULike](/src/publication-library/index.md) page. diff --git a/content/news/galaxy-current-protocols/index.md b/content/news/galaxy-current-protocols/index.md index 97d6ec8c0b..b8829c7ff1 100644 --- a/content/news/galaxy-current-protocols/index.md +++ b/content/news/galaxy-current-protocols/index.md @@ -7,10 +7,10 @@ date: "2012-06-18" Two new Galaxy-related papers are now available in [Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html): **["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html)** - [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Daniel Blankenberg](/src/people/dan/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), [Galaxy Team](/src/galaxy-team/index.md).
+ [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 10.5.

**["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html)** - [Enis Afgan](/src/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/index.md).
+ [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 11.9. Both papers feature hands-on, step by step protocols, accompanied by numerous and detailed figures at each step. diff --git a/content/news/galaxy-czars-first-call/index.md b/content/news/galaxy-czars-first-call/index.md index f518e2c6b0..d712c0c692 100644 --- a/content/news/galaxy-czars-first-call/index.md +++ b/content/news/galaxy-czars-first-call/index.md @@ -14,4 +14,4 @@ The group decided to have calls every other month, with the next on in September Many, many thanks to Ann Black-Ziegelbein for getting the group off to a great start. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-czars-survey/index.md b/content/news/galaxy-czars-survey/index.md index 343b8cd07b..c1dbcb282b 100644 --- a/content/news/galaxy-czars-survey/index.md +++ b/content/news/galaxy-czars-survey/index.md @@ -15,4 +15,4 @@ The email post "[Interested in speaking with other institutions deploying Galaxy The resulting community, now dubbed [GalaxyCzars](/src/community/GalaxyCzars/index.md), welcomes anyone who cares about Galaxy deployments and wants to share their experience, or learn from others. If that describes you, please help us get started by **[taking this short survey](https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ)**. This will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public on the [GalaxyCzars](/src/community/GalaxyCzars/index.md) and [Capacity Planning](/src/admin/capacity-planning/index.md) pages. -[Dave Clements](/src/people/dave-clements/index.md) (channeling Ann Black-Ziegelbein) +[Dave Clements](/people/dave-clements/) (channeling Ann Black-Ziegelbein) diff --git a/content/news/galaxy-deployment-catalog/index.md b/content/news/galaxy-deployment-catalog/index.md index 0ef01c5df9..da59fc9b0a 100644 --- a/content/news/galaxy-deployment-catalog/index.md +++ b/content/news/galaxy-deployment-catalog/index.md @@ -10,6 +10,6 @@ If you have a Galaxy deployment then please take a few minutes to describe your Thanks a bunch, and please let us know if you have any questions. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) *2020-12-04 Update: The Deployment catalog is no longer available.* diff --git a/content/news/galaxy-events-pageand-calendar/index.md b/content/news/galaxy-events-pageand-calendar/index.md index 3d26919838..7d6a879c93 100644 --- a/content/news/galaxy-events-pageand-calendar/index.md +++ b/content/news/galaxy-events-pageand-calendar/index.md @@ -13,4 +13,4 @@ The page also contains a link to the new [Galaxy Events Google Calendar](https:/ If you know of events that either have significant Galaxy content, or are of interest to the overall community, please send them to outreach@galaxyproject.org and they will be added to the [Events](/src/events/index.md) page and the calendar. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-gmod-biocuration2013/index.md b/content/news/galaxy-gmod-biocuration2013/index.md index 18e655c7b5..dfdedbd174 100644 --- a/content/news/galaxy-gmod-biocuration2013/index.md +++ b/content/news/galaxy-gmod-biocuration2013/index.md @@ -16,4 +16,4 @@ The second is that registration is now open for the [2013 GMOD Meeting](http://g Finally, [Biocuration 2013](http://www.ebi.ac.uk/biocuration2013/home) is immediately after the GMOD Meeting, and also in Cambridge. Biocuration will feature a [GO Galaxy Workshop](http://wiki.geneontology.org/index.php/GO_Galaxy_Workshop_at_Biocuration_2013) about using Galaxy to reason with ontologies. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-google-calendars/index.md b/content/news/galaxy-google-calendars/index.md index eca150e3d3..d67c04514b 100644 --- a/content/news/galaxy-google-calendars/index.md +++ b/content/news/galaxy-google-calendars/index.md @@ -18,4 +18,4 @@ This split allows us to present Galaxy events in a much sparser calendar, that i And we will continue to link to past Galaxy events (and presentations, videos, examples, ...) from the *[Events Archive](/src/events/index.md#past-events)*. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-ismb-eccb-bosc2011/index.md b/content/news/galaxy-ismb-eccb-bosc2011/index.md index 8e09ae6fc4..6957b29982 100644 --- a/content/news/galaxy-ismb-eccb-bosc2011/index.md +++ b/content/news/galaxy-ismb-eccb-bosc2011/index.md @@ -13,4 +13,4 @@ either about Galaxy or featuring Galaxy. See the [Events/ISMB-ECCB-BOSC 2011](/ One of the workshops, *Genomics for Non-Model Organisms* is organized by Galaxy and features 4 talks that use Galaxy (including a newly added talk by Marc Bras of INRA that uses Galaxy for SNP detection in grapevine). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-linked-in-group-created/index.md b/content/news/galaxy-linked-in-group-created/index.md index 674600ca99..05d84bb93a 100644 --- a/content/news/galaxy-linked-in-group-created/index.md +++ b/content/news/galaxy-linked-in-group-created/index.md @@ -10,4 +10,4 @@ A [Galaxy Group now exists on LinkedIn](http://bit.ly/gxyLinkedIn). The group i If you are on LinkedIn, please consider [joining the group](http://bit.ly/gxyLinkedIn) today. -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/galaxy-on-mobile/index.md b/content/news/galaxy-on-mobile/index.md index dc80f1e5ff..791184d213 100644 --- a/content/news/galaxy-on-mobile/index.md +++ b/content/news/galaxy-on-mobile/index.md @@ -10,7 +10,7 @@ date: "2016-02-02" The app has been in development for over a year at the University of Oslo as part of [Claus Børnich's masters thesis](https://www.duo.uio.no/handle/10852/44701) and is described in - Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/src/people/marten/index.md), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 + Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, [Martin Čech](/people/marten/), and Geir Kjetil Sandve. [Galaxy Portal: Interacting with the Galaxy platform through mobile devices](http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btw042.abstract). *Bioinformatics* first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 A [user manual](https://github.com/Tarostar/QMLGalaxyPortal/raw/master/GalaxyPortalUserGuide.pdf), additional information, and the full source are [available on GitHub](https://github.com/Tarostar/QMLGalaxyPortal). diff --git a/content/news/galaxy-pag2012/index.md b/content/news/galaxy-pag2012/index.md index 5ac0fce971..a46185681f 100644 --- a/content/news/galaxy-pag2012/index.md +++ b/content/news/galaxy-pag2012/index.md @@ -6,9 +6,9 @@ date: "2012-01-06" [Plant and Animal Genome XX (PAG2012)](/src/events/pag2012/index.md) starts in San Diego on January 14. If you are attending PAG then you will have (at least) [a half-dozen opportunities](/src/events/pag2012/index.md) to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the [Galaxy @ PAG2012 page](/src/events/pag2012/index.md) and the [conference website](http://www.intlpag.org/) for more information. -Dannon Baker and [Dave Clements](/src/people/dave-clements/index.md) from the [Galaxy Team](/src/galaxy-team/index.md) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. +Dannon Baker and [Dave Clements](/people/dave-clements/index.md) from the [Galaxy Team](/src/galaxy-team/) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, -[Dave Clements](/src/people/dave-clements/index.md) and Dannon Baker
+[Dave Clements](/people/dave-clements/) and Dannon Baker
[Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/galaxy-project-grant-support/index.md b/content/news/galaxy-project-grant-support/index.md index 448562de94..ab02ebb048 100644 --- a/content/news/galaxy-project-grant-support/index.md +++ b/content/news/galaxy-project-grant-support/index.md @@ -21,4 +21,4 @@ Any other information you want to provide would be helpful. Not only will this s Many thanks, -[James Taylor](/src/people/james-taylor/index.md) and [Anton Nekrutenko](/src/people/anton/index.md), on behalf of the [Galaxy Team](/src/galaxy-team/index.md) +[James Taylor](/people/james-taylor/index.md) and [Anton Nekrutenko](/people/anton/), on behalf of the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/galaxy-project-openings/index.md b/content/news/galaxy-project-openings/index.md index f656713aff..373cb2077c 100644 --- a/content/news/galaxy-project-openings/index.md +++ b/content/news/galaxy-project-openings/index.md @@ -10,4 +10,4 @@ Galaxy a great project with a [great community](/src/events/gcc2013/index.md). I As always, please let me, or [any of us](/src/galaxy-team/index.md), know if you have any questions. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-tour-de-france2012/index.md b/content/news/galaxy-tour-de-france2012/index.md index 64a2044a1e..3828bc506f 100644 --- a/content/news/galaxy-tour-de-france2012/index.md +++ b/content/news/galaxy-tour-de-france2012/index.md @@ -4,10 +4,10 @@ date: "2012-04-25" ---
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/src/people/nate/index.md), [Anton Nekrutenko](/src/people/anton/index.md) and [James Taylor](/src/people/james-taylor/index.md). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/index.md), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. The Tour is generously sponsored and hosted by the [Laboratoire de Biologie Intégrative des Organismes Marins](http://biom.obs-banyuls.fr/fr/index.html), the [Laboratoire Biométrie et Biologie Evolutive](http://lbbe.univ-lyon1.fr/), and the [Inserm - Mines ParisTech - Institut Curie - Bioinformatics and Computational Systems Biology of Cancer](http://u900.curie.fr/). Further support for the workshops is provided by an [Amazon Web Services (AWS) Education Grant](http://aws.amazon.com/education). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-workshops-in-south-africa/index.md b/content/news/galaxy-workshops-in-south-africa/index.md index 8a8bd57ee3..9378a26b94 100644 --- a/content/news/galaxy-workshops-in-south-africa/index.md +++ b/content/news/galaxy-workshops-in-south-africa/index.md @@ -36,4 +36,4 @@ In addition, there will be a keynote talk on Galaxy at the [South African Geneti **1 July** [Early registration deadline](http://genetics.cmc-uct.co.za/?page_id=7) for the [South African Genetics & Bioinformatics Society Joint Conference](http://genetics.cmc-uct.co.za/) -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/gcc2012-abstract-submission-open/index.md b/content/news/gcc2012-abstract-submission-open/index.md index 334fe56cec..b775ff16d8 100644 --- a/content/news/gcc2012-abstract-submission-open/index.md +++ b/content/news/gcc2012-abstract-submission-open/index.md @@ -17,4 +17,4 @@ See the [GCC2011 program](/src/events/gcc2011/index.md) for an idea of the bread GCC2012 is hosted by the [University of Illinois at Chicago](http://uic.edu/), the [University of Illinois at Urbana-Champaign](http://illinois.edu/), and the [Computation Institute](http://www.ci.anl.gov/). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/gcc2012-registration-is-open/index.md b/content/news/gcc2012-registration-is-open/index.md index 3422e08679..e6d04c3c6b 100644 --- a/content/news/gcc2012-registration-is-open/index.md +++ b/content/news/gcc2012-registration-is-open/index.md @@ -17,4 +17,4 @@ There are several [registration levels](/src/events/gcc2012/register/index.md), GCC2012 is hosted by the [University of Illinois at Chicago](http://uic.edu/), the [University of Illinois at Urbana-Champaign](http://illinois.edu/), and the [Computation Institute](http://www.ci.anl.gov/). -[Dave Clements](/src/people/dave-clements/index.md), on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/index.md) +[Dave Clements](/people/dave-clements/index.md), on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) diff --git a/content/news/gcc2012-registration-open/index.md b/content/news/gcc2012-registration-open/index.md index 130666a896..8103940315 100644 --- a/content/news/gcc2012-registration-open/index.md +++ b/content/news/gcc2012-registration-open/index.md @@ -24,4 +24,4 @@ Finally, [abstract submission](/src/events/gcc2012/abstracts/index.md) is also o Looking forward to seeing you in Chicago! -[Dave Clements](/src/people/dave-clements/index.md) on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/index.md) +[Dave Clements](/people/dave-clements/index.md) on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) diff --git a/content/news/gcc2012-scheduled/index.md b/content/news/gcc2012-scheduled/index.md index 00be66e573..536ccfc7b9 100644 --- a/content/news/gcc2012-scheduled/index.md +++ b/content/news/gcc2012-scheduled/index.md @@ -12,4 +12,4 @@ Some things will be the same as in previous years, but we are also using feedbac Please reserve July 25-27 on your calendars! -[Dave Clements](/src/people/dave-clements/index.md) and [Neil Bahroos](/src/NeilBahroos/index.md) +[Dave Clements](/people/dave-clements/index.md) and [Neil Bahroos](/src/NeilBahroos/) diff --git a/content/news/gcc2014-hackathon/index.md b/content/news/gcc2014-hackathon/index.md index 1e866f81a7..5c7c6ad055 100644 --- a/content/news/gcc2014-hackathon/index.md +++ b/content/news/gcc2014-hackathon/index.md @@ -16,4 +16,4 @@ Finally, we are very happy to have **[Curoverse](https://curoverse.com/) on boar We hope to see you in June, and can't wait to see what we can accomplish! --[Dannon Baker](/src/people/dannon-baker/index.md) on behalf of the [GCC2014 Hackathon Organizing Committee](/src/events/gcc2014/organizers/index.md#hackathon-committee) +-[Dannon Baker](/people/dannon-baker/index.md) on behalf of the [GCC2014 Hackathon Organizing Committee](/src/events/gcc2014/organizers/#hackathon-committee) diff --git a/content/news/gcc2015-data-wrangling-hackathon/index.md b/content/news/gcc2015-data-wrangling-hackathon/index.md index ac921c715f..15c23f573c 100644 --- a/content/news/gcc2015-data-wrangling-hackathon/index.md +++ b/content/news/gcc2015-data-wrangling-hackathon/index.md @@ -12,4 +12,4 @@ We are inviting Galaxy power end-users as well as scientists and bioinformatics Questions, Feedback, or Hack idea? **[Post here](https://biostar.usegalaxy.org/p/12106/)** or contact the Data Hack Organizers. -[Jennifer Hillman Jackson](/src/people/jennifer-jackson/index.md) and the [Data Wrangling Hackathon Organising Committee](http://gcc2015.tsl.ac.uk/organisers/#Data_Wrangling_Hackathon_Committee) +[Jennifer Hillman Jackson](/people/jennifer-jackson/) and the [Data Wrangling Hackathon Organising Committee](http://gcc2015.tsl.ac.uk/organisers/#Data_Wrangling_Hackathon_Committee) diff --git a/content/news/gcc2015-registration-open/index.md b/content/news/gcc2015-registration-open/index.md index bb07de4416..26a426914b 100644 --- a/content/news/gcc2015-registration-open/index.md +++ b/content/news/gcc2015-registration-open/index.md @@ -12,6 +12,6 @@ You can also sign up for [conference housing](http://gcc2015.tsl.ac.uk/logistics We apologize profusely for the delay in opening registration, and we thank you for your patience and faith. We promise the conference will again [be spectacular](/src/galaxy-project/statistics/index.md#events). -[Dave Clements](/src/people/dave-clements/index.md) and [Martin Page](http://www.tsl.ac.uk/staff/martin-page/), on behalf of the [GCC2015 Organising Committee](http://gcc2015.tsl.ac.uk/organisers/). +[Dave Clements](/people/dave-clements/) and [Martin Page](http://www.tsl.ac.uk/staff/martin-page/), on behalf of the [GCC2015 Organising Committee](http://gcc2015.tsl.ac.uk/organisers/). PS: *And don't forget the [poster abstract](http://gcc2015.tsl.ac.uk/Abstracts) submission deadline is 1 May.* diff --git a/content/news/gcc2016-call-for-host/index.md b/content/news/gcc2016-call-for-host/index.md index 2f0e251e9c..4cc6661c4a 100644 --- a/content/news/gcc2016-call-for-host/index.md +++ b/content/news/gcc2016-call-for-host/index.md @@ -36,4 +36,4 @@ Hosts get copious (and enthusiastic) organizational support from Galaxy's Outrea Hoping to work with you in 2016! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/gcc2017-call-for-host/index.md b/content/news/gcc2017-call-for-host/index.md index d2f91b0469..a688f8c078 100644 --- a/content/news/gcc2017-call-for-host/index.md +++ b/content/news/gcc2017-call-for-host/index.md @@ -45,4 +45,4 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2017! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/gcc2018-call-for-host/index.md b/content/news/gcc2018-call-for-host/index.md index 9cf7c26992..7c49440df3 100644 --- a/content/news/gcc2018-call-for-host/index.md +++ b/content/news/gcc2018-call-for-host/index.md @@ -45,4 +45,4 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2018! -[Dave Clements](/src/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/index.md) +[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/gtn-joins-goblet/index.md b/content/news/gtn-joins-goblet/index.md index 0ef04c9949..911136e6d7 100644 --- a/content/news/gtn-joins-goblet/index.md +++ b/content/news/gtn-joins-goblet/index.md @@ -15,12 +15,12 @@ GTN's GOBLET membership will raise the visibility of Galaxy, Galaxy training, an This membership was made possible by a unique arrangement where five GTN members each contributed 20% of the cost of a Bronze Organizational Membership: -* [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), [Friedrich Miescher Institute (FMI)](http://www.fmi.ch/), Switzerland -* [Björn Grüning](/src/people/bjoern-gruening/index.md), [University of Freiburg](http://www.uni-freiburg.de/), Germany +* [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Friedrich Miescher Institute (FMI)](http://www.fmi.ch/), Switzerland +* [Björn Grüning](/people/bjoern-gruening/), [University of Freiburg](http://www.uni-freiburg.de/), Germany * [Mark Crowe](http://www.qfab.org/mark-crowe/), [QFAB](http://www.qfab.org/), Australia * [UC Davis Bioinformatics Core Training Program](http://training.bioinformatics.ucdavis.edu/), United States * [Galaxy Project](http://galaxyproject.org/), United States Many thanks to these GTN members for making this happen, and to the GOBLET Executive for this opportunity. -[Dave Clements](/src/people/dave-clements/index.md), on behalf of the [Galaxy Training Network](https://training.galaxyproject.org/) +[Dave Clements](/people/dave-clements/), on behalf of the [Galaxy Training Network](https://training.galaxyproject.org/) diff --git a/content/news/ismb2011-slides-now-available/index.md b/content/news/ismb2011-slides-now-available/index.md index 81e1732e25..794f929944 100644 --- a/content/news/ismb2011-slides-now-available/index.md +++ b/content/news/ismb2011-slides-now-available/index.md @@ -12,4 +12,4 @@ Slides for for 10 of the Galaxy-related presentations at [ISMB/ECCB/BOSC 2011](/ plus many more. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/iuc-collections-codefest/index.md b/content/news/iuc-collections-codefest/index.md index 8f360106ff..deeb75e2f2 100644 --- a/content/news/iuc-collections-codefest/index.md +++ b/content/news/iuc-collections-codefest/index.md @@ -16,7 +16,7 @@ which the IUC would like to repeat more often. A list of all awesome contributions from all participants is given below. Tools: -* Swap all repeats to multiple='True' where appropriate by [Helena Rasche](/src/people/helena-rasche/index.md) (@erasche) +* Swap all repeats to multiple='True' where appropriate by [Helena Rasche](/people/helena-rasche/) (@erasche) * https://github.com/galaxyproject/tools-iuc/pull/276 * https://github.com/bgruening/galaxytools/issues/246 * https://github.com/galaxyproject/tools-devteam/issues/226 @@ -27,9 +27,9 @@ Tools: * [Trim Galore update to use and produce collections](https://github.com/bgruening/galaxytools/pull/245) * [Most of the unix text processing tools should be collection ready](https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing) * [Michael Crusoe](https://impactstory.org/MichaelRCrusoe) ([@mr-c](https://github.com/mr-c)) worked on the [khmer wrappers to accept and produce collections](https://github.com/galaxyproject/tools-iuc/pull/80) -* To replace most of the repeat parameters we actually needed [support for min/max attributes in the multiple data input parameter](https://github.com/galaxyproject/galaxy/issues/765.), which was implemented in Galaxy by [John Chilton](/src/people/john-chilton/index.md) ([@jmchilton](https://github.com/jmchilton)) +* To replace most of the repeat parameters we actually needed [support for min/max attributes in the multiple data input parameter](https://github.com/galaxyproject/galaxy/issues/765.), which was implemented in Galaxy by [John Chilton](/people/john-chilton/) ([@jmchilton](https://github.com/jmchilton)) * Michael Crusoe (@mr-c) [described more of Galaxy's new collection features in the tool XSD project](https://github.com/JeanFred/Galaxy-XSD/pull/4) which was [integrated in planemo](https://github.com/galaxyproject/planemo/pull/309) -* [John Chilton](/src/people/john-chilton/index.md) (@jmchilton) made significant progress toward [allowing a multiple data parameter to reduce many collections simultaneously](https://github.com/galaxyproject/galaxy/pull/805). This will greatly simplify wrappers such as cuffmerge which includes a confusing repeat for supplying additional dataset lists beyond the first. +* [John Chilton](/people/john-chilton/) (@jmchilton) made significant progress toward [allowing a multiple data parameter to reduce many collections simultaneously](https://github.com/galaxyproject/galaxy/pull/805). This will greatly simplify wrappers such as cuffmerge which includes a confusing repeat for supplying additional dataset lists beyond the first. [Peter Van Heusden](https://twitter.com/pvanheus) (@pvanheus) wrote a nice summary about his experience during the IUC Codefest and data collections in his blog titled ["Adventures in Galaxy output collections"](http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/). diff --git a/content/news/jan2012-distribution-news-brief/index.md b/content/news/jan2012-distribution-news-brief/index.md index b9e6774e34..f9f1386ee9 100644 --- a/content/news/jan2012-distribution-news-brief/index.md +++ b/content/news/jan2012-distribution-news-brief/index.md @@ -21,6 +21,6 @@ upgrade: % hg pull -u -r 63bc46cc73b7 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/jan272012-distribution-news-brief/index.md b/content/news/jan272012-distribution-news-brief/index.md index ee0219a43f..003b832576 100644 --- a/content/news/jan272012-distribution-news-brief/index.md +++ b/content/news/jan272012-distribution-news-brief/index.md @@ -24,6 +24,6 @@ upgrade: % hg pull -u -r 26920e20157f **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/january2012-galaxy-events/index.md b/content/news/january2012-galaxy-events/index.md index c471fdc29f..ec651bb66a 100644 --- a/content/news/january2012-galaxy-events/index.md +++ b/content/news/january2012-galaxy-events/index.md @@ -21,13 +21,13 @@ There are Galaxy-related events on (at least) 3 continents next month:
- + - + @@ -39,7 +39,7 @@ There are Galaxy-related events on (at least) 3 continents next month: - + @@ -54,4 +54,4 @@ There are Galaxy-related events on (at least) 3 continents next month: And I apologize in advance if I messed up the translation of the [event at DDBJ](http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ)! -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/jhu-apl-bioinformaticist/index.md b/content/news/jhu-apl-bioinformaticist/index.md index f64208aa90..b9e57bfe81 100644 --- a/content/news/jhu-apl-bioinformaticist/index.md +++ b/content/news/jhu-apl-bioinformaticist/index.md @@ -9,4 +9,4 @@ The [Johns Hopkins University Applied Physics Laboratory (APL)](http://www.jhuap If you are a US citizen with Unix chops, programming experience, analysis skills, and have "*Familiarity with the Galaxy platform for bioinformatic analysis, to include experience administering a local Galaxy instance*" then please [give them a shout](https://jhuapl.taleo.net/careersection/2/jobdetail.ftl?job=11077). -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/jul202012-distribution-news-brief/index.md b/content/news/jul202012-distribution-news-brief/index.md index 6a3e860c90..7cae4ff88e 100644 --- a/content/news/jul202012-distribution-news-brief/index.md +++ b/content/news/jul202012-distribution-news-brief/index.md @@ -22,6 +22,6 @@ upgrade: % hg pull -u -r ec29ce8e27a1 **Thanks for using Galaxy!** We hope to see everyone in *Chicago* @ **GCC2012**!! -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/liste-de-diffusion-galaxy-france/index.md b/content/news/liste-de-diffusion-galaxy-france/index.md index eecb527c42..a17f264450 100644 --- a/content/news/liste-de-diffusion-galaxy-france/index.md +++ b/content/news/liste-de-diffusion-galaxy-france/index.md @@ -28,6 +28,6 @@ Pour vous aider dans votre utilisation de Galaxy, voici une liste de liens utile A très bientôt sur la liste Galaxy France, -Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/src/people/dave-clements/index.md) & [Jennifer Jackson](/src/people/jennifer-jackson/index.md). +Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/people/dave-clements/index.md) & [Jennifer Jackson](/src/people/jennifer-jackson/). Alban Lermine diff --git a/content/news/mar122012-distribution-news-brief/index.md b/content/news/mar122012-distribution-news-brief/index.md index 5d3f18752c..3e66f19f12 100644 --- a/content/news/mar122012-distribution-news-brief/index.md +++ b/content/news/mar122012-distribution-news-brief/index.md @@ -24,6 +24,6 @@ upgrade: % hg pull -u -r 40f1816d6857 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/may112012-distribution-news-brief/index.md b/content/news/may112012-distribution-news-brief/index.md index bd7c634838..74e1d82661 100644 --- a/content/news/may112012-distribution-news-brief/index.md +++ b/content/news/may112012-distribution-news-brief/index.md @@ -23,6 +23,6 @@ upgrade: % hg pull -u -r 17d57db9a7c0 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/new-galaxy-announce-mailing-list/index.md b/content/news/new-galaxy-announce-mailing-list/index.md index 46e5b45623..c868778e56 100644 --- a/content/news/new-galaxy-announce-mailing-list/index.md +++ b/content/news/new-galaxy-announce-mailing-list/index.md @@ -18,4 +18,4 @@ To subscribe to the list please go to the [Galaxy-Announce Mailman page](http:// See [Mailing Lists](/src/mailing-lists/index.md) for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/new-galaxy-group-cite-u-like/index.md b/content/news/new-galaxy-group-cite-u-like/index.md index 2420c4cdd1..144a619a76 100644 --- a/content/news/new-galaxy-group-cite-u-like/index.md +++ b/content/news/new-galaxy-group-cite-u-like/index.md @@ -12,4 +12,4 @@ If you want to help other Galaxy users and sites find papers that are relevant t *Update: Thanks to the efforts of [Stephen Turner at the University of Virginia](http://twitter.com/genetics_blog), the Galaxy CiteULike group is now mirrored on Mendeley.* -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/nov2011-distribution-news-brief/index.md b/content/news/nov2011-distribution-news-brief/index.md index ff32794b19..f68b71764d 100644 --- a/content/news/nov2011-distribution-news-brief/index.md +++ b/content/news/nov2011-distribution-news-brief/index.md @@ -22,6 +22,6 @@ upgrade: % hg pull -u -r b258de1e6cea **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/november2011-galaxy-events/index.md b/content/news/november2011-galaxy-events/index.md index 5717ffbf5e..11cfb91211 100644 --- a/content/news/november2011-galaxy-events/index.md +++ b/content/news/november2011-galaxy-events/index.md @@ -19,31 +19,31 @@ There are several Galaxy related events going on at Cold Spring Harbor Laborator - + - + - + - + - + @@ -57,4 +57,4 @@ There are several Galaxy related events going on at Cold Spring Harbor Laborator
Thanks,
-[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/oct2011-distribution-news-brief/index.md b/content/news/oct2011-distribution-news-brief/index.md index 13232d4562..420940643f 100644 --- a/content/news/oct2011-distribution-news-brief/index.md +++ b/content/news/oct2011-distribution-news-brief/index.md @@ -22,6 +22,6 @@ upgrade: % hg pull -u -r 338ead4737ba **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/october2011-galaxy-events/index.md b/content/news/october2011-galaxy-events/index.md index 23306dc600..782dcf0559 100644 --- a/content/news/october2011-galaxy-events/index.md +++ b/content/news/october2011-galaxy-events/index.md @@ -22,25 +22,25 @@ There are (at least) three [Galaxy related events](/src/events/index.md) going o - + - + - +
Presentations Galaxy at Pathogen Portal
Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update
Dannon Baker
 Galaxy at Pathogen Portal
Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update
Dannon Baker
Links January 8-21 2012 Workshop on Genomics
Features Galaxy and much more.
 Český Krumlov, Czech Republic James Taylor James Taylor
January 14-18 Galaxy Session @ GMOD Workshop, and
The Galaxy Platform: Running Analyses in the Cloud @ Cloud Computing Session 		PAG 2012, San Diego, California, United States Dave Clements
Dannon Baker 		Dave Clements
Dannon Baker
January 17 January 23 Galaxy Developer Workshop
Application deadline is December 15.
Český Krumlov, Czech Republic, immediately following the Workshop on Genomics, (which also features Galaxy content) James Taylor James Taylor
January 26 November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes Genome Informatics 2011, Cold Spring Harbor, New York, United States Dan Blankenberg Dan Blankenberg
November 8-21 Advanced Sequencing Technologies & Applications Course
Features Galaxy and much more. 		Cold Spring Harbor Laboratory, New York, United States James Taylor James Taylor
November 9-15 Compuational & Comparative Genomics Course
Features Galaxy and much more. 		Cold Spring Harbor Laboratory, New York, United States James Taylor James Taylor
January 8-21 2012 2012 Workshop on Genomics
Features Galaxy and much more.
Application deadline is November 1. 		Český Krumlov, Czech Republic James Taylor James Taylor
January 14-18 2012 Galaxy Session @ GMOD Workshop PAG 2012, San Diego, California, United States Dave Clements Dave Clements
January 17 2012 Exploit your Data: Galaxy and the GMOD Tool Suite AMATA 2011, Canberra, Australia This workshop will cover both Galaxy and provide an overview of the http://gmod.org/wiki/|GMOD tool suite. Many thanks to CSIRO and AMATA for sponsoring this workshop Dave Clements Dave Clements
October 12-14 October 2011 GMOD Meeting and Galaxy Workshop Ontario Institute for Cancer Research (OICR), Toronto, Canada Dan will give a Galaxy update at the meeting, and then lead a satellite workshop on Galaxy the day following the meeting. (Or, if you already know all about Galaxy you could attend workshops on http://gmod.org/wiki/BioMart and http://gmod.org/wiki/InterMine, two data sources for Galaxy.) Register now as the meeting and associated workshop have limited space. Dan Blankenberg Dan Blankenberg
October 23-24 The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool BioVis 2011, Providence, Rhode Island, United States Learn about Trackster and other biological visualization. This is part of VisWeek 2011. Jeremy Goecks Jeremy Goecks

Thanks,
-[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/poweredby-galaxy/index.md b/content/news/poweredby-galaxy/index.md index aae386f54e..1d298ce066 100644 --- a/content/news/poweredby-galaxy/index.md +++ b/content/news/poweredby-galaxy/index.md @@ -13,4 +13,4 @@ This, along with [Citing Galaxy](/src/Citing Galaxy/index.md), are two easy thin Thanks, -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/s-g2014-report/index.md b/content/news/s-g2014-report/index.md index fef7000542..ee26dff08b 100644 --- a/content/news/s-g2014-report/index.md +++ b/content/news/s-g2014-report/index.md @@ -11,8 +11,8 @@ More than 40 people registered for the event, signing up for one, two or all thr The [last day](/src/events/germany2014/index.md) was a very interactive day discussing the latest developments in Galaxy. Have a look at the [wiki pages](/src/events/sg2014/index.md) for copies of the presentations. -We would like to thank for the financial support we got from [SystemsX.ch](http://www.systemsx.ch/) and for all the help we got from the Galaxy team, especially for sending [Dannon](/src/people/dannon-baker/index.md) over to Europe. It was great to have him, and the event profited a lot from him. +We would like to thank for the financial support we got from [SystemsX.ch](http://www.systemsx.ch/) and for all the help we got from the Galaxy team, especially for sending [Dannon](/people/dannon-baker/) over to Europe. It was great to have him, and the event profited a lot from him. Running the event at two different places caused some logistical problems - some participants even learned about European geography. But the event was again a great success and we got a lot of great feedback. We are looking forward to the next Swiss German Galaxy Tour. -[Björn](/src/people/bjoern-gruening/index.md) and [Hans-Rudolf](/src/people/hansrudolf-hotz/index.md) +[Björn](/people/bjoern-gruening/index.md) and [Hans-Rudolf](/src/people/hansrudolf-hotz/) diff --git a/content/news/sep072012-distribution-news-brief/index.md b/content/news/sep072012-distribution-news-brief/index.md index e42806e6ae..5008f95847 100644 --- a/content/news/sep072012-distribution-news-brief/index.md +++ b/content/news/sep072012-distribution-news-brief/index.md @@ -24,6 +24,6 @@ upgrade: $ hg pull -u -r e6444e7a1685 **Thanks for using Galaxy!** -[Jennifer Jackson](/src/people/jennifer-jackson/index.md) +[Jennifer Jackson](/people/jennifer-jackson/) [Galaxy Team](/src/galaxy-team/index.md) diff --git a/content/news/september2011-galaxy-events/index.md b/content/news/september2011-galaxy-events/index.md index 8cd7e485bf..37346acfe0 100644 --- a/content/news/september2011-galaxy-events/index.md +++ b/content/news/september2011-galaxy-events/index.md @@ -19,13 +19,13 @@ There are (at least) three [Galaxy related events](/src/events/index.md) going o September 15-16 Galaxy: A Web-based Platform for Accessible, Reproducible, and Transparent High-throughput Biology and Galaxy Workshop UAB Research Computing Day, Birmingham, Alabama, United States - Jeremy Goecks + Jeremy Goecks September 19-22 Transparent, accessible, reproducible analysis with Galaxy Genome Informatics Workshop @ Beyond the Genome 2011, Washington DC, United States - James Taylor + James Taylor September 22 @@ -39,4 +39,4 @@ There are (at least) three [Galaxy related events](/src/events/index.md) going o See the [Events](/src/events/index.md) page for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach@galaxyproject.org and we will help you get the word out. Thanks,
-[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/south-africa-workshop-tour2013/index.md b/content/news/south-africa-workshop-tour2013/index.md index e7c9ddc160..2baaa64a36 100644 --- a/content/news/south-africa-workshop-tour2013/index.md +++ b/content/news/south-africa-workshop-tour2013/index.md @@ -25,4 +25,4 @@ The [Cape Town event](/src/events/u-cape-town2013/index.md) is hosted by the [Af If you are interested, then please apply by 17 September! -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/updated-galaxy-project.org-site/index.md b/content/news/updated-galaxy-project.org-site/index.md index 56abc8bb49..7cf56f01ff 100644 --- a/content/news/updated-galaxy-project.org-site/index.md +++ b/content/news/updated-galaxy-project.org-site/index.md @@ -16,4 +16,4 @@ Please continue to use these wherever appropriate. Thanks, -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/watchthe-gcc2011-talks-online/index.md b/content/news/watchthe-gcc2011-talks-online/index.md index 98dc0ffc9c..95960b775c 100644 --- a/content/news/watchthe-gcc2011-talks-online/index.md +++ b/content/news/watchthe-gcc2011-talks-online/index.md @@ -7,4 +7,4 @@ NBIC, the host and co-sponsor of the [2011 Galaxy Community Conference (GCC2011) We had several requests for this, and I would like to thank NBIC for making this happen. -[Dave Clements](/src/people/dave-clements/index.md) +[Dave Clements](/people/dave-clements/) diff --git a/content/news/whole-genome-mult-alignments-paper/index.md b/content/news/whole-genome-mult-alignments-paper/index.md index 112c2898af..d99582d77e 100644 --- a/content/news/whole-genome-mult-alignments-paper/index.md +++ b/content/news/whole-genome-mult-alignments-paper/index.md @@ -5,6 +5,6 @@ date: "2011-07-28"
Bioinformatics Jorunal
-A new paper, "[Making whole genome multiple alignments usable for biologists](http://bioinformatics.oxfordjournals.org/content/early/2011/07/19/bioinformatics.btr398.abstract)," by [Daniel Blankenberg](/src/people/dan/index.md), *[et al](/src/galaxy-team/index.md).* has been published (early access) in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface." +A new paper, "[Making whole genome multiple alignments usable for biologists](http://bioinformatics.oxfordjournals.org/content/early/2011/07/19/bioinformatics.btr398.abstract)," by [Daniel Blankenberg](/people/dan/index.md), *[et al](/src/galaxy-team/).* has been published (early access) in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface." The methods are [described on a Galaxy Page](http://usegalaxy.org/u/dan/p/maf) as well. diff --git a/content/news/workshop-zagreb201503/index.md b/content/news/workshop-zagreb201503/index.md index 21474b3159..bdc6875f6f 100644 --- a/content/news/workshop-zagreb201503/index.md +++ b/content/news/workshop-zagreb201503/index.md @@ -12,7 +12,7 @@ date: "2015-02-13"
Ruđer Bošković Institute (RBI)
-This [2-day workshop](http://www.irb.hr/eng/Research/Divisions-and-Centers/Centre-for-Informatics-and-Computing/News/FREE-Workshop-Bioinformatics-Methods-in-Genomics) will cover a spread of topics in genomics. The first day will present a set of lectures and the second day will host two hands-on workshop sessions, including ***Introduction to RNA-Seq analysis with Galaxy*** presented by [Enis Afgan](/src/people/enis-afgan/index.md) & Davor Davidović (RBI). The event will be offered in English. +This [2-day workshop](http://www.irb.hr/eng/Research/Divisions-and-Centers/Centre-for-Informatics-and-Computing/News/FREE-Workshop-Bioinformatics-Methods-in-Genomics) will cover a spread of topics in genomics. The first day will present a set of lectures and the second day will host two hands-on workshop sessions, including ***Introduction to RNA-Seq analysis with Galaxy*** presented by [Enis Afgan](/people/enis-afgan/) & Davor Davidović (RBI). The event will be offered in English. **Who is this for?** diff --git a/content/people/dave-clements/index.md b/content/people/dave-clements/index.md index 09e6645190..30b281b3f3 100644 --- a/content/people/dave-clements/index.md +++ b/content/people/dave-clements/index.md @@ -38,10 +38,10 @@ My pre-bioinformatics career included ## Publications -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/src/people/enis-afgan/index.md), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/src/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Vahid Jalili](/src/people/vahid-jalili/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Daniel Blankenberg](/src/people/dan/index.md). -* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/src/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/index.md), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/index.md), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/index.md), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md). -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/src/people/dan/index.md), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Carl Eberhard](/src/people/carl-eberhard/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Greg Von Kuster](/src/people/greg_vonkuster/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Jeremy Goecks](/src/people/jeremy-goecks/index.md) -* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Daniel Blankenberg](/src/people/dan/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), [Galaxy Team](/src/galaxy-team/index.md) +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/index.md), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). +* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) +* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/) * [The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data](http://database.oxfordjournals.org/content/2011/bar051.full), in *[Database](http://database.oxfordjournals.org/)*, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main * [Organization of the pronephric kidney revealed by large-scale gene expression mapping](http://genomebiology.com/2008/9/5/R84); in *[Genome Biology](http://genomebiology.com/2008/9/5/)*, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli * [A high-resolution anatomical ontology of the developing murine genitourinary tract](https://doi.org/10.1016/j.modgep.2007.03.002); in *[Gene Expression Patterns](http://www.elsevier.com/locate/modgep)*, 7(6), pp. 680-699 (June 2007). Melissa H. Little, Jane Brennan, Kylie Georgas, Jamie A. Davies, Duncan R. Davidson, Richard A. Baldock, Annemiek Beverdam, John F. Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Cullen-McEwen, Jean Fleming, Thierry Gilbert, Doris Herzlinger, Derek Houghton, Matt H. Kaufman, Elena Kleymenova, Peter A. Koopman, Alfor G. Lewis, Andrew P. McMahon, Cathy L. Mendelsohn, Eleanor K. Mitchell, Bree A. Rumballe, Derina E. Sweeney, M. Todd Valerius, Gen Yamada, Yiya Yang and Jing Yu @@ -317,7 +317,7 @@ Are coming, the next time I need to do a biosketch. March 7 - Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam + Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam University of Georgia, Athens, Georgia, United States Slides
diff --git a/content/people/delphine-lariviere/index.md b/content/people/delphine-lariviere/index.md index 2a477f6e13..56e3d7c074 100644 --- a/content/people/delphine-lariviere/index.md +++ b/content/people/delphine-lariviere/index.md @@ -1,5 +1,5 @@
- + Delphine Lariviere
diff --git a/content/people/fubar/index.md b/content/people/fubar/index.md index 29bab8fa76..cc20dc9e85 100644 --- a/content/people/fubar/index.md +++ b/content/people/fubar/index.md @@ -2,7 +2,7 @@ Email: [GG ross.lazarus AT gmail DOT com MMM ](mailto:GG ross.lazarus AT gmail DOT com MMM )
![](/src/images/people/team/ross.jpg)
-Ross Lazarus is an Australian medical academic who served as an Associate Professor in Population Medicine at Harvard Medical School and Director of Bioinformatics at the Channing Laboratory for 12 years before returning to take up a position as Head of Computational Biology at the [BakerIDI](http://www.bakeridi.edu.au/) in Melbourne in 2011. While based at HMS, he badgered [Anton](/src/people/anton/index.md) and [James](/src/people/james-taylor/index.md) until they let him join the very new [Galaxy Team](/src/galaxy-team/index.md) after he was smitten at first sight of the [source code](https://github.com/galaxyproject/galaxy). He helps take care of Picard and other NGS tool wrappers and is developing a [comprehensive toolkit](https://bitbucket.org/fubar/rgalaxy/src/94584ac7c10f/tools/rgenetics) for digital differential expression, exposing edgeR/DESeq, miRDeep2 and GSEA in a convenient way starting with aligned bam files and an interval file specifying contigs for read counts. For those times when you need a few lines of R or python quickly wrapped into a new Galaxy tool for your local users, you might enjoy a Galaxy tool he recently published that [generates new Galaxy tools from scripts](https://bitbucket.org/fubar/galaxytoolfactory/overview). Ross is often responsible for sending grumpy responses to the lists at times when most other team members are asleep*. In preparing for these roles, he has at various times worked as a public health and family physician, public health informatician, NIH/NSF funded researcher, bioinformatician, genetic epidemiologist and computer wonk. +Ross Lazarus is an Australian medical academic who served as an Associate Professor in Population Medicine at Harvard Medical School and Director of Bioinformatics at the Channing Laboratory for 12 years before returning to take up a position as Head of Computational Biology at the [BakerIDI](http://www.bakeridi.edu.au/) in Melbourne in 2011. While based at HMS, he badgered [Anton](/people/anton/index.md) and [James](/people/james-taylor/) until they let him join the very new [Galaxy Team](/src/galaxy-team/) after he was smitten at first sight of the [source code](https://github.com/galaxyproject/galaxy). He helps take care of Picard and other NGS tool wrappers and is developing a [comprehensive toolkit](https://bitbucket.org/fubar/rgalaxy/src/94584ac7c10f/tools/rgenetics) for digital differential expression, exposing edgeR/DESeq, miRDeep2 and GSEA in a convenient way starting with aligned bam files and an interval file specifying contigs for read counts. For those times when you need a few lines of R or python quickly wrapped into a new Galaxy tool for your local users, you might enjoy a Galaxy tool he recently published that [generates new Galaxy tools from scripts](https://bitbucket.org/fubar/galaxytoolfactory/overview). Ross is often responsible for sending grumpy responses to the lists at times when most other team members are asleep*. In preparing for these roles, he has at various times worked as a public health and family physician, public health informatician, NIH/NSF funded researcher, bioinformatician, genetic epidemiologist and computer wonk. diff --git a/content/people/tori-r/index.md b/content/people/tori-r/index.md index df3b638ab0..9b16d4f942 100644 --- a/content/people/tori-r/index.md +++ b/content/people/tori-r/index.md @@ -4,7 +4,7 @@ # Tori I am a 4th grader at [Family School](http://www.family.4j.lane.edu/FamilySchool/Splash.html) in Eugene, Oregon. -I did a programming mentorship with [Dave Clements](/src/people/dave-clements/index.md) to help him updating the Galaxy wiki +I did a programming mentorship with [Dave Clements](/people/dave-clements/) to help him updating the Galaxy wiki less boring and not take so long. diff --git a/content/toolshed/contributions/2015-04/index.md b/content/toolshed/contributions/2015-04/index.md index 6c72b571e8..b75d5401cb 100644 --- a/content/toolshed/contributions/2015-04/index.md +++ b/content/toolshed/contributions/2015-04/index.md @@ -29,7 +29,7 @@ title: April 2015 Tool Shed Contributions * [samtools_calmd](https://toolshed.g2.bx.psu.edu/view/devteam/samtools_calmd): recalculate MD/NM tags Generates the MD tag using ``samtools calmd`` command. * [data_manager_bowtie2_index_builder](https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_bowtie2_index_builder): Data Manager for building bowtie2 indexes Data Manager for building bowtie2 indexes * [samtools_sort](https://toolshed.g2.bx.psu.edu/view/devteam/samtools_sort): Sort alignments by leftmost coordinates or read name. This tool uses the SAMtools toolkit to sort alignments by leftmost coordinates or read names. - * Repository-Maintainer: [Björn Grüning](/src/people/bjoern-gruening/index.md) + * Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/) * Repository-Development: https://github.com/bgruening/galaxytools * [samtools_idxstats](https://toolshed.g2.bx.psu.edu/view/devteam/samtools_idxstats): BAM mapping statistics (using samtools idxstats) Runs "samtools idxstats" to get mapping statistics from a sorted index BAM file as a tabular output file. * [samtools_split](https://toolshed.g2.bx.psu.edu/view/devteam/samtools_split): Split a BAM file by read group This tool runs the samtools split command in the SAMtools toolkit to split BAM files by read group. diff --git a/content/use/basic-sequence/index.md b/content/use/basic-sequence/index.md index 96e5b4f5c4..237021a61f 100644 --- a/content/use/basic-sequence/index.md +++ b/content/use/basic-sequence/index.md @@ -17,5 +17,5 @@ quotas: citations: pub_libraries: sponsors: - - "[Björn Grüning](/src/people/bjoern-gruening/index.md)" + - "[Björn Grüning](/people/bjoern-gruening/)" --- diff --git a/content/use/blast/index.md b/content/use/blast/index.md index bff94a001f..f2f000cd49 100644 --- a/content/use/blast/index.md +++ b/content/use/blast/index.md @@ -17,5 +17,5 @@ quotas: citations: pub_libraries: sponsors: - - "[Björn Grüning](/src/people/bjoern-gruening/index.md) and Peter Cock" + - "[Björn Grüning](/people/bjoern-gruening/) and Peter Cock" --- diff --git a/content/use/ewas-galaxy/index.md b/content/use/ewas-galaxy/index.md index 1cfc4d0545..0631eaada9 100644 --- a/content/use/ewas-galaxy/index.md +++ b/content/use/ewas-galaxy/index.md @@ -15,7 +15,7 @@ user_support: quotas: - "None." citations: - - "[EWAS-Galaxy: a tools suite for population epigenetics integrated into Galaxy](https://doi.org/10.1101/553784 ), Katarzyna Murat, [Björn Grüning](/src/people/bjoern-gruening/index.md), Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J Tobin, Krzysztof Poterlowicz. *bioRxiv* 553784; doi:doi.org/10.1101/553784 " + - "[EWAS-Galaxy: a tools suite for population epigenetics integrated into Galaxy](https://doi.org/10.1101/553784 ), Katarzyna Murat, [Björn Grüning](/people/bjoern-gruening/), Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J Tobin, Krzysztof Poterlowicz. *bioRxiv* 553784; doi:doi.org/10.1101/553784 " pub_libraries: - "EWAS-Galaxy" sponsors: diff --git a/content/use/exome-seq/index.md b/content/use/exome-seq/index.md index 52b5810271..9077745d4c 100644 --- a/content/use/exome-seq/index.md +++ b/content/use/exome-seq/index.md @@ -17,5 +17,5 @@ quotas: citations: pub_libraries: sponsors: - - "[Björn Grüning](/src/people/bjoern-gruening/index.md) and Bérénice Batut" + - "[Björn Grüning](/people/bjoern-gruening/) and Bérénice Batut" --- diff --git a/content/use/g-onramp/index.md b/content/use/g-onramp/index.md index 3cdadbbb7f..561738c3fd 100644 --- a/content/use/g-onramp/index.md +++ b/content/use/g-onramp/index.md @@ -22,7 +22,7 @@ user_support: quotas: - "None" citations: - - "[G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation](https://doi.org/10.1101/499558), Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, [Jeremy Goecks](/src/people/jeremy-goecks/index.md), *bioRxiv* 499558; doi: 10.1101/499558" + - "[G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation](https://doi.org/10.1101/499558), Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, [Jeremy Goecks](/people/jeremy-goecks/), *bioRxiv* 499558; doi: 10.1101/499558" pub_libraries: - "G-OnRamp" sponsors: diff --git a/content/use/galaxy-test/index.md b/content/use/galaxy-test/index.md index 0b59679f2b..598cd0b215 100644 --- a/content/use/galaxy-test/index.md +++ b/content/use/galaxy-test/index.md @@ -16,7 +16,7 @@ user_support: quotas: - "Storage and computational quotas. See [Test](/src/test/index.md) for details" citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/src/people/dan/index.md), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Carl Eberhard](/src/people/carl-eberhard/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Greg Von Kuster](/src/people/greg_vonkuster/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Jeremy Goecks](/src/people/jeremy-goecks/index.md). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "[Project tagged publications](https://www.zotero.org/groups/1732893/galaxy/tags/%2BProject) in [Galaxy Publication library](/src/publication-library/index.md)." - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: diff --git a/content/use/graphclust/index.md b/content/use/graphclust/index.md index f102e08770..bb54b14812 100644 --- a/content/use/graphclust/index.md +++ b/content/use/graphclust/index.md @@ -24,7 +24,7 @@ quotas: - "Docker Container: None" - "Public Server: Storage and computational quotas." citations: - - "[GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering](https://doi.org/10.1101/550335), Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, [Björn Grüning](/src/people/bjoern-gruening/index.md), Rolf Backofen + - "[GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering](https://doi.org/10.1101/550335), Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, [Björn Grüning](/people/bjoern-gruening/), Rolf Backofen *bioRxiv* 550335; doi: 10.1101/550335" pub_libraries: - "GraphClust" diff --git a/content/use/hic-explorer/index.md b/content/use/hic-explorer/index.md index bad74ccc56..c77e9a84fb 100644 --- a/content/use/hic-explorer/index.md +++ b/content/use/hic-explorer/index.md @@ -21,7 +21,7 @@ quotas: - "Storage and computational quotas." citations: - "[Galaxy HiCExplorer: a web server for reproducible -Hi-C data analysis, quality control and visualization](https://academic.oup.com/nar/article/46/W1/W11/5036837), Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, and [Björn A Grüning](/src/people/bjoern-gruening/index.md), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi:10.1093/nar/gky504" +Hi-C data analysis, quality control and visualization](https://academic.oup.com/nar/article/46/W1/W11/5036837), Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, and [Björn A Grüning](/people/bjoern-gruening/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi:10.1093/nar/gky504" pub_libraries: - "HiCExplorer" sponsors: diff --git a/content/use/imaging/index.md b/content/use/imaging/index.md index cd8f5d8851..6ca7f5da62 100644 --- a/content/use/imaging/index.md +++ b/content/use/imaging/index.md @@ -26,6 +26,6 @@ citations: pub_libraries: - "Imaging EU" sponsors: - - "[Greg von Kuster](/src/people/greg_vonkuster/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md) and Thomas Wollmann" + - "[Greg von Kuster](/people/greg_vonkuster/index.md), [Björn Grüning](/src/people/bjoern-gruening/) and Thomas Wollmann" - "The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/freiburg/) but also collectively by groups and individuals from across Europe" --- diff --git a/content/use/metaproteomics-gateway/index.md b/content/use/metaproteomics-gateway/index.md index 37b57dfad5..cc8fc5d135 100644 --- a/content/use/metaproteomics-gateway/index.md +++ b/content/use/metaproteomics-gateway/index.md @@ -18,7 +18,7 @@ quotas: - "Can be accessed anonymously." - "Supports account creation." citations: - - "[Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework](https://doi.org/10.3390/proteomes6010007), Clemens Blank, Caleb Easterly, [Bjoern Gruening](/src/people/bjoern-gruening/index.md), James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. *Proteomes* 2018, 6(1), 7; doi:10.3390/proteomes6010007" + - "[Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework](https://doi.org/10.3390/proteomes6010007), Clemens Blank, Caleb Easterly, [Bjoern Gruening](/people/bjoern-gruening/), James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. *Proteomes* 2018, 6(1), 7; doi:10.3390/proteomes6010007" pub_libraries: - "Metaproteomics Gateway" sponsors: diff --git a/content/use/proteogenomics-gateway/index.md b/content/use/proteogenomics-gateway/index.md index 4adb745c50..07454ae3e4 100644 --- a/content/use/proteogenomics-gateway/index.md +++ b/content/use/proteogenomics-gateway/index.md @@ -17,7 +17,7 @@ quotas: - "Can be accessed anonymously." - "Supports account creation." citations: - - "[An Accessible Proteogenomics Informatics Resource for Cancer Researchers](http://cancerres.aacrjournals.org/content/77/21/e43.long), Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, [Björn Grüning](/src/people/bjoern-gruening/index.md), Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. *Cancer Research*, DOI: 10.1158/0008-5472.CAN-17-0331" + - "[An Accessible Proteogenomics Informatics Resource for Cancer Researchers](http://cancerres.aacrjournals.org/content/77/21/e43.long), Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, [Björn Grüning](/people/bjoern-gruening/), Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. *Cancer Research*, DOI: 10.1158/0008-5472.CAN-17-0331" pub_libraries: - "Proteogenomics Gateway" sponsors: diff --git a/content/use/quantp/index.md b/content/use/quantp/index.md index f46cf0246f..12065669b4 100644 --- a/content/use/quantp/index.md +++ b/content/use/quantp/index.md @@ -17,7 +17,7 @@ user_support: quotas: - "None" citations: - - "[QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics](https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727), Kumar P, Panigrahi P, Johnson J, Weber WJ, Mehta S, Sajulga R, Easterly C, Crooker BA, [Heydarian M](/src/people/mo-heydarian/index.md), Anamika K, Griffin TJ, Jagtap P., *Journal of Proteome Research*, 2018 Dec 24. doi: 10.1021/acs.jproteome.8b00727" + - "[QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics](https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727), Kumar P, Panigrahi P, Johnson J, Weber WJ, Mehta S, Sajulga R, Easterly C, Crooker BA, [Heydarian M](/people/mo-heydarian/), Anamika K, Griffin TJ, Jagtap P., *Journal of Proteome Research*, 2018 Dec 24. doi: 10.1021/acs.jproteome.8b00727" pub_libraries: - "QuanTP" sponsors: diff --git a/content/use/usegalaxy-au/index.md b/content/use/usegalaxy-au/index.md index e8f4da25d7..d7d4bf6431 100644 --- a/content/use/usegalaxy-au/index.md +++ b/content/use/usegalaxy-au/index.md @@ -22,7 +22,7 @@ quotas: - "Registered users get 100GB" - "Australian users get 600GB" citations: - - "[Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140829) [Afgan E](/src/people/enis-afgan/index.md), Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A., *PLoS One.* 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829." + - "[Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140829) [Afgan E](/people/enis-afgan/), Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A., *PLoS One.* 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829." - "[Nectar Virtual Labs investment has huge economic and research impact](https://nectar.org.au/vls-have-huge-economic-research-impact/)" pub_libraries: - "GVL-QLD" diff --git a/content/use/usegalaxy-eu/index.md b/content/use/usegalaxy-eu/index.md index 0362f714d5..099b43e019 100644 --- a/content/use/usegalaxy-eu/index.md +++ b/content/use/usegalaxy-eu/index.md @@ -18,7 +18,7 @@ user_support: quotas: - "Storage and computational quotas." citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/src/people/dan/index.md), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Carl Eberhard](/src/people/carl-eberhard/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Greg Von Kuster](/src/people/greg_vonkuster/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Jeremy Goecks](/src/people/jeremy-goecks/index.md). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.eu" diff --git a/content/use/usegalaxy-org/index.md b/content/use/usegalaxy-org/index.md index 6eca24c670..b600bb404c 100644 --- a/content/use/usegalaxy-org/index.md +++ b/content/use/usegalaxy-org/index.md @@ -11,7 +11,7 @@ summary: "The [Galaxy Project](/galaxy-project/) free public server; biomedical comments: - "Strong on genomics; good central repository for shared Galaxy objects. See [Main](/main/) for more." citations: - - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/src/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/src/people/dave-bouvier/index.md), [Martin Čech](/src/people/marten/index.md), [John Chilton](/src/people/john-chilton/index.md), [Dave Clements](/src/people/dave-clements/index.md), [Nate Coraor](/src/people/nate/index.md), [Björn Grüning](/src/people/bjoern-gruening/index.md), [Aysam Guerler](/src/people/guerler/index.md), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md), [Vahid Jalili](/src/people/vahid-jalili/index.md), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/index.md), [James Taylor](/src/people/james-taylor/index.md), [Anton Nekrutenko](/src/people/anton/index.md), and [Daniel Blankenberg](/src/people/dan/index.md). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" + - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.org" From 88777344be8629304c6e297187a3adc34db0c808 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 16:52:28 -0400 Subject: [PATCH 05/24] More people link fixes --- .../index.md | 2 +- .../dev-news-briefs/2015-01-13/index.md | 4 +- content/blog/2019-07-galaxy-twitter/index.md | 2 +- content/citing-galaxy/index.md | 18 +++--- .../galaxy-admins/meetups/2013-11-20/index.md | 2 +- .../galaxy-admins/meetups/2015-02-19/index.md | 4 +- .../galaxy-admins/meetups/2015-04-16/index.md | 4 +- .../galaxy-admins/meetups/2015-06-18/index.md | 2 +- .../galaxy-admins/meetups/2015-08-20/index.md | 2 +- .../community/galaxy-admins/meetups/index.md | 2 +- content/develop/gsoc/2015-ideas/index.md | 18 +++--- content/events/2017-ismb-bosc/index.md | 4 +- content/events/2018-europe-dev/index.md | 2 +- content/events/2019-04-bioit/index.md | 2 +- content/events/2019-09-gateways/index.md | 2 +- content/events/2019-09-incob/index.md | 2 +- content/events/2019-sacnas/index.md | 4 +- content/events/2020-pag/index.md | 2 +- content/events/archive/wayback/index.md | 64 +++++++++---------- content/events/caltech2013/index.md | 2 +- content/events/eccb2014/index.md | 2 +- .../events/galaxy-tour-de-france2012/index.md | 2 +- content/events/gaw2014/index.md | 2 +- content/events/gcc2012/abstracts/index.md | 4 +- .../breakouts/automation-strategies/index.md | 2 +- .../program/breakouts/end-users/index.md | 4 +- 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content/news/2019-01-galaxy-update/index.md | 8 +-- content/news/2019-02-galaxy-update/index.md | 4 +- content/news/2019-03-galaxy-update/index.md | 2 +- content/news/2019-06-galaxy-update/index.md | 2 +- content/news/2019-08-incob-building/index.md | 2 +- content/news/2019-10-galaxy-update/index.md | 2 +- content/news/2019-10-hacktoberfest/index.md | 2 +- .../index.md | 2 +- content/news/baltimore-meetup201501/index.md | 2 +- content/news/bio-blend-v0.5.2/index.md | 2 +- content/news/bio-blend-v0.5.3/index.md | 2 +- content/news/cloudman-release201401/index.md | 2 +- content/news/cloudman-release201408/index.md | 2 +- .../conda-dependency-codefest-report/index.md | 2 +- .../news/galaxy-current-protocols/index.md | 4 +- .../galaxy-linked-in-group-created/index.md | 2 +- content/news/galaxy-pag2012/index.md | 2 +- .../galaxy-project-grant-support/index.md | 2 +- .../news/galaxy-tour-de-france2012/index.md | 2 +- .../gcc2012-registration-is-open/index.md | 2 +- .../news/gcc2012-registration-open/index.md | 2 +- content/news/gcc2012-scheduled/index.md | 2 +- content/news/gcc2014-hackathon/index.md | 2 +- content/news/gcc2016-call-for-host/index.md | 2 +- content/news/gcc2017-call-for-host/index.md | 2 +- content/news/gcc2018-call-for-host/index.md | 2 +- .../liste-de-diffusion-galaxy-france/index.md | 2 +- content/news/s-g2014-report/index.md | 2 +- .../index.md | 2 +- content/people/dave-clements/index.md | 10 +-- content/people/fubar/index.md | 2 +- content/use/galaxy-test/index.md | 2 +- content/use/imaging/index.md | 2 +- content/use/usegalaxy-eu/index.md | 2 +- content/use/usegalaxy-org/index.md | 2 +- 203 files changed, 387 insertions(+), 387 deletions(-) diff --git a/content/admin/tools/external-display-applications-tutorial/index.md b/content/admin/tools/external-display-applications-tutorial/index.md index 645f40c954..52e1f6e700 100644 --- a/content/admin/tools/external-display-applications-tutorial/index.md +++ b/content/admin/tools/external-display-applications-tutorial/index.md @@ -13,7 +13,7 @@ There are many services available that allow users to upload their own data for ## Citation -If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x * * * diff --git a/content/archive/dev-news-briefs/2015-01-13/index.md b/content/archive/dev-news-briefs/2015-01-13/index.md index 0050e11369..a86484d943 100644 --- a/content/archive/dev-news-briefs/2015-01-13/index.md +++ b/content/archive/dev-news-briefs/2015-01-13/index.md @@ -71,7 +71,7 @@ Galaxy’s mobile interface, in addition to being vulnerable to XSS attacks, has ## IPython Integration -Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/index.md) and [Helena Rasche](/src/people/helena-rasche/), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. +Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/) and [Helena Rasche](/src/people/helena-rasche/), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. ## Tool Form Upgrade (for Beta Testing) @@ -148,7 +148,7 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Fixed composite Datatypes issue related to renaming individual parts of paired Datasets. [https://trello.com/c/ExOMfxtT](https://trello.com/c/ExOMfxtT) 1. Fixed issue where Dataset download links were being incorrectly populated by regenerating `dataset-model` URLs upon fetching (even when silent). Plus a corrections for cases where the `to_ext` value was missing. [https://trello.com/c/ngLd7M4u](https://trello.com/c/ngLd7M4u) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) 1. Fix Slurm job post-mortem for »clusters« functionality added to `slurm-drmaa` (and currently in use on [http://usegalaxy.org](http://usegalaxy.org)). [https://trello.com/c/OuNEdZLc](https://trello.com/c/OuNEdZLc) -1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/people/nicola-soranzo/index.md) & [Björn Grüning](/src/people/bjoern-gruening/). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) +1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/people/nicola-soranzo/) & [Björn Grüning](/src/people/bjoern-gruening/). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) 1. Fixed import bug for `run_reports.sh`. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/ZmTmQTZl](https://trello.com/c/ZmTmQTZl) 1. Fixed a parameter parsing issue in the Data Libraries API (recently introduced while refactoring Data Managers). [https://trello.com/c/1ZTlAVlT](https://trello.com/c/1ZTlAVlT) 1. Corrected a temporary issue where Import was omitted from the original release of `latest_2014.10.06`. [https://trello.com/c/iJwFduar](https://trello.com/c/iJwFduar) diff --git a/content/blog/2019-07-galaxy-twitter/index.md b/content/blog/2019-07-galaxy-twitter/index.md index 4f784a039b..5390b102ad 100644 --- a/content/blog/2019-07-galaxy-twitter/index.md +++ b/content/blog/2019-07-galaxy-twitter/index.md @@ -106,4 +106,4 @@ We recommend [TweetDeck](https://tweetdeck.twitter.com/) for using Twitter. Twe See you on Twitter, -[Dave Clements](/people/dave-clements/index.md), [Martin Cech](/people/marten/index.md), [Mo Heydarian](/src/people/mo-heydarian/), [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) and Nicola Soranzo +[Dave Clements](/people/dave-clements/), [Martin Cech](/people/marten/), [Mo Heydarian](/src/people/mo-heydarian/), [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) and Nicola Soranzo diff --git a/content/citing-galaxy/index.md b/content/citing-galaxy/index.md index ce7d8edcdc..5afcd73fad 100644 --- a/content/citing-galaxy/index.md +++ b/content/citing-galaxy/index.md @@ -40,7 +40,7 @@ Some excellent examples (*emphasis added*): If you use, extend or reference Galaxy in your published work, please cite this publication: -* [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 This and other references are also [available in GitHub](https://github.com/galaxyproject/galaxy/blob/dev/CITATION) as a [CITATION file](http://software-carpentry.org/blog/2013/09/introducing-citation-files.html). @@ -54,37 +54,37 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## Cloud -* [Enis Afgan](/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. +* [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. **[CloudLaunch: Discover and deploy cloud applications](https://doi.org/10.1016/j.future.2018.04.037)**, *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 ## Data Managers -* [Daniel Blankenberg](/people/dan/index.md), James E. Johnson, The [Galaxy Team](/src/galaxy-team/index.md), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 +* [Daniel Blankenberg](/people/dan/), James E. Johnson, The [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 ## DataSource Tools -* [Daniel Blankenberg](/people/dan/index.md), [Nate Coraor](/people/nate/index.md), [Gregory Von Kuster](/people/greg_vonkuster/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. +* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. ## External Display Applications -* [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +* [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x ## Interactive Environments -* [Björn Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 +* [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 ## Reproducibility -* [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/people/john-chilton/index.md), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). +* [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). **[Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014)**, *Cell Systems*, Volume 6, Issue 6, 2018, Pages 631-635, ISSN 2405-4712, doi:10.1016/j.cels.2018.03.014. ## ToolShed -* [Daniel Blankenberg](/people/dan/index.md), [Gregory Von Kuster](/people/greg_vonkuster/index.md), [Emil Bouvier](/people/dave-bouvier/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 +* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 ## Training & Education -* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 ### Online Education diff --git a/content/community/galaxy-admins/meetups/2013-11-20/index.md b/content/community/galaxy-admins/meetups/2013-11-20/index.md index a96933dd43..dda34ec620 100644 --- a/content/community/galaxy-admins/meetups/2013-11-20/index.md +++ b/content/community/galaxy-admins/meetups/2013-11-20/index.md @@ -19,7 +19,7 @@ - + diff --git a/content/community/galaxy-admins/meetups/2015-02-19/index.md b/content/community/galaxy-admins/meetups/2015-02-19/index.md index 70facd57f1..35562d277a 100644 --- a/content/community/galaxy-admins/meetups/2015-02-19/index.md +++ b/content/community/galaxy-admins/meetups/2015-02-19/index.md @@ -20,7 +20,7 @@ - + @@ -33,7 +33,7 @@ # GalaxyAdmins is Back! -Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Thanks to the efforts of [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/) *is back.* Starting in February 2015, we will resume our bi-monthly web meetups. +Except for a [meetup at GCC2014](/src/events/gcc2014/bofs/galaxy-admins/index.md), the [GalaxyAdmins group](/src/community/galaxy-admins/index.md) has been hiatus for a while. Thanks to the efforts of [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), the [GalaxyAdmins group](/src/community/galaxy-admins/) *is back.* Starting in February 2015, we will resume our bi-monthly web meetups. *[GalaxyAdmins](/src/community/galaxy-admins/index.md)* is a discussion group for Galaxy community members who are responsible for Galaxy installations. diff --git a/content/community/galaxy-admins/meetups/2015-04-16/index.md b/content/community/galaxy-admins/meetups/2015-04-16/index.md index 680a9d292f..ec719c8002 100644 --- a/content/community/galaxy-admins/meetups/2015-04-16/index.md +++ b/content/community/galaxy-admins/meetups/2015-04-16/index.md @@ -20,7 +20,7 @@ - + @@ -41,7 +41,7 @@ ## Galaxy Project Update: Galaxy's new tool form support -[Sam Guerler](/people/guerler/index.md) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work to update Galaxy's tool forms. +[Sam Guerler](/people/guerler/) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work to update Galaxy's tool forms. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/2015-06-18/index.md b/content/community/galaxy-admins/meetups/2015-06-18/index.md index abdadf4264..8df6120b78 100644 --- a/content/community/galaxy-admins/meetups/2015-06-18/index.md +++ b/content/community/galaxy-admins/meetups/2015-06-18/index.md @@ -20,7 +20,7 @@ - + diff --git a/content/community/galaxy-admins/meetups/2015-08-20/index.md b/content/community/galaxy-admins/meetups/2015-08-20/index.md index fc265aa8d4..9b0186cf42 100644 --- a/content/community/galaxy-admins/meetups/2015-08-20/index.md +++ b/content/community/galaxy-admins/meetups/2015-08-20/index.md @@ -45,7 +45,7 @@ ## Adding transparency and automation into the Galaxy tool installation process -[Enis Afgan](/people/enis-afgan/index.md) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work on *[Adding transparency and automation into the Galaxy tool installation process](https://github.com/afgane/ansible-tools)* via Ansible. The talk will discuss process of unifying the tool installation approach within the Galaxy project and how it can be used by anyone to to install potentially hundreds of tools in an automated fashion. +[Enis Afgan](/people/enis-afgan/) of the [Galaxy Team](/src/galaxy-team/) will discuss recent work on *[Adding transparency and automation into the Galaxy tool installation process](https://github.com/afgane/ansible-tools)* via Ansible. The talk will discuss process of unifying the tool installation approach within the Galaxy project and how it can be used by anyone to to install potentially hundreds of tools in an automated fashion. ## Call Technology diff --git a/content/community/galaxy-admins/meetups/index.md b/content/community/galaxy-admins/meetups/index.md index 34abee0a13..c8c0370f68 100644 --- a/content/community/galaxy-admins/meetups/index.md +++ b/content/community/galaxy-admins/meetups/index.md @@ -66,7 +66,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * [2013-03-20 Web Meetup](/src/community/galaxy-admins/meetups/2013-03-20/index.md) * [Hailiang Leon Mei](mailto:hailiang DOT mei AT nbic DOT nl) discuss NBIC's recent experiences deploying the [NBIC Galaxy](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/). [Dan Blankenberg](/people/dan/) discusses the new release policy and upcoming *Data Manager* features. * [2013-01-16 Web Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) - * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/people/greg_vonkuster/index.md) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/) + * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/people/greg_vonkuster/) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/) **2012** diff --git a/content/develop/gsoc/2015-ideas/index.md b/content/develop/gsoc/2015-ideas/index.md index 0f1a9be8c6..aa3cf518bd 100644 --- a/content/develop/gsoc/2015-ideas/index.md +++ b/content/develop/gsoc/2015-ideas/index.md @@ -32,7 +32,7 @@ Galaxy supports running jobs in Docker containers for running jobs on a single n **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy and/or Kubernetes, bioinformatics knowledge -**Possible Mentors** Kyle Ellrott, [John Chilton](/people/john-chilton/index.md), [Dannon Baker](/src/people/dannon-baker/) +**Possible Mentors** Kyle Ellrott, [John Chilton](/people/john-chilton/), [Dannon Baker](/src/people/dannon-baker/) ## GA4GH Container and Workflows Integration @@ -53,7 +53,7 @@ The [Global Alliance for Genomics Health](http://genomicsandhealth.org/) (GA4GH) **Potentially Helpful Skills** Familiarity with Galaxy and/or other Workflow Management Systems -**Possible Mentors** [John Chilton](/people/john-chilton/index.md), [Daniel Blankenberg](/src/people/dan/) +**Possible Mentors** [John Chilton](/people/john-chilton/), [Daniel Blankenberg](/src/people/dan/) ## Docker Swarm and Compose @@ -75,7 +75,7 @@ By making complex applications easier to deploy and doing so reproducibly, the o **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy, Docker, and/or Fig, bioinformatics knowledge -**Possible Mentors** [John Chilton](/people/john-chilton/index.md), [Björn Grüning](/people/bjoern-gruening/), [Dannon Baker](/src/people/dannon-baker/) +**Possible Mentors** [John Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), [Dannon Baker](/src/people/dannon-baker/) ## Fostering Bioconductor Collaborations @@ -92,7 +92,7 @@ The [RGalaxy](http://www.bioconductor.org/packages/release/bioc/html/RGalaxy.htm * Implement automated scripts (for use with cron jobs or CI tools such as Jenkins or Buildbot) to automate the release and publication of such artifacts. * Build and publish workflows demonstrating these tools with actual data. -**Possible Mentors** [Nitesh Turaga](/people/nitesh-turaga/index.md), [Björn Grüning](/src/people/bjoern-gruening/), Daniel Blankenberg +**Possible Mentors** [Nitesh Turaga](/people/nitesh-turaga/), [Björn Grüning](/src/people/bjoern-gruening/), Daniel Blankenberg **Required Skills** Python programming @@ -244,7 +244,7 @@ Once familiar with pages - there are at least two paths this project could diver **Potentially Helpful Skills** Familiarity with Galaxy and IPython -**Possible Mentors** [Carl Eberhard](/people/carl-eberhard/index.md), [Martin Cech](/src/people/marten/) +**Possible Mentors** [Carl Eberhard](/people/carl-eberhard/), [Martin Cech](/src/people/marten/) ## Easier or More Robust History Imports and Exports @@ -266,7 +266,7 @@ that can be pasted into an import the history from another Galaxy instance. * Split this process in pieces to allow tracking/resuming the transfers. * Rework the API and UI to provide pleasant progress bar tracking progress and estimating time remaining. -**Possible Mentors** [Martin Cech](/people/marten/index.md), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/src/people/dan/) +**Possible Mentors** [Martin Cech](/people/marten/), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/src/people/dan/) **Required Skills** Python programming @@ -303,7 +303,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Convert Galaxy to run on Python 3. * Once all dependencies are upgraded, package Galaxy for [Debian Med](https://www.debian.org/devel/debian-med/). -**Possible Mentors** [Nate Coraor](/people/nate/index.md), [Tim Booth](https://github.com/tbooth), [John Chilton](/src/people/john-chilton/) +**Possible Mentors** [Nate Coraor](/people/nate/), [Tim Booth](https://github.com/tbooth), [John Chilton](/src/people/john-chilton/) **Required Skills:** * Knowledge of DPKG, BASH scripting, Makefiles, and the layout of files on a standard Linux filesystem (/etc, /var, /usr, ...) @@ -326,7 +326,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Integrate the authentication mechanism with [Globus Nexus](https://www.globus.org/platform/services). -**Possible Mentors** [Martin Cech](/people/marten/index.md), [Enis Afgan](/people/enis-afgan/), [Nitesh Turaga](/src/people/nitesh-turaga/) +**Possible Mentors** [Martin Cech](/people/marten/), [Enis Afgan](/people/enis-afgan/), [Nitesh Turaga](/src/people/nitesh-turaga/) **Required Skills** Python Programming @@ -371,7 +371,7 @@ Recently Interactive Environments (IEs) were developed for Galaxy. These consist * Unit test framework for IEs to ensure the proxy works ([some progress](https://github.com/hexylena/vagrant-galaxy-casperjs) exists but it's not very generic). -**Possible Mentors** [Helena Rasche](/people/helena-rasche/index.md), [John Chilton](/src/people/john-chilton/) +**Possible Mentors** [Helena Rasche](/people/helena-rasche/), [John Chilton](/src/people/john-chilton/) **Required Skills** Docker, NodeJS diff --git a/content/events/2017-ismb-bosc/index.md b/content/events/2017-ismb-bosc/index.md index d45d08482c..43a39305cb 100644 --- a/content/events/2017-ismb-bosc/index.md +++ b/content/events/2017-ismb-bosc/index.md @@ -19,7 +19,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | -| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | +| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | ## 22 July, Saturday @@ -51,7 +51,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | -| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Bjorn Gruning](/src/people/bjoern-gruening/), [James Taylor](/src/people/james-taylor/) | Meeting Hall V | | +| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/), [James Taylor](/src/people/james-taylor/) | Meeting Hall V | | | 18:00 | [B-079: Development of a bioinformatics pipeline for the routine analysis of viral whole genome sequencing data](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=H#B-079) | Qiang Fu | Congress Foyer, Level 2 | [Poster]( https://depot.galaxyproject.org/hub/attachments/documents/posters/2017_ismb_viral_wgs_fu.pdf) | | 18:00 | [B-365: Comparison of open source (galaxy based) and commercial pipelines for RNA-Seq data analysis](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=P#B-365) | Slave Trajanoski | Congress Foyer, Level 2 | [Poster](https://depot.galaxyproject.org/hub/attachments/documents/posters/ismb2017-trajanoski.pdf) | | 20:00 | [Galaxy Community Dinner](http://bit.ly/gxyismb2017bdinner) | [Martin Čech](/people/marten/) | [VYŠEHRADSKÝ RESTAURANT KANDELÁBR](http://bit.ly/gxyismb2017bdinner) | | diff --git a/content/events/2018-europe-dev/index.md b/content/events/2018-europe-dev/index.md index 5331a928f2..06b7d2b59e 100644 --- a/content/events/2018-europe-dev/index.md +++ b/content/events/2018-europe-dev/index.md @@ -132,5 +132,5 @@ http://www.vag-freiburg.de/fahrplan-linien/netzplaene/liniennetzplan.html ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) (hrh@fmi.ch) or [Björn Grüning](/people/bjoern-gruening/) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/src/people/jeanfrancois-dufayard/) (jean-francois.dufayard@cirad.fr) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) (hrh@fmi.ch) or [Björn Grüning](/people/bjoern-gruening/) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/src/people/jeanfrancois-dufayard/) (jean-francois.dufayard@cirad.fr) diff --git a/content/events/2019-04-bioit/index.md b/content/events/2019-04-bioit/index.md index 22914abd18..74102678e8 100644 --- a/content/events/2019-04-bioit/index.md +++ b/content/events/2019-04-bioit/index.md @@ -21,5 +21,5 @@ Going to [BioIT World 2019](https://www.bio-itworldexpo.com/)? Galaxy is there | Mon 4/15 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 4:15 | Hackathon Report Outs: Integrating Globus into Galaxy to Enable FAIRifying Data | Track 6: FAIR Data | Globus Genomics | -| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/people/enis-afgan/index.md) & [Vahid Jalili](/src/people/vahid-jalili/) | +| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/people/enis-afgan/) & [Vahid Jalili](/src/people/vahid-jalili/) | | Thu 4/18 | 10:40 | [Longitudinal and Context Visualization for Precision Oncology](http://www.giiconference.com/chi653337/data-visualization.shtml) | Track 8: Data Visualization & Exploration Tools | [Jeremy Goecks](/people/jeremy-goecks/) | diff --git a/content/events/2019-09-gateways/index.md b/content/events/2019-09-gateways/index.md index 023d97083c..c123ed75d6 100644 --- a/content/events/2019-09-gateways/index.md +++ b/content/events/2019-09-gateways/index.md @@ -22,6 +22,6 @@ There are several Galaxy related presentations at [Gateways 2019](https://scienc ## Find out more -Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/people/mo-heydarian/index.md) or [Dave Clements](/src/people/dave-clements/). +Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/people/mo-heydarian/) or [Dave Clements](/src/people/dave-clements/). diff --git a/content/events/2019-09-incob/index.md b/content/events/2019-09-incob/index.md index 0e187a46f9..dabbc7c2da 100644 --- a/content/events/2019-09-incob/index.md +++ b/content/events/2019-09-incob/index.md @@ -52,4 +52,4 @@ The session will conclude with a commitment to grow a community of interested pa Galaxy is a widely used and deployed open-source platform that integrates thousands of analysis tools, and supports data integration and analysis, workflow creation, data visualization, and sharing and publishing your analyses and pipelines. Galaxy is also *a global community* of researchers, programmers, trainers, and users all doing and supporting data intensive research. Interested? Then we hope to see you at INCOB.
-[Dave Clements](/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) +[Dave Clements](/people/dave-clements/), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) diff --git a/content/events/2019-sacnas/index.md b/content/events/2019-sacnas/index.md index f6e1e06727..15ac13e8e8 100644 --- a/content/events/2019-sacnas/index.md +++ b/content/events/2019-sacnas/index.md @@ -56,8 +56,8 @@ The goals of this workshop are to ## Instructors -- [Dave Clements](/people/dave-clements/index.md), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) -- [Mo Heydarian](/people/mo-heydarian/index.md), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) +- [Dave Clements](/people/dave-clements/), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) +- [Mo Heydarian](/people/mo-heydarian/), [Galaxy Project](/src/) and [Johns Hopkins University](http://jhu.edu) ## Registration diff --git a/content/events/2020-pag/index.md b/content/events/2020-pag/index.md index a77df0739a..37aec4719b 100644 --- a/content/events/2020-pag/index.md +++ b/content/events/2020-pag/index.md @@ -35,4 +35,4 @@ In addition, there was be a [GMOD Codefest](http://gmod.org/wiki/Codefest_2020) | | 7:13-7:25 | [Eukaryotic Pathogen, Vector & Host Informatics Resources (VEuPathDB) - a Merged International Approach Towards Achieving Sustainability](https://plan.core-apps.com/pag_2020/event/06b15a6d8bf3d42e3dbaf3d39ebad5d7) | [Data Resource Sustainability and Funding](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb048f4a), East 1 | | [Jessica Kissinger](http://mango.ctegd.uga.edu/jkissingLab/) | | **Tuesday, January 14** | 4:00-4:20 | **[Introduction to Galaxy and the Galaxy Ecosystem](https://plan.core-apps.com/pag_2020/event/a8f1e9dbae7dc0d6d1e5f05d4657f89d)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-intro-slides.pdf) | [Dave Clements](/people/dave-clements/) | | | 4:20-4:50 | **[Galaxy for Excellence in Breeding](https://plan.core-apps.com/pag_2020/event/0faacece23744ad32bb082ce6b8c5e27)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-eib-slides.pdf) | [Star Yanxin Gao](https://twitter.com/stargao3) | -| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/people/mo-heydarian/index.md), [Dave Clements](/src/people/dave-clements/), Umesh Rosyara, Jose Crossa, Mathias Lorieux | +| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/people/mo-heydarian/), [Dave Clements](/src/people/dave-clements/), Umesh Rosyara, Jose Crossa, Mathias Lorieux | diff --git a/content/events/archive/wayback/index.md b/content/events/archive/wayback/index.md index 2186052b03..2f8caf67a1 100644 --- a/content/events/archive/wayback/index.md +++ b/content/events/archive/wayback/index.md @@ -97,7 +97,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -237,7 +237,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -258,7 +258,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -272,7 +272,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -418,7 +418,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -564,7 +564,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -745,7 +745,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -787,7 +787,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -872,7 +872,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -904,7 +904,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1126,7 +1126,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1217,7 +1217,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1556,7 +1556,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1680,7 +1680,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1790,7 +1790,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1893,7 +1893,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -1992,14 +1992,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + - + @@ -2038,7 +2038,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -2444,7 +2444,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -2889,7 +2889,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -2910,7 +2910,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -2941,7 +2941,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -3165,7 +3165,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -3298,7 +3298,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -3371,7 +3371,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -3458,7 +3458,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -3634,7 +3634,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -4008,7 +4008,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -4040,7 +4040,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -4259,7 +4259,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + @@ -4634,7 +4634,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + diff --git a/content/events/caltech2013/index.md b/content/events/caltech2013/index.md index 357e619d19..3285cf0c15 100644 --- a/content/events/caltech2013/index.md +++ b/content/events/caltech2013/index.md @@ -89,7 +89,7 @@ This workshop is generously supported by an [AWS in Education](http://aws.amazon **[Dave Clements](/people/dave-clements/)**
**Emory University**

-This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/people/dannon-baker/index.md) and [Nate Coraor](/src/people/nate/), two members of the [core Galaxy development team](/src/galaxy-team/). +This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/people/dannon-baker/) and [Nate Coraor](/src/people/nate/), two members of the [core Galaxy development team](/src/galaxy-team/). *This discussion is open to any member of the Caltech community. It is free, but space is limited and advanced registration is strongly encouraged.* diff --git a/content/events/eccb2014/index.md b/content/events/eccb2014/index.md index 2bb562ea35..50e0c24cd0 100644 --- a/content/events/eccb2014/index.md +++ b/content/events/eccb2014/index.md @@ -68,6 +68,6 @@ There were several sessions and posters featuring Galaxy at the [13th European C - +
Presentations GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
 GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
Links
Topics GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
 GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
Links
Topics IU Galaxies - tips and tricks (Slides)
Carrie Ganote, National Center for Genome Analysis Support (NCGAS), Pervasive Technology Institute, Indiana University
Galaxy Project Update: Galaxy's new tool form support (Slides)
Aysam Guerler, Galaxy, Johns Hopkins University
 IU Galaxies - tips and tricks (Slides)
Carrie Ganote, National Center for Genome Analysis Support (NCGAS), Pervasive Technology Institute, Indiana University
Galaxy Project Update: Galaxy's new tool form support (Slides)
Aysam Guerler, Galaxy, Johns Hopkins University
Links
Topics Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
Links December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online Dannon Baker, Dave Clements Dannon Baker, Dave Clements
October 25-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy Dannon Baker, Björn Grüning Dannon Baker, Björn Grüning
October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening Hans-Rudolf Hotz and Bjoern Gruening
October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening Hans-Rudolf Hotz and Bjoern Gruening
August 18 GalaxyAdmins Web Meetup Around the World Online Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements Slides
June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements Slides
April 21 The Galaxy Portal: Accessing Galaxy from Mobile Devices and Tool Development Developments Around the World GalaxyAdmins Web Meetup, Online Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz
April 4 IUC Hackathon - Conda dependencies Around the World Online Björn Grüning, Rémi Marenco, Nitesh Turaga Björn Grüning, Rémi Marenco, Nitesh Turaga
February 18 GalaxyAdmins Web Meetup Around the World Online Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements
January 21, 22 Introduction to Galaxy Workshop North America Icahn School of Medicine at Mt. Sinai, New York, New York, United States
Training offered by GTN Member
Dave Clements, Andrew Sharp
Training offered by GTN Member
Dave Clements, Andrew Sharp 		Slides
November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States
Training offered by GTN Member
Dan Blankenberg, John Chilton
Training offered by GTN Member
Dan Blankenberg, John Chilton
October 15 October Galaxy Admins Meetup Around the World Online David Kovalic, Hans-Rudolf Hotz, Dave Clements David Kovalic, Hans-Rudolf Hotz, Dave Clements Video, Slides
June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester Around the World June 2015 GalaxyAdmins Web Meetup, Online Peter Briggs, John Chilton, Hans-Rudolf Hotz Peter Briggs, John Chilton, Hans-Rudolf Hotz Slides
May 15 RNA-Seq Galaxy Workshop North America Penn State University, State College, Pennsylvania, United States
Training offered by GTN Member
Martin Cech, Anton Nekrutenko
Training offered by GTN Member
Martin Cech, Anton Nekrutenko 		Slides
April 16 GalaxyAdmins April 2015 Meetup Online Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler Slides, video
March 17 Using Galaxy Workshop Penn State University, State College, Pennsylvania, United States
Training offered by GTN Member
Martin Cech, Anton Nekrutenko
Training offered by GTN Member
Martin Cech, Anton Nekrutenko
February 19 February 2015 GalaxyAdmins Web Meetup Online Hans-Rudolf Hotz, Dave Clements Hans-Rudolf Hotz, Dave Clements Slides, Video
February 18 Baltimore Area Galaxy Meetup Baltimore, Maryland, United States Enis Afgan, Nitesh Turaga Enis Afgan, Nitesh Turaga Slides
January 22 Baltimore Area Galaxy Meetup
This meetup is now full.
 Baltimore, Maryland, United States Enis Afgan, Nitesh Turaga Enis Afgan, Nitesh Turaga Slides
Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany Slides Hans-Rudolf Hotz and Bjoern Gruening Hans-Rudolf Hotz and Bjoern Gruening
(second Swiss) Galaxy Workshop Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
 Drosophila Research Conference, San Diego, California, United States Anton Nekrutenko, Jen Jackson Anton Nekrutenko, Jen Jackson
March 24-25 Galaxy Workshop University of Georgia, Athens, Georgia, United States Slides Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam
Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States Anton Nekrutenko, JamesTaylor Anton Nekrutenko, JamesTaylor
February 10-14 November GalaxyAdmins Meetup Online Slides, Screencast Dave Clements, Srinivas Maddhi, Nate Coraor Dave Clements, Srinivas Maddhi, Nate Coraor
November 19
High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
 Polymorphism Detection and Visualization Anton Nekrutenko, Jennifer Jackson Anton Nekrutenko, Jennifer Jackson
Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States Galaxy 101 NGS: Introduction to Polymorphism Detection, Managing a Local Galaxy Instance Anton Nekrutenko, Jennifer Jackson, Anushka Brownley Anton Nekrutenko, Jennifer Jackson, Anushka Brownley
October 14-18 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia Ross Lazarus, Dan Blankenberg Ross Lazarus, Dan Blankenberg
September 27 WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 6-7 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Slides
Tutorial 		Jeremy Goecks, Jennifer Jackson Jeremy Goecks, Jennifer Jackson
Working with High-Throughput Data and Data Visualization Galaxy 101 and RNA-seq Analysis and Visualization QB3 - Computational Genomics Resource Laboratory, Univ of California Berkeley Slides
Tutorials: Galaxy101, RNA-seq		 Jeremy Goecks, Jennifer Jackson Jeremy Goecks, Jennifer Jackson
October 28 - November 2 Galaxy Tour de France 2012 Perpignan, Montpellier, Lyon, Paris Nate Coraor, Anton Nekrutenko, JamesTaylor Nate Coraor, Anton Nekrutenko, JamesTaylor
May 23-25 Management and Analysis of Second and Third Generation Sequencing Data with Galaxy
AGBT 2011 		Marco Island, Florida, United States Slides Anton Nekrutenko, James Taylor Anton Nekrutenko, James Taylor
January 15-19 14:00-14:30 ID02: A panel of European Public Galaxy Instances
1. Galaxy Project Introduction
2. deepTools: user-friendly tools for data visualization
3. The Nebula ChIP-Seq web service
4. The French Institute of Bioinformatics (IFB) academic cloud infrastructure for life sciences
1. Slides
2. Slides 		Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet
diff --git a/content/events/galaxy-tour-de-france2012/index.md b/content/events/galaxy-tour-de-france2012/index.md index 6273af66aa..85431f43af 100644 --- a/content/events/galaxy-tour-de-france2012/index.md +++ b/content/events/galaxy-tour-de-france2012/index.md @@ -110,7 +110,7 @@ If you attend both workshops and plan to eat in the area, there are many choices ## Meet the Team! -
Nate Coraor!   Anton Nekrutenko!   James Taylor!
+
Nate Coraor!   Anton Nekrutenko!   James Taylor!
* [Nate Coraor](/people/nate/) * [Anton Nekrutenko](/people/anton/) diff --git a/content/events/gaw2014/index.md b/content/events/gaw2014/index.md index adc7f59616..2735d363fc 100644 --- a/content/events/gaw2014/index.md +++ b/content/events/gaw2014/index.md @@ -87,7 +87,7 @@ GAW 2014 also included poster session and keynote speakers. 16:20-17:00 - Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan + Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index 21aa6a5181..2b98c3727b 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -18,7 +18,7 @@ Abstracts for talks that were presented at the [GCC2012 main sessions](/src/even
 
-**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -229,7 +229,7 @@ Contact: support@oqtans.org; ratschg@mskcc.org
-**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/people/dan/index.md)2, [Anton Nekrutenko](/src/people/anton/)2 and Oliver Hobert1
+**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/people/dan/)2, [Anton Nekrutenko](/src/people/anton/)2 and Oliver Hobert1
1 Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
2 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA, USA
diff --git a/content/events/gcc2012/program/breakouts/automation-strategies/index.md b/content/events/gcc2012/program/breakouts/automation-strategies/index.md index 323f42553c..d3437cf820 100644 --- a/content/events/gcc2012/program/breakouts/automation-strategies/index.md +++ b/content/events/gcc2012/program/breakouts/automation-strategies/index.md @@ -7,7 +7,7 @@ title: Automation strategies for Data, Tools, & Config -A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/people/john-chilton/index.md), [Enis Afgan](/people/enis-afgan/index.md), [Dave Bouvier](/src/people/dave-bouvier/) and [Jen Jackson](/src/people/jennifer-jackson/) +A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/people/john-chilton/), [Enis Afgan](/people/enis-afgan/), [Dave Bouvier](/src/people/dave-bouvier/) and [Jen Jackson](/src/people/jennifer-jackson/) This involves turning the base Galaxy into a production machine: * download of associated genomes and data files, diff --git a/content/events/gcc2012/program/breakouts/end-users/index.md b/content/events/gcc2012/program/breakouts/end-users/index.md index ef407f775f..d0b9757699 100644 --- a/content/events/gcc2012/program/breakouts/end-users/index.md +++ b/content/events/gcc2012/program/breakouts/end-users/index.md @@ -15,11 +15,11 @@ title: Galaxy End Users * Karen Reddy * -* [Anton](/people/anton/index.md), [Dan](/people/dan/index.md), Rémi, and [Jen](/src/people/jennifer-jackson/) from [Galaxy Team](/src/galaxy-team/) +* [Anton](/people/anton/), [Dan](/people/dan/), Rémi, and [Jen](/src/people/jennifer-jackson/) from [Galaxy Team](/src/galaxy-team/) # Notes -These are a merged grouping of [Anton's](/people/anton/index.md), [Dan's](/people/dan/), and [Jen's](/src/people/jennifer-jackson/) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. +These are a merged grouping of [Anton's](/people/anton/), [Dan's](/people/dan/), and [Jen's](/src/people/jennifer-jackson/) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. ## Platforms diff --git a/content/events/gcc2012/program/breakouts/index.md b/content/events/gcc2012/program/breakouts/index.md index 71f490c621..6fc051cf8e 100644 --- a/content/events/gcc2012/program/breakouts/index.md +++ b/content/events/gcc2012/program/breakouts/index.md @@ -5,7 +5,7 @@ Breakouts are informal, open discussion sessions where participants interested i GalaxyCzars
Ann Black-Ziegelbein - Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson + Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson Bioinformatics Training and Teaching with Galaxy
Dave Clements diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index 4d0b0878d5..68f9da3883 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -35,9 +35,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -46,7 +46,7 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 11:00 WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
WS6: Galaxy API
Dannon Baker
@@ -55,9 +55,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 @@ -84,7 +84,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | **8:00-9:00** | Continental Breakfast, Registration Open | | **9:00-9:10** | **Welcome:** [William Hendrickson](http://www.uic.edu/depts/mcmi/faculty/hendrickson/), [University of Illinois at Chicago (UIC)](http://www/uic.edu/) | | **9:10-10:40** | **Session 1:** Moderator: [Tin Lap Lee](http://www.sbs.cuhk.edu.hk/TeachingStaffDetails.asp?TE_NAME=LEE%20Tin%20Lap), [Chinese University of Hong Kong](http://www.cuhk.edu.hk/) | -| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/people/anton/index.md) and [James Taylor](/src/people/james-taylor/), Galaxy Project
| +| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/), Galaxy Project
| | 9:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Luo.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 31:55)*
*[Integration of S-MART, a toolbox to aid RNA-seq data analysis in Galaxy](/src/events/gcc2012/abstracts/index.md#integration-of-s-mart-a-toolbox-to-aid-rna-seq-data-analysis-in-galaxy)*
Yufei Luo, Unité de recherche en Génomique-Info, INRA
| | 10:00 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Park.pdf), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ xx:yy), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5)*
*[Connecting Galaxy to a Data Repository](/src/events/gcc2012/abstracts/index.md#connecting-galaxy-to-a-data-repository)*
Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School
| | 10:20 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/MaillolDufayard.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5) (starts @ 11:45)*
*[Role of Galaxy in a bioinformatic plant breeding platform](/src/events/gcc2012/abstracts/index.md#role-of-galaxy-in-a-bioinformatic-plant-breeding-platform)*
Vincent Maillol and Jean-Francois Dufayard, INRA and CIRAD
| @@ -142,7 +142,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.ppt), Video*
*Galaxy-P*
Pratik Jagtap, University of Minnesota
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Sandve.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421)*
*The Genomic Hyperbrowser: Prove Your Point*
Geir Kjetil Sandve, University of Oslo
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Gruning.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 6:10)*
*[ChemicalToolBox](/src/chemical-tool-box/index.md)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| -| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/index.md), Penn State University, [James Taylor](/src/people/james-taylor/), Emory University
| +| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/), Penn State University, [James Taylor](/src/people/james-taylor/), Emory University
| | **2:55-3:15** | **Break** | | **3:15-5:00** | **Session 8: Breakouts**
Moderator: Dave Clements, [Emory University](http://www.emory.edu/)
[Breakouts](/src/eents/gcc2012/program/breakouts/index.md) | | **5:00** | **[2012 Galaxy Community Conference](/src/events/gcc2012/index.md) ends** | diff --git a/content/events/gcc2012/sponsorships/index.md b/content/events/gcc2012/sponsorships/index.md index 688096e915..a6ba7fbcb1 100644 --- a/content/events/gcc2012/sponsorships/index.md +++ b/content/events/gcc2012/sponsorships/index.md @@ -16,7 +16,7 @@ Sponsorships are available at four different levels. Ion Torrent - Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss + Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss diff --git a/content/events/gcc2012/training-day/index.md b/content/events/gcc2012/training-day/index.md index 55bf71c920..0c95a11d00 100644 --- a/content/events/gcc2012/training-day/index.md +++ b/content/events/gcc2012/training-day/index.md @@ -29,9 +29,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -40,7 +40,7 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 11:00 WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
WS6: Galaxy API
Dannon Baker
@@ -49,9 +49,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index 1ce639dfb9..bee3bf198c 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -39,7 +39,7 @@ Victoria is an assistant professor of [Statistics](http://www.stat.columbia.edu/
-**[Ross Lazarus](/people/fubar/index.md)1**, Antony Kaspi1, Mark Ziemann1 and The [Galaxy Team](/src/galaxy-team/) 2. +**[Ross Lazarus](/people/fubar/)1**, Antony Kaspi1, Mark Ziemann1 and The [Galaxy Team](/src/galaxy-team/) 2. 1 BakerIDI Heart and Diabetes Research Institute, 75 Commercial Rd, Melbourne, VIC 3004, Australia
2 http://wiki.galaxyproject.org[/GalaxyTeam](/src/events/gcc2013/abstracts/talks/GalaxyTeam/index.md) @@ -271,7 +271,7 @@ Ion Torrent has invented the first device—a new semiconductor chip—capable o
 
-**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -430,7 +430,7 @@ We will present an overview of the requirements to move Galaxy into the Clinical
Greg Von Kuster
-**[Greg von Kuster](/people/greg_vonkuster/index.md)**, [Daniel Blankenberg](/src/people/dan/) +**[Greg von Kuster](/people/greg_vonkuster/)**, [Daniel Blankenberg](/src/people/dan/) Penn State / Galaxy Team *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/VonKusterToolShed.pdf), [Vimeo](https://vimeo.com/74347850)* @@ -451,7 +451,7 @@ To ensure the quality of the Tool Shed and the available contributed Utilities,
-**[Carl Eberhard](/people/carl-eberhard/index.md)**1, [Jeremy Goecks](/people/jeremy-goecks/index.md)1, [The Galaxy Team](/src/galaxy-team/index.md)1,2, [Anton Nekrutenko](/src/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 +**[Carl Eberhard](/people/carl-eberhard/)**1, [Jeremy Goecks](/people/jeremy-goecks/)1, [The Galaxy Team](/src/galaxy-team/)1,2, [Anton Nekrutenko](/src/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 1 Emory University
2 Penn State University @@ -486,7 +486,7 @@ Data Managers can be defined locally or installed automatically from a Tool Shed
-**[Dannon Baker](/people/dannon-baker/index.md)**1, [Nate Coraor](/people/nate/)2, [John Chilton](/src/people/john-chilton/)3 +**[Dannon Baker](/people/dannon-baker/)**1, [Nate Coraor](/people/nate/)2, [John Chilton](/src/people/john-chilton/)3 1 Emory University
2 Penn State
diff --git a/content/events/gcc2013/lightning/index.md b/content/events/gcc2013/lightning/index.md index ae4146581f..3501125bdf 100644 --- a/content/events/gcc2013/lightning/index.md +++ b/content/events/gcc2013/lightning/index.md @@ -7,7 +7,7 @@ title: Lightning Talks -Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/people/fubar/index.md)) and [Session 8 on Tuesday](/src/events/gcc2013/program/index.md#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/)). **No more than half the lightning talk slots will be allocated before the meeting.** +Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/people/fubar/)) and [Session 8 on Tuesday](/src/events/gcc2013/program/#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/)). **No more than half the lightning talk slots will be allocated before the meeting.** If you wish to give a lightning talk, please send an abstract to [GCC2013 Scientific Committee](mailto:gcc2013-sci AT galaxyproject DOT org), either * any time before the start of [Session 2](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (to be considered for Monday or Tuesday slots), or diff --git a/content/events/gcc2013/program/index.md b/content/events/gcc2013/program/index.md index 6a182a3b07..e0a6ac0b08 100644 --- a/content/events/gcc2013/program/index.md +++ b/content/events/gcc2013/program/index.md @@ -33,11 +33,11 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 9:00 - Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
+ Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
- Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00 @@ -45,11 +45,11 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 12:30 - The Galaxy API
Nate Coraor, Carl Eberhard
- Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
+ The Galaxy API
Nate Coraor, Carl Eberhard
+ Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30 @@ -57,8 +57,8 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 15:00 - Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
- Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
+ Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
+ Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
@@ -297,7 +297,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - + diff --git a/content/events/gcc2013/training-day/index.md b/content/events/gcc2013/training-day/index.md index 2f66e311b9..7f15b03ea8 100644 --- a/content/events/gcc2013/training-day/index.md +++ b/content/events/gcc2013/training-day/index.md @@ -39,11 +39,11 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - + - - + + @@ -51,11 +51,11 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - - + + - + @@ -63,8 +63,8 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - - + + @@ -114,7 +114,7 @@ See each individual workshop's list of prerequisite for specifics.
9:10
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
9:40
9:00 Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
 Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
 Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
 Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00
12:30 The Galaxy API
Nate Coraor, Carl Eberhard
 Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
 The Galaxy API
Nate Coraor, Carl Eberhard
 Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
 RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30
15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
- + @@ -144,7 +144,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University 		Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University
Content
- + @@ -336,7 +336,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University 		Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University
Content
- + @@ -371,7 +371,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI 		Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI
Content
- + @@ -405,7 +405,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University 		Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University
Content
- + @@ -446,7 +446,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University 		Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University
Content
- + @@ -480,7 +480,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Nate Coraor, Penn State University
Carl Eberhard, Emory University 		Nate Coraor, Penn State University
Carl Eberhard, Emory University
Content
- + diff --git a/content/events/gcc2014/abstracts/talks/index.md b/content/events/gcc2014/abstracts/talks/index.md index eeba71c826..cbef643d60 100644 --- a/content/events/gcc2014/abstracts/talks/index.md +++ b/content/events/gcc2014/abstracts/talks/index.md @@ -136,7 +136,7 @@ As a trusted industry leader in designing and implementing effective scientific
 
-**[Anton Nekrutenko](/people/anton/index.md)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -167,7 +167,7 @@ An overview of where the Galaxy Project is and where it is going.
Greg Von Kuster
-**[Greg von Kuster](/people/greg_vonkuster/index.md)1** and the [Galaxy Team](/src/galaxy-team/) +**[Greg von Kuster](/people/greg_vonkuster/)1** and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu/), State College, Pennsylvania, United States
@@ -230,7 +230,7 @@ We present a Galaxy based web server for processing and visualizing deeply seque
GCC2014 Hackathon Participants
-**[Dannon Baker](/people/dannon-baker/index.md)1, [Brad Chapman](http://bcbio.wordpress.com/)2, [John Chilton](/people/john-chilton/)3, [Kyle Ellrott](http://www.soe.ucsc.edu/people/kellrott)4, and [GCC2014 Hackathon Participants](/src/events/gcc2014/hackathon/)** +**[Dannon Baker](/people/dannon-baker/)1, [Brad Chapman](http://bcbio.wordpress.com/)2, [John Chilton](/people/john-chilton/)3, [Kyle Ellrott](http://www.soe.ucsc.edu/people/kellrott)4, and [GCC2014 Hackathon Participants](/src/events/gcc2014/hackathon/)** 1 [Johns Hopkins University](http://jhu.edu/), Baltimore Maryland, United States
2 [Harvard University](http://harvard.edu), Cambridge, Massachusetts, United States
@@ -249,7 +249,7 @@ In this talk, we’ll very briefly describe our Galaxy Hackathon goals and provi
Dan Blenkenberg
-**[Daniel Blankenberg](/people/dan/index.md)1** and the [Galaxy Team](/src/galaxy-team/)2 +**[Daniel Blankenberg](/people/dan/)1** and the [Galaxy Team](/src/galaxy-team/)21 [Penn State University](http://psu.edu), State College, Pennsylvania, United States
2 [http://galaxyproject.org/](http://galaxyproject.org/) @@ -268,7 +268,7 @@ Here, we describe a new set of resources that aim to rectify this situation. The
John Chilton
-**[John Chilton](/people/john-chilton/index.md)1** and the [Galaxy Team](/src/galaxy-team/) +**[John Chilton](/people/john-chilton/)1** and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu), State College, Pennsylvania, United States @@ -303,7 +303,7 @@ Dataset collections are a powerful new feature that greatly enhance the expressi
Martin Čech
-**[Martin Čech](/people/marten/index.md)1**, [Pavel Švéda](http://www.linkedin.com/in/pavelsveda)1, [Ondřej Fabián](https://www.linkedin.com/pub/ondrej-fabian/33/6a5/1b8)1 and the [Galaxy Team](/src/galaxy-team/) +**[Martin Čech](/people/marten/)1**, [Pavel Švéda](http://www.linkedin.com/in/pavelsveda)1, [Ondřej Fabián](https://www.linkedin.com/pub/ondrej-fabian/33/6a5/1b8)1 and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu), State College, Pennsylvania, United States diff --git a/content/events/gcc2014/bofs/heterogeneous/index.md b/content/events/gcc2014/bofs/heterogeneous/index.md index da1bca27b3..75b8b5073e 100644 --- a/content/events/gcc2014/bofs/heterogeneous/index.md +++ b/content/events/gcc2014/bofs/heterogeneous/index.md @@ -13,7 +13,7 @@ When: Tuesday, July 1, 5:45pm Where: Salon A -Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/people/john-chilton/index.md), [Nate Coraor](/src/people/nate/), Carrie Ganote +Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Carrie Ganote ## Description diff --git a/content/events/gcc2014/program/index.md b/content/events/gcc2014/program/index.md index 69434e1e45..ac64f08bb6 100644 --- a/content/events/gcc2014/program/index.md +++ b/content/events/gcc2014/program/index.md @@ -40,10 +40,10 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + - + @@ -53,7 +53,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -66,7 +66,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -197,7 +197,7 @@ Moderator: [Liisa Koski](https://www.linkedin.com/pub/liisa-koski/70/164/b0b), [
Instructors James Taylor, Emory University
Nate Coraor, Penn State University 		James Taylor, Emory University
Nate Coraor, Penn State University
Content
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
 3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
- + @@ -315,7 +315,7 @@ Moderator: [Mohammad Heydarian](http://epigenetics.jhu.edu/?section=personnelPag - + diff --git a/content/events/gcc2014/training-day/admin-walkthrough/index.md b/content/events/gcc2014/training-day/admin-walkthrough/index.md index 4c9a409f61..d5736ab6a0 100644 --- a/content/events/gcc2014/training-day/admin-walkthrough/index.md +++ b/content/events/gcc2014/training-day/admin-walkthrough/index.md @@ -9,7 +9,7 @@ title: "Tutorial: Galaxy Installation and Administration"
GCC2014 Training Day
-[Nate Coraor](/people/nate/index.md) and [John Chilton](/src/people/john-chilton/) +[Nate Coraor](/people/nate/) and [John Chilton](/src/people/john-chilton/)
diff --git a/content/events/gcc2014/training-day/index.md b/content/events/gcc2014/training-day/index.md index fbe5b1c922..e240422651 100644 --- a/content/events/gcc2014/training-day/index.md +++ b/content/events/gcc2014/training-day/index.md @@ -36,10 +36,10 @@ Meeting participants select which Training Day topics to attend when they [regis - + - + @@ -49,7 +49,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -62,7 +62,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -212,7 +212,7 @@ See each individual workshop's list of prerequisite for specifics.
1:15 State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
1:50
9:10 The GCC2014 Hackathon
Dannon Baker, Brad Chapman, John Chilton, Kyle Ellrott, and GCC2014 Hackathon Participants
The GCC2014 Hackathon
Dannon Baker, Brad Chapman, John Chilton, Kyle Ellrott, and GCC2014 Hackathon Participants
9:30
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
 3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
- + @@ -257,7 +257,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Jeremy Goecks, George Washington University
Aysam Guerler, Johns Hopkins University 		Jeremy Goecks, George Washington University
Aysam Guerler, Johns Hopkins University
Content
- + @@ -306,7 +306,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Nate Coraor, Penn State University
John Chilton, Penn State University 		Nate Coraor, Penn State University
John Chilton, Penn State University
Content
- + diff --git a/content/events/gcc2015/bofs/galaxy-admins/index.md b/content/events/gcc2015/bofs/galaxy-admins/index.md index 52e80d3f2a..b123adc9e3 100644 --- a/content/events/gcc2015/bofs/galaxy-admins/index.md +++ b/content/events/gcc2015/bofs/galaxy-admins/index.md @@ -17,7 +17,7 @@ When:: Tuesday, 7 July, 18:20 Where:: Franklin Room, JICCC -Contact:: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), [Dave Clements](/src/people/dave-clements/) +Contact:: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Dave Clements](/src/people/dave-clements/) # Audience @@ -102,4 +102,4 @@ This BoF will meet on **Tuesday, 7 July at 18:20, in the Franklin Room, at the J # Questions? -Send them to [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/) +Send them to [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/src/people/dave-clements/) diff --git a/content/events/germany2014/index.md b/content/events/germany2014/index.md index 40c80a4d9f..bce3092490 100644 --- a/content/events/germany2014/index.md +++ b/content/events/germany2014/index.md @@ -39,4 +39,4 @@ We have created a [small map of places to find food and drinks](https://mapsengi ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/germany2016/index.md b/content/events/germany2016/index.md index f659d0ee18..691a6ef033 100644 --- a/content/events/germany2016/index.md +++ b/content/events/germany2016/index.md @@ -39,4 +39,4 @@ Please let us know what you are interesting in. ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/indiana-u2012/index.md b/content/events/indiana-u2012/index.md index c834e4dcdf..cf89d97250 100644 --- a/content/events/indiana-u2012/index.md +++ b/content/events/indiana-u2012/index.md @@ -110,7 +110,7 @@ This is a hands-on workshop. **Please bring a wifi-enabled laptop with a curren **[Dave Clements](/people/dave-clements/)**
**Emory University**

-This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/index.md) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/people/nate/) and [Dannon Baker](/src/people/dannon-baker/) of the Galaxy development team. +This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/people/nate/) and [Dannon Baker](/src/people/dannon-baker/) of the Galaxy development team. *Registration is open to any member of the Indiana University community. The workshop is free, but space is limited and advanced registration is required.* diff --git a/content/events/ismb2012/index.md b/content/events/ismb2012/index.md index 1c1728dc49..f34eb29ead 100644 --- a/content/events/ismb2012/index.md +++ b/content/events/ismb2012/index.md @@ -19,7 +19,7 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B - + diff --git a/content/events/meetups/baltimore/2015-01-22/index.md b/content/events/meetups/baltimore/2015-01-22/index.md index 2097e71cc0..b45e34b62f 100644 --- a/content/events/meetups/baltimore/2015-01-22/index.md +++ b/content/events/meetups/baltimore/2015-01-22/index.md @@ -13,7 +13,7 @@ The first Galaxy meetup or social gathering held in Baltimore was sold out. It w The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis](/people/enis-afgan/index.md) & [Nitesh](/src/people/nitesh-turaga/) +[Enis](/people/enis-afgan/) & [Nitesh](/src/people/nitesh-turaga/) ## There's a meetup! @@ -21,7 +21,7 @@ Hey Everyone, We are looking forward to kicking off our first [Galaxy Project](http://galaxyproject.org) Meetup! We will meet at one of the Galaxy project hubs - the Department of Biology of Johns Hopkins University for a general introduction to Galaxy in form of a social gathering. This will be an informal meeting open to anyone interested in data analysis, tools, computer infrastructure, programming - regardless. -[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be kicking things off with a discussion on Galaxy and how researchers around the world are leveraging it. +[Enis Afgan](/people/enis-afgan/) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be kicking things off with a discussion on Galaxy and how researchers around the world are leveraging it. Thanks and hope to see you there! diff --git a/content/events/meetups/baltimore/2015-02-18/index.md b/content/events/meetups/baltimore/2015-02-18/index.md index 6b6e769d58..937ed92ddc 100644 --- a/content/events/meetups/baltimore/2015-02-18/index.md +++ b/content/events/meetups/baltimore/2015-02-18/index.md @@ -12,7 +12,7 @@ Hey Everyone, We are looking forward to a [follow-up Meetup](https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22) by the [Galaxy Project](http://galaxyproject.org)! We will meet at one of the Galaxy project hubs - the Department of Biology of Johns Hopkins University. This time around, we will briefly take a look at how to get started using Galaxy. Again, this will be an informal meeting open to anyone interested in data analysis, tools, computer infrastructure, programming. -[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be delivering a short introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint (and will be available for any additional questions). +[Enis Afgan](/people/enis-afgan/) and [Nitesh Turaga](/people/nitesh-turaga/) of the [Galaxy team](/src/galaxy-team/) will be delivering a short introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint (and will be available for any additional questions). Thanks and hope to see you there! diff --git a/content/events/meetups/psu/2015-03/index.md b/content/events/meetups/psu/2015-03/index.md index c3a6fde365..fc1da5d2b3 100644 --- a/content/events/meetups/psu/2015-03/index.md +++ b/content/events/meetups/psu/2015-03/index.md @@ -8,7 +8,7 @@ title: March 2015 Penn State Using Galaxy Workshop Hey Everyone, This will be an informal meeting open to anyone interested in data analysis, genomic tools and biology workflows. -[Anton Nekrutenko](/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint. Multiple Galaxy Team members will be available for any additional questions. +[Anton Nekrutenko](/people/anton/) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to the resources available to start using the Galaxy application from a practitioner's viewpoint. Multiple Galaxy Team members will be available for any additional questions. Thanks and hope to see you there! diff --git a/content/events/meetups/psu/2015-05/index.md b/content/events/meetups/psu/2015-05/index.md index 5b574083ad..72ba6fab00 100644 --- a/content/events/meetups/psu/2015-05/index.md +++ b/content/events/meetups/psu/2015-05/index.md @@ -12,7 +12,7 @@ title: May 2015 Penn State RNA-Seq Galaxy Workshop Hey Everyone, This meeting is open to anyone interested in RNA-Seq analysis and biology workflows. -[Anton Nekrutenko](/people/anton/index.md) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to RNA-Seq resources available at Galaxy from a practitioner's viewpoint. +[Anton Nekrutenko](/people/anton/) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to RNA-Seq resources available at Galaxy from a practitioner's viewpoint. [Galaxy Team members](/src/galaxy-team/index.md) will be available for any additional questions. diff --git a/content/events/sg2014/index.md b/content/events/sg2014/index.md index bbd4c87495..8b33720619 100644 --- a/content/events/sg2014/index.md +++ b/content/events/sg2014/index.md @@ -10,7 +10,7 @@ title: Swiss German Galaxy Tour 2014 There will be a *Swiss-German Galaxy Tour* this fall featuring a range of events over 3 days in two locations. ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Events @@ -39,4 +39,4 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/sg2016/index.md b/content/events/sg2016/index.md index 7b5bafcb39..df03c2fe4a 100644 --- a/content/events/sg2016/index.md +++ b/content/events/sg2016/index.md @@ -51,4 +51,4 @@ The [second day](/src/events/germany2016/index.md), October 21st, is ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/switzerland2014/index.md b/content/events/switzerland2014/index.md index 6fbc2d7e70..85e18c58c3 100644 --- a/content/events/switzerland2014/index.md +++ b/content/events/switzerland2014/index.md @@ -27,7 +27,7 @@ Following the workshop, we organise a [Developers Day](/src/events/germany2014/i ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Preliminary Schedule @@ -35,7 +35,7 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | | 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/SG2014T__State_of_the_Galaxy.pdf) | | 10:30 - 10:50 | coffee Break | | 10:50 - 11:40 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | Galaxy: putting pieces together | [whiteboard](/src/events/switzerland2014/Bjoern_whiteboard.jpg) | @@ -48,7 +48,7 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf | 15:00 - 15:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Using Galaxy for NGS analysis in a collaborative environment | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/hrh_20141001.pdf) | | 15:30 - 15:45 | Tim-Christoph Roloff ([FMI](http://www.fmi.ch/)) | Genomics analysis at FMI | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Galaxy_Workshop_Bern_2014_Tim_Roloff.pdf) | | 15:45 - 16:00 | Torsten Houwaart ([University of Freiburg](http://www.uni-freiburg.de/)) | RNA structure visualized in Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Torsten_Bern01.10.2014.pdf) | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | @@ -69,4 +69,4 @@ This workshop is generously supported by [SyBIT](https://wiki.systemsx.ch/displa ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/switzerland2014/trainingday/index.md b/content/events/switzerland2014/trainingday/index.md index 26575abf6a..69a52a960f 100644 --- a/content/events/switzerland2014/trainingday/index.md +++ b/content/events/switzerland2014/trainingday/index.md @@ -27,7 +27,7 @@ Topics covered: | Time | Speaker | Title | Type | Slides | | ---- | -------- | ------ | ----- | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:40 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | +| 9:30 - 9:40 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | | 9:40 - 9:50 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | demo | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/intro_20140930.pdf) | | 9:50 - 10:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | datatypes, histories, datasets, tools, data sharing | hands-on | | | 10:30 - 11:00 | coffee Break | @@ -38,7 +38,7 @@ Topics covered: | 14:40 - 15:00| coffee Break | | 15:00 - 15:30 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | NGS-analaysis: a Chip-Seq example | hands-on | | | 15:30 - 16:00 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | visualizations | hands-on | | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | This schedule will most likely change. It will be adapted according to the progress we make during the day @@ -50,7 +50,7 @@ The training day will be held in the [UniS-Building (room: A -119) of the Univer ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you.
diff --git a/content/events/switzerland2016/index.md b/content/events/switzerland2016/index.md index 6186a0833c..d35eaafd77 100644 --- a/content/events/switzerland2016/index.md +++ b/content/events/switzerland2016/index.md @@ -20,7 +20,7 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | | 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) | State of the Galaxy Project - priorities, plans, and community | | | 10:30 - 11:00 | Coffee Break | | 11:00 - 11:20 | Nicola Soranzo | News from the [IUC](/src/iuc/index.md) and the Galaxy tool ecosystem | | @@ -35,7 +35,7 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | 15:20 - 15:40 | Nikolay Vazov | Customizing Galaxy for Large Institutions | | | 15:40 - 16:00 | TBA | | | | 16:00 - 17:00 | lightening talks | | | -| 17:00 - 17:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md), [Björn Grüning](/src/people/bjoern-gruening/) | concluding remarks | | +| 17:00 - 17:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Björn Grüning](/src/people/bjoern-gruening/) | concluding remarks | | | 17:01 - 17:15 | ...going to the pub | @@ -45,4 +45,4 @@ The workshop will be held at the Universität of Freiburg in Germany (see the [m ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/events/uga2014/index.md b/content/events/uga2014/index.md index 5cc77649e5..768a2ca9a1 100644 --- a/content/events/uga2014/index.md +++ b/content/events/uga2014/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
March 7, 2014
-**Instructors
[Carl Eberhard](/people/carl-eberhard/index.md), [Dave Clements](/people/dave-clements/), [Dannon Baker](/src/people/dannon-baker/), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) +**Instructors
[Carl Eberhard](/people/carl-eberhard/), [Dave Clements](/people/dave-clements/), [Dannon Baker](/src/people/dannon-baker/), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) 8:30-17:00
[University of Georgia](http://www.uga.edu/), Athens, GA** diff --git a/content/galaxy-updates/2012-02/index.md b/content/galaxy-updates/2012-02/index.md index f354e5d628..3a7c07cbef 100644 --- a/content/galaxy-updates/2012-02/index.md +++ b/content/galaxy-updates/2012-02/index.md @@ -18,7 +18,7 @@ New papers of note for the Galaxy community: * Thomas Hentrich, Julia M. Schulze, Eldon Emberly, and Michael S. Kobor, "[CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures](http://bioinformatics.oxfordjournals.org/content/early/2012/01/10/bioinformatics.bts007.short)." *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* -* Jeremy Goecks, Kanwei Li, [Dave Clements](/people/dave-clements/index.md), The [Galaxy Team](/src/galaxy-team/), James Taylor, "[The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool](http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6094046)." *[Biological Data Visualization (BioVis), 2011 IEEE Symposium on](http://www.biovis.net/)* +* Jeremy Goecks, Kanwei Li, [Dave Clements](/people/dave-clements/), The [Galaxy Team](/src/galaxy-team/), James Taylor, "[The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool](http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6094046)." *[Biological Data Visualization (BioVis), 2011 IEEE Symposium on](http://www.biovis.net/)* Plus [27 other papers](http://www.citeulike.org/group/16008/library) that use, reference, or are about Galaxy. diff --git a/content/galaxy-updates/2012-05/index.md b/content/galaxy-updates/2012-05/index.md index f7bccf3b44..ab76ce94a7 100644 --- a/content/galaxy-updates/2012-05/index.md +++ b/content/galaxy-updates/2012-05/index.md @@ -38,7 +38,7 @@ Also, if you are interested in presenting a topic, especially a "how to use Gala
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/index.md), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See [Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md) for details and links. diff --git a/content/galaxy-updates/2012-07/index.md b/content/galaxy-updates/2012-07/index.md index 9b9d1608db..2e4fc065f4 100644 --- a/content/galaxy-updates/2012-07/index.md +++ b/content/galaxy-updates/2012-07/index.md @@ -52,9 +52,9 @@ Welcome to the July 2012 edition of *[Galaxy Update](/src/galaxy-updates/index.m These papers may be of interest to the Galaxy community: -* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. +* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. -* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. +* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. These papers were among [31 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md) (for a total of 348 papers in the last ~16 months). The new papers are spread [across 8 categories](http://www.citeulike.org/group/16008/tags). diff --git a/content/galaxy-updates/2012-09/index.md b/content/galaxy-updates/2012-09/index.md index 7ab0b9ed3d..a8061a3667 100644 --- a/content/galaxy-updates/2012-09/index.md +++ b/content/galaxy-updates/2012-09/index.md @@ -50,7 +50,7 @@ Welcome to the September 2012 edition of *[Galaxy Update](/src/galaxy-updates/in These papers may be of interest to the Galaxy community: -* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/people/anton/index.md) & [Taylor](/src/people/james-taylor/), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) +* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/people/anton/) & [Taylor](/src/people/james-taylor/), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) * "[IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis](https://doi.org/10.1186/1471-2105-13-S14-S5)", by Merelli, Viti, Milanesi, *BMC Bioinformatics*, Vol. 13, No. Suppl 14. (2011), S5 @@ -190,7 +190,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-10/index.md b/content/galaxy-updates/2012-10/index.md index 924fcfce6c..759c591f8a 100644 --- a/content/galaxy-updates/2012-10/index.md +++ b/content/galaxy-updates/2012-10/index.md @@ -156,7 +156,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-11/index.md b/content/galaxy-updates/2012-11/index.md index eeadde32ca..d458317d74 100644 --- a/content/galaxy-updates/2012-11/index.md +++ b/content/galaxy-updates/2012-11/index.md @@ -64,7 +64,7 @@ These papers may be of interest to the Galaxy community: * "[G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes](https://doi.org/10.1186/1471-2105-13-253)," Danielle Lemay, William Martin, Angie Hinrichs, Monique Rijnkels, J. German, Ian Korf, Katherine Pollard, *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)*, Vol. 13, No. 1. (28 September 2012), 253

-* "[Creating re-usable tools from scripts: The Galaxy Tool Factory](https://doi.org/10.1093/bioinformatics/bts573)," [Ross Lazarus](/people/fubar/index.md), Antony Kaspi, Mark Ziemann, [The Galaxy Team](/src/galaxy-team/), *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* (28 September 2012) +* "[Creating re-usable tools from scripts: The Galaxy Tool Factory](https://doi.org/10.1093/bioinformatics/bts573)," [Ross Lazarus](/people/fubar/), Antony Kaspi, Mark Ziemann, [The Galaxy Team](/src/galaxy-team/), *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)* (28 September 2012) These papers were among [44 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md). @@ -137,7 +137,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-12/index.md b/content/galaxy-updates/2012-12/index.md index 5c42e4bfeb..6f09003ba5 100644 --- a/content/galaxy-updates/2012-12/index.md +++ b/content/galaxy-updates/2012-12/index.md @@ -45,8 +45,8 @@ These papers may be of interest to the Galaxy community: -* [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman and [James Taylor](/src/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

-* [Jeremy Goecks](/people/jeremy-goecks/index.md), [Nate Coraor](/people/nate/index.md), [The Galaxy Team](/src/galaxy-team/index.md), [Anton Nekrutenko](/src/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

+* [Enis Afgan](/people/enis-afgan/), Brad Chapman and [James Taylor](/src/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

+* [Jeremy Goecks](/people/jeremy-goecks/), [Nate Coraor](/people/nate/), [The Galaxy Team](/src/galaxy-team/), [Anton Nekrutenko](/src/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

* Samantha Baldwin, Roopashree Revanna, Susan Thomson, *et al.*, "[A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)](https://doi.org/10.1186/1471-2164-13-637)," *BMC Genomics*, Vol. 13, No. 1. (2012), 637

* Jeremy C. Morgan, Robert W. Chapman, Paul E. Anderson, "[A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources](https://doi.org/10.1145/2382936.2383033). Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

* Bo Liu, Borja Sotomayor, Ravi Madduri, Kyle Chard, "[Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision](http:// bit.ly/UPBbRI)." [Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012)](http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/) diff --git a/content/galaxy-updates/2013-01/index.md b/content/galaxy-updates/2013-01/index.md index e9af47d04f..8f15ea3df2 100644 --- a/content/galaxy-updates/2013-01/index.md +++ b/content/galaxy-updates/2013-01/index.md @@ -188,7 +188,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-02/index.md b/content/galaxy-updates/2013-02/index.md index f218596bda..5488f7c4cf 100644 --- a/content/galaxy-updates/2013-02/index.md +++ b/content/galaxy-updates/2013-02/index.md @@ -204,7 +204,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-03/index.md b/content/galaxy-updates/2013-03/index.md index 999a7633f3..8c96ecf84d 100644 --- a/content/galaxy-updates/2013-03/index.md +++ b/content/galaxy-updates/2013-03/index.md @@ -200,7 +200,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-04/index.md b/content/galaxy-updates/2013-04/index.md index 7ff06a9955..fdfe520842 100644 --- a/content/galaxy-updates/2013-04/index.md +++ b/content/galaxy-updates/2013-04/index.md @@ -275,7 +275,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-05/index.md b/content/galaxy-updates/2013-05/index.md index 1e24df6395..17228d333c 100644 --- a/content/galaxy-updates/2013-05/index.md +++ b/content/galaxy-updates/2013-05/index.md @@ -181,7 +181,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-06/index.md b/content/galaxy-updates/2013-06/index.md index 80a9bcd78c..f67d4de7e4 100644 --- a/content/galaxy-updates/2013-06/index.md +++ b/content/galaxy-updates/2013-06/index.md @@ -193,7 +193,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-07/index.md b/content/galaxy-updates/2013-07/index.md index 5533c17554..25ca5cd79a 100644 --- a/content/galaxy-updates/2013-07/index.md +++ b/content/galaxy-updates/2013-07/index.md @@ -126,7 +126,7 @@ This installation of Galaxy has been configured such that anonymous users can op A record 53 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in June. These papers may be particularly interesting to the Galaxy community -* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/index.md), [Carl Eberhard](/people/carl-eberhard/index.md), Tomithy Too, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 +* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/), [Carl Eberhard](/people/carl-eberhard/), Tomithy Too, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 * "[Detection of non-coding RNA in Bacteria and Archaea using the DETR’PROK Galaxy pipeline](https://doi.org/10.1016/j.ymeth.2013.06.003)" by Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret, *[Methods](http://www.sciencedirect.com/science/journal/10462023)* (June 2013) * "[Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data](https://doi.org/10.1002/gepi.21739)" by Nicholas A. Davis, Caleb A. Lareau, Bill C. White, *et al.* *Genetic Epidemiology* (June 2013) * "[A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America](https://doi.org/10.1093/bib/bbt033)" by Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza, *Briefings in Bioinformatics* (30 May 2013) @@ -356,7 +356,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + @@ -368,7 +368,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - +
Instructors Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University 		Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University
Content Wednesday July 11 OpenBio Codefest 2012 All Day Enis Afgan and Dannon Baker of the the Galaxy Team will participate. Enis Afgan and Dannon Baker of the the Galaxy Team will participate. Report
November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization November 6-10 Galaxy 101: Data Integration, Analysis and Sharing
Sold out
 American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization
Sold out
 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 13-14 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 9-13 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 9-13 September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia Jennifer Jackson, Ross Lazarus Jennifer Jackson, Ross Lazarus
October 1-3 October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States James Taylor, Jennifer Jackson James Taylor, Jennifer Jackson
diff --git a/content/galaxy-updates/2013-08/index.md b/content/galaxy-updates/2013-08/index.md index 57294317d4..05f7be69a6 100644 --- a/content/galaxy-updates/2013-08/index.md +++ b/content/galaxy-updates/2013-08/index.md @@ -103,7 +103,7 @@ The QBRC galaxy server tools are constantly being updated. Please contact author 47 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in July. These papers may be particularly interesting to the Galaxy community -* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/people/james-taylor/index.md), [Anton Nekrutenko](/people/anton/), [Nate Coraor](/src/people/nate/), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) +* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Nate Coraor](/src/people/nate/), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) * "[Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE](https://doi.org/10.1186/1471-2164-14-494)" by Quang Trinh, Fei Y. Jen, Ziru Zhou, *et al.*, *BMC Genomics,* Vol. 14, No. 1. (2013), 494 * "[The Banana Genome Hub](https://doi.org/10.1093/database/bat035)" by Droc, *et al.*, *Database*, Vol. 2013 (01 January 2013), @@ -193,7 +193,7 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Jennifer Jackson, Ross Lazarus + Jennifer Jackson, Ross Lazarus September 30 - October 2 @@ -233,7 +233,7 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson diff --git a/content/galaxy-updates/2013-09/index.md b/content/galaxy-updates/2013-09/index.md index 1c036ce627..82513dfd5f 100644 --- a/content/galaxy-updates/2013-09/index.md +++ b/content/galaxy-updates/2013-09/index.md @@ -180,7 +180,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg September 30 - October 2 @@ -224,7 +224,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu High Throughput Data Analysis and Visualization with Galaxy' - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson January 11-15 diff --git a/content/galaxy-updates/2013-10/index.md b/content/galaxy-updates/2013-10/index.md index babb4244e7..fbabf49091 100644 --- a/content/galaxy-updates/2013-10/index.md +++ b/content/galaxy-updates/2013-10/index.md @@ -186,7 +186,7 @@ In the next 3 months there are no less than 13 talks and workshops at at least 5 September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg October 13-16 @@ -327,7 +327,7 @@ And don't worry, you won't have to travel to Australia during its spring just to October 22 Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson, Anushka Brownley + Anton Nekrutenko, Jennifer Jackson, Anushka Brownley October 22-26 @@ -337,7 +337,7 @@ And don't worry, you won't have to travel to Australia during its spring just to High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
- Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders diff --git a/content/galaxy-updates/2013-11/index.md b/content/galaxy-updates/2013-11/index.md index 8d41f78d27..7dfe3f8bf2 100644 --- a/content/galaxy-updates/2013-11/index.md +++ b/content/galaxy-updates/2013-11/index.md @@ -97,7 +97,7 @@ And ... ## Ten Simple Rules for Reproducible Computational Research -[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/people/anton/index.md), [James Taylor](/src/people/james-taylor/), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October. +[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October.
PLoS Computational Biology: Ten Simple Rules for Reproducible Computational Research
diff --git a/content/galaxy-updates/2014-01/index.md b/content/galaxy-updates/2014-01/index.md index be78987f49..0aaa423eca 100644 --- a/content/galaxy-updates/2014-01/index.md +++ b/content/galaxy-updates/2014-01/index.md @@ -306,7 +306,7 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 diff --git a/content/galaxy-updates/2014-02/index.md b/content/galaxy-updates/2014-02/index.md index 793ab1365e..9081a5f6db 100644 --- a/content/galaxy-updates/2014-02/index.md +++ b/content/galaxy-updates/2014-02/index.md @@ -217,7 +217,7 @@ GMOD Malaysia 2014 is made possible by the generous support of the [National Evo March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 @@ -381,7 +381,7 @@ bringing the number of log entries to 12. # Galaxy is now at Johns Hopkins and GWU (and Penn State!) -In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/src/galaxy-team/index.md) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/index.md) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. +In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/src/galaxy-team/index.md) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are [still hiring](/src/galaxy-is-hiring/index.md), but now at three universities instead of two. diff --git a/content/galaxy-updates/2014-03/index.md b/content/galaxy-updates/2014-03/index.md index e52e39f0f3..ceaa2ba6fd 100644 --- a/content/galaxy-updates/2014-03/index.md +++ b/content/galaxy-updates/2014-03/index.md @@ -9,7 +9,7 @@ Welcome to the March 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *54 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in Febrary. Some papers that may be particularly interesting to the Galaxy community: -* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/index.md), [Von Kuster](/people/greg_vonkuster/index.md), [Bouvier](/people/dave-bouvier/index.md), [Baker](/people/dannon-baker/index.md), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/src/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 +* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/src/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 * [Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis](https://doi.org/10.1371/journal.pone.0087301), by Khushi, *et al.,* *PLoS ONE*, Vol. 9, No. 2. (12 February 2014), e87301, doi:10.1371/journal.pone.0087301 @@ -188,7 +188,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson April 15-17 @@ -287,7 +287,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-04/index.md b/content/galaxy-updates/2014-04/index.md index de21ce1b9f..462413daf6 100644 --- a/content/galaxy-updates/2014-04/index.md +++ b/content/galaxy-updates/2014-04/index.md @@ -9,9 +9,9 @@ Welcome to the April 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *63 papers* (a new monthly record) were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in March. Some papers that may be particularly interesting to the Galaxy community: -* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/people/dan/index.md), James E. Johnson, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 +* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/people/dan/), James E. Johnson, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 -* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/people/dan/index.md), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) +* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/people/dan/), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) * "[Orione, a web-based framework for NGS analysis in microbiology](https://doi.org/10.1093/bioinformatics/btu135)," Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia, *Bioinformatics* (Oxford, England) (10 March 2014), doi:10.1093/bioinformatics/btu135 diff --git a/content/galaxy-updates/2014-05/index.md b/content/galaxy-updates/2014-05/index.md index 5bd56aec07..a616bbf970 100644 --- a/content/galaxy-updates/2014-05/index.md +++ b/content/galaxy-updates/2014-05/index.md @@ -41,7 +41,7 @@ Galaxy Biostar was launched on April 23. We hope you like the change and look f *47 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in April. Some papers that may be particularly interesting to the Galaxy community: -* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/people/dan/index.md) and [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 +* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/people/dan/) and [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 * "[Support for data-intensive computing with CloudMan](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6596260)," Yousef Kowsar and [Enis Afgan](/people/enis-afgan/), *[Information & Communication Technology Electronics & Microelectronics (MIPRO), 2013 36th International Convention on](http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6588635),* (May 2013), pp. 243-248 diff --git a/content/galaxy-updates/2014-07/index.md b/content/galaxy-updates/2014-07/index.md index ebedc7056f..9b972a1bad 100644 --- a/content/galaxy-updates/2014-07/index.md +++ b/content/galaxy-updates/2014-07/index.md @@ -116,7 +116,7 @@ Over the rest of the summer there are other [Galaxy related events](/src/events/ September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-08/index.md b/content/galaxy-updates/2014-08/index.md index 9c17189f09..6ef62ad2a0 100644 --- a/content/galaxy-updates/2014-08/index.md +++ b/content/galaxy-updates/2014-08/index.md @@ -201,7 +201,7 @@ Over the rest of the few months there are many [Galaxy related events](/src/even September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-09/index.md b/content/galaxy-updates/2014-09/index.md index f2f91114a1..31b2ced88f 100644 --- a/content/galaxy-updates/2014-09/index.md +++ b/content/galaxy-updates/2014-09/index.md @@ -94,7 +94,7 @@ These events are a great way to meet other Galaxy users and developers and learn September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-10/index.md b/content/galaxy-updates/2014-10/index.md index 38a1155d17..a43551a3d3 100644 --- a/content/galaxy-updates/2014-10/index.md +++ b/content/galaxy-updates/2014-10/index.md @@ -61,7 +61,7 @@ There are [upcoming events](/src/events/index.md) in Switzerland, Germany, Austr September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2015-02/index.md b/content/galaxy-updates/2015-02/index.md index a7e85f26fe..f0ab66fbe0 100644 --- a/content/galaxy-updates/2015-02/index.md +++ b/content/galaxy-updates/2015-02/index.md @@ -19,11 +19,11 @@ Welcome to the February *[Galaxy Update](/src/galaxy-updates/index.md)*, a summa 55 new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in January. Some highlights: * [Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines](https://doi.org/10.1002/cam4.360) - [Jeremy Goecks](/people/jeremy-goecks/index.md), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/src/people/james-taylor/), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 + [Jeremy Goecks](/people/jeremy-goecks/), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/src/people/james-taylor/), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 * [Merging OpenLifeData with SADI services using Galaxy and Docker](http://www.biorxiv.org/content/biorxiv/early/2015/01/10/013615) Mikel E. Aranguren, *bioRxiv* * [NCBI BLAST+ integrated into Galaxy](http://www.biorxiv.org/content/early/2015/01/21/014043) - Peter J. A. Cock, [John M. Chilton](/people/john-chilton/index.md), [Björn Grüning](/people/bjoern-gruening/), James E. Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/), *bioRxiv* + Peter J. A. Cock, [John M. Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), James E. Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/), *bioRxiv* * [SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations](http://www.gigasciencejournal.com/content/4/1/1/abstract) Wilfried M Guiblet, Kai Zhao, Stephen J O'Brien, Steven E Massey, Alfred L Roca and Taras K Oleksyk, *[GigaScience](http://www.gigasciencejournal.com/)* 2015, 4:1
[Supplementary materials](http://gigagalaxy.net/u/gigascience/g/wguiblet2014) (as a Galaxy Page) @@ -162,7 +162,7 @@ Please let the organisers know if you are interested in helping make this event The first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) will happen online on Thursday, 19 February. [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) will lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/), and [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) will lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. @@ -174,7 +174,7 @@ The [first Baltimore Area Galaxy meetup](/src/events/meetups/baltimore/2015-01-2 The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis Afgan](/people/enis-afgan/index.md) & [Nitesh Turaga](/src/people/nitesh-turaga/) +[Enis Afgan](/people/enis-afgan/) & [Nitesh Turaga](/src/people/nitesh-turaga/) ## Other Events @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 5 countries on 4 continents February 19 February 2015 GalaxyAdmins Web Meetup Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements @@ -386,7 +386,7 @@ Several *critical* security vulnerabilities were recently discovered by Bartlomi **IPython Integration** -Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/index.md) and [Helena Rasche](/people/helena-rasche/), [Galaxy now features integration with the popular IPython project](/src/archive/dev-news-briefs/2015-01-13/#ipython-integration). The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. +Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/) and [Helena Rasche](/people/helena-rasche/), [Galaxy now features integration with the popular IPython project](/src/archive/dev-news-briefs/2015-01-13/#ipython-integration). The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. ** Tool Form Upgrade (for Beta Testing) ** @@ -463,20 +463,20 @@ In no particular order: * [snpsift_dbnsfp_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_datatypes): Galaxy applicable data formats for SnpSift. snpsift_dbnsfp tool Allows for the creation of a snpsift dbnsfp Galaxy dataset from a tabular file that can be used by SnpSift dbnsfp to annotate a vcf formatted file. * [snpeff_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpeff_datatypes): Galaxy applicable data formats for SnpEff tools Galaxy applicable data formats for SnpEff tools. The snpeffdb datatype provides the means to represent a SnpEff genome database in a Galaxy dataset. * [snpsift_dbnsfp](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp): snpEff SnpSift dbnsfp tool from Pablo Cingolani Annotates variants on genes using the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.) http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift): snpEff SnpSift tools from Pablo Cingolani Variant annotation and effect prediction tools. It annotates and predicts the effects of variants on genes. This repository should manage tool dependencies. There are data managers for the Galaxy admin to download genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed /
* [snpsift_genesets](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_genesets): snpEff SnpSift genesets tool from Pablo Cingolani Annotates variants with GeneSets, such as Gene Ontology (GO), KEGG, Reactome, etc.; http://snpeff.sourceforge.net/SnpSift.html#geneSets !SnpEff and !SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift_dbnsfp_generic](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_generic): snpEff SnpSift dbnsfp tool that can use any dbnsfp-like annotation data Annotates variants on genes using a tabular set of annotation values such as those from the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.)
This tool determines the available annotations from the input, so it can be used for other organisms other than human or other annotation values than available from dbNSFP. http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP
SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * *From [amawla](https://toolshed.g2.bx.psu.edu/view/amawla):* @@ -532,7 +532,7 @@ In no particular order: * *From [iuc](https://toolshed.g2.bx.psu.edu/view/iuc/): * * [data_manager_snpeff](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_snpeff): Manage SnpEff genome reference data Data managers for the Galaxy admin to download SnpEff genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/index.md), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ ### Packages / Tool Dependency Definitions diff --git a/content/galaxy-updates/2015-03/index.md b/content/galaxy-updates/2015-03/index.md index cfdfef96d4..1e0f8807a0 100644 --- a/content/galaxy-updates/2015-03/index.md +++ b/content/galaxy-updates/2015-03/index.md @@ -22,7 +22,7 @@ Welcome to the March 2015 *[Galaxy Update](/src/galaxy-updates/index.md)*, a sum Jorrit Boeke, [John M Chilton](/people/john-chilton/), Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, *Nature Biotechnology*, Vol. 33, No. 2. (6 February 2015) * [Online Resources for Genomic Analysis Using High-Throughput Sequencing](https://doi.org/10.1101/pdb.top083667) - [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 + [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 * [Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud](https://doi.org/10.12694/scpe.v16i1.1058) Philip Church, Andrzej Goscinski, *Scalable Computing: Practice and Experience*, Vol. 16, No. 1. (07 February 2015), doi:10.12694/scpe.v16i1.1058 @@ -197,17 +197,17 @@ A hands-on, 4 day workshop on *[RNA-Seq and ChIP-Seq Analysis with Galaxy](http: [Video and slides](/src/community/galaxy-admins/meetups/2015-02-19/index.md) from the first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) are now available online. -[Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) also lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. +[Hans-Rudolf Hotz](/people/hansrudolf-hotz/) also lead a short discussion on *[GalaxyAdmins](/src/community/galaxy-admins/) direction*. [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. Our next meetup will be in April. ### Fall 2014 Questionnaire Summaries -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) was presented by [Dave Clements](/people/dave-clements/index.md). A [summary of the admin/devel questionnaire](/src/community/galaxy-admins/surveys/2014/) is now available online. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) was presented by [Dave Clements](/people/dave-clements/). A [summary of the admin/devel questionnaire](/src/community/galaxy-admins/surveys/2014/) is now available online. ### Gravity -[Nate Coraor](/people/nate/index.md) introduced [Gravity](/src/community/galaxy-admins/meetups/2015-02-19/#galaxy-project-update-gravity), a process manager (supervisor) for Galaxy servers. +[Nate Coraor](/people/nate/) introduced [Gravity](/src/community/galaxy-admins/meetups/2015-02-19/#galaxy-project-update-gravity), a process manager (supervisor) for Galaxy servers. ## Other Events diff --git a/content/galaxy-updates/2015-04/index.md b/content/galaxy-updates/2015-04/index.md index f259c1996d..09a3d474b0 100644 --- a/content/galaxy-updates/2015-04/index.md +++ b/content/galaxy-updates/2015-04/index.md @@ -208,7 +208,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents April 16 GalaxyAdmins April 2015 Meetup Online - Hans-Rudolf Hotz, Dave Clements, Carrie Ganote + Hans-Rudolf Hotz, Dave Clements, Carrie Ganote April 20-21 @@ -493,7 +493,7 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) +[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) ## Planemo 0.6.0 diff --git a/content/galaxy-updates/2015-05/index.md b/content/galaxy-updates/2015-05/index.md index 1364ffc382..ea0f3d1b63 100644 --- a/content/galaxy-updates/2015-05/index.md +++ b/content/galaxy-updates/2015-05/index.md @@ -28,7 +28,7 @@ Welcome to the May 2015 *[Galactic News](/src/galaxy-updates/index.md)*, a summa Halfdan Rydbeck, Geir Kjetil K. Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig, *PloS one*, Vol. 10, No. 4. (2015) * [StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo](https://doi.org/10.1093/bioinformatics/btv213) - Yin Tang, [Emil Bouvier](/people/dave-bouvier/index.md), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/src/people/anton/), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 + Yin Tang, [Emil Bouvier](/people/dave-bouvier/), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/src/people/anton/), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 The new papers were tagged with: @@ -244,7 +244,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents May 15 RNA-Seq Galaxy Workshop Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko May 22, 29 diff --git a/content/galaxy-updates/2015-09/index.md b/content/galaxy-updates/2015-09/index.md index acd3511dd0..57fa4a18a4 100644 --- a/content/galaxy-updates/2015-09/index.md +++ b/content/galaxy-updates/2015-09/index.md @@ -248,7 +248,7 @@ There are [upcoming events](/src/events/index.md) in five countries on three con october 15 October Galaxy Admins Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements October 19 diff --git a/content/galaxy-updates/2015-10/index.md b/content/galaxy-updates/2015-10/index.md index 72eef5bff8..73950652ce 100644 --- a/content/galaxy-updates/2015-10/index.md +++ b/content/galaxy-updates/2015-10/index.md @@ -158,7 +158,7 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2017! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) ---- @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents October 15 October Galaxy Admins Meetup Around the World Online - David Kovalic, Hans-Rudolf Hotz, Dave Clements + David Kovalic, Hans-Rudolf Hotz, Dave Clements October 28-29 @@ -245,7 +245,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Anton Nekrutenko, James Taylor + Training offered by GTN Member Anton Nekrutenko, James Taylor Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations Workshop @@ -395,7 +395,7 @@ Thanks to everyone who helped put these together. **Release Highlights ** * **Interactive Environments** - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by [Helena Rasche](/people/helena-rasche/). * **Workflow Editor Enhancements** - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections. -* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/people/bjoern-gruening/index.md), [Nicola Soranzo](/people/nicola-soranzo/), and [Helena Rasche](/src/people/helena-rasche/). +* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/people/bjoern-gruening/), [Nicola Soranzo](/people/nicola-soranzo/), and [Helena Rasche](/src/people/helena-rasche/). * And *[much more](http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html)* ## Mid 2015 Galaxy CloudMan Release diff --git a/content/galaxy-updates/2015-11/index.md b/content/galaxy-updates/2015-11/index.md index 9aa651666a..e9d4caf9fb 100644 --- a/content/galaxy-updates/2015-11/index.md +++ b/content/galaxy-updates/2015-11/index.md @@ -205,7 +205,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Dan Blankenberg, John Chilton + Training offered by GTN Member Dan Blankenberg, John Chilton Common Workflow Language on Galaxy
Part of Portable Bioinformatics Workshop @@ -521,6 +521,6 @@ Ran out of time to compile these. Look for a double batch in December. Galaxy codebase -In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/people/helena-rasche/index.md) originally submitted by team member [Nate Coraor](/src/people/nate/). +In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/people/helena-rasche/) originally submitted by team member [Nate Coraor](/src/people/nate/). Our thanks go to the community and the team alike. diff --git a/content/galaxy-updates/2016-02/index.md b/content/galaxy-updates/2016-02/index.md index d6b0ec103e..c25c2002c7 100644 --- a/content/galaxy-updates/2016-02/index.md +++ b/content/galaxy-updates/2016-02/index.md @@ -215,7 +215,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. February 18 GalaxyAdmins Web Meetup Around the World Online - Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements + Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements February 20-23 diff --git a/content/galaxy-updates/2016-04/index.md b/content/galaxy-updates/2016-04/index.md index 593c43d33b..e79790c38c 100644 --- a/content/galaxy-updates/2016-04/index.md +++ b/content/galaxy-updates/2016-04/index.md @@ -175,7 +175,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. April 21 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements April 22-26 diff --git a/content/galaxy-updates/2016-05/index.md b/content/galaxy-updates/2016-05/index.md index 7c36e88c4a..0bdf3cf0cc 100644 --- a/content/galaxy-updates/2016-05/index.md +++ b/content/galaxy-updates/2016-05/index.md @@ -262,7 +262,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth June 16 GalaxyAdmins Web Meetup Around the World Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 25-29 @@ -464,11 +464,11 @@ Variant calling is a complex field that was significantly propelled by advances
Reference based RNA seq
-Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). +Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Reference based RNA seq -**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/people/bjoern-gruening/index.md) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). +**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Dataset Collections diff --git a/content/galaxy-updates/2016-06/index.md b/content/galaxy-updates/2016-06/index.md index ff2ad06293..71f0619326 100644 --- a/content/galaxy-updates/2016-06/index.md +++ b/content/galaxy-updates/2016-06/index.md @@ -175,7 +175,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 20 diff --git a/content/galaxy-updates/2016-07/index.md b/content/galaxy-updates/2016-07/index.md index 4cfe638cc4..a4605f80d2 100644 --- a/content/galaxy-updates/2016-07/index.md +++ b/content/galaxy-updates/2016-07/index.md @@ -185,7 +185,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -227,13 +227,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-08/index.md b/content/galaxy-updates/2016-08/index.md index 49b98b6bbe..6ea89953ed 100644 --- a/content/galaxy-updates/2016-08/index.md +++ b/content/galaxy-updates/2016-08/index.md @@ -92,7 +92,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -152,13 +152,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-09/index.md b/content/galaxy-updates/2016-09/index.md index 064b4c3826..46204cd05b 100644 --- a/content/galaxy-updates/2016-09/index.md +++ b/content/galaxy-updates/2016-09/index.md @@ -154,13 +154,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening @@ -266,7 +266,7 @@ Some highlights from last month: Matt Chambers. * **[CloudBridge: a Simple Cross-Cloud Python Library](https://s3.amazonaws.com/cloudbridgelib/CloudBridge.pdf)** - Nuwan Goonasekera, Andrew Lonie, [James Taylor](/people/james-taylor/index.md), [Enis Afgan](/src/people/enis-afgan/). XSEDE16. + Nuwan Goonasekera, Andrew Lonie, [James Taylor](/people/james-taylor/), [Enis Afgan](/src/people/enis-afgan/). XSEDE16. * **[DISMISS: detection of stranded methylation in MeDIP-Seq data](http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1158-7)** Umar Niazi, Kathrin K Geyer, Martin J Vickers, Karl F Hoffmann, Martin T Swain. *BMC Bioinformatics*, Vol. 17, No. 1. (2016), pp. 1-12, doi:10.1186/s12859-016-1158-7 diff --git a/content/galaxy-updates/2016-10/index.md b/content/galaxy-updates/2016-10/index.md index 69a32ad1d1..cca84f9bf7 100644 --- a/content/galaxy-updates/2016-10/index.md +++ b/content/galaxy-updates/2016-10/index.md @@ -217,19 +217,19 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 24-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy - Dannon Baker, Björn Grüning + Dannon Baker, Björn Grüning @@ -361,7 +361,7 @@ Some highlights from last month: Annette McGrath, Steve McMahon, Sean Li, Joel Ludbey, Tim Ho. *Journal of Grid Computing* (2016), pp. 1-11, doi:10.1007/s10723-016-9379-6 **[Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter](http://biorxiv.org/content/early/2016/09/22/075457)** - [Björn Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 + [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 **[Genotyping of evolving prokaryotic populations](https://doi.org/10.7287/peerj.preprints.2449v1)** Markus Zojer, Lisa N. Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei. *PeerJ Preprints* (14 September 2016), doi:10.7287/peerj.preprints.2449v1 diff --git a/content/galaxy-updates/2016-12/index.md b/content/galaxy-updates/2016-12/index.md index 5a7d6b500d..ac52cce31f 100644 --- a/content/galaxy-updates/2016-12/index.md +++ b/content/galaxy-updates/2016-12/index.md @@ -100,13 +100,13 @@ There are [a plenitude of Galaxy related events coming up](/src/events/index.md) December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online - Dannon Baker, Dave Clements + Dannon Baker, Dave Clements December 15 Galaxy Training Materials: Community creation, curation, and use and The new Galaxy Hub: Community creation, curation, and use Online Online - Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements + Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements December 15-16 @@ -180,7 +180,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth Some highlights from last month: -* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/index.md), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) +* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) * [How Are You – and How’s Your Microbiome?](https://theanalyticalscientist.com/issues/1116/how-are-you-and-hows-your-microbiome/), Pratik Jagtap, *The Analytical Scientist*, November 2016 * [Computational workflow for the fine-grained analysis of metagenomic samples](https://doi.org/10.1186/s12864-016-3063-x), Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles, *BMC Genomics*, Vol. 17, No. S8. (25 October 2016), doi:10.1186/s12864-016-3063-x * [Big Data Smart Socket (BDSS): A System that Abstracts Data Transfer Habits from End Users](https://doi.org/10.1093/bioinformatics/btw679), Nick A. Watts, Frank A. Feltus, *Bioinformatics* (26 October 2016), btw679, doi:10.1093/bioinformatics/btw679 diff --git a/content/galaxy-updates/2017-03/index.md b/content/galaxy-updates/2017-03/index.md index 7ebafcfca8..041e6c9800 100644 --- a/content/galaxy-updates/2017-03/index.md +++ b/content/galaxy-updates/2017-03/index.md @@ -260,7 +260,7 @@ Some highlights from the past two months: Connor Wytko, Brian Soto, Stephen P. Ficklin. *Database*, Vol. 2017 (10 January 2017), baw154, doi:10.1093/database/baw154 * [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://doi.org/10.12688/f1000research.9821.1) - [Nitesh Turaga](/people/nitesh-turaga/index.md), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/index.md), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 + [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 * [MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets](https://doi.org/10.1007/s41048-016-0033-4) Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan. *Biophysics Reports* (2017), pp. 1-10, doi:10.1007/s41048-016-0033-4 diff --git a/content/galaxy-updates/2017-06/index.md b/content/galaxy-updates/2017-06/index.md index bf829d87c5..0837d59252 100644 --- a/content/galaxy-updates/2017-06/index.md +++ b/content/galaxy-updates/2017-06/index.md @@ -31,7 +31,7 @@ If you missed the May 31 regular registration deadline then don't worry because **The Galaxy Project: from the Planck epoch to Montpellier** -[Dr. Anton Nekrutenko](/people/anton/index.md) and [Dr. James Taylor](/src/people/james-taylor/) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. +[Dr. Anton Nekrutenko](/people/anton/) and [Dr. James Taylor](/src/people/james-taylor/) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. If you are reading this, you probably already know who they are. If not, see their [bios here](https://gcc2017.sciencesconf.org/). @@ -211,7 +211,7 @@ Some highlights from the papers added last month: *Nucleic Acids Research* (02 May 2017), doi:10.1093/nar/gkx315 * [Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](https://doi.org/10.1371/journal.pcbi.1005425) - [Björn A. Grüning](/people/bjoern-gruening/index.md), [Helena Rasche](/people/helena-rasche/index.md), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/index.md), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 + [Björn A. Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 * [MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization](https://doi.org/10.1093/bioinformatics/btx320) Katherine M. McCoy, Margaret L. Antonio, Tim van Opijnen. *Bioinformatics* (11 May 2017), doi:10.1093/bioinformatics/btx320 diff --git a/content/galaxy-updates/2017-09/index.md b/content/galaxy-updates/2017-09/index.md index 6ebd80c28d..b309296e61 100644 --- a/content/galaxy-updates/2017-09/index.md +++ b/content/galaxy-updates/2017-09/index.md @@ -17,7 +17,7 @@ Welcome to the September 2017 *[Galactic News](/src/galaxy-updates/index.md)*, a Some highlights from the recently added pubs: * [2017 Galaxy community update](https://doi.org/10.7490/f1000research.1114388.1) - [Dan Blankenberg](/people/dan/index.md), [Jeremy Goecks](/src/people/jeremy-goecks/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 + [Dan Blankenberg](/people/dan/), [Jeremy Goecks](/src/people/jeremy-goecks/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 * [Approaches for small RNA-seq in Galaxy](https://doi.org/10.7490/f1000research.1114423.1) Mallory Freeberg, [James Taylor](/people/james-taylor/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114423.1 @@ -26,7 +26,7 @@ Some highlights from the recently added pubs: Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis. *GigaScience*, Vol. 6, No. 8. (August 2017), pp. 1-7, doi:10.1093/gigascience/gix048 * [Building an open, collaborative, online infrastructure for bioinformatics training](https://doi.org/10.7490/f1000research.1114447.1) - Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/people/dave-clements/index.md), [Björn Grüning](/src/people/bjoern-gruening/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 + Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/people/dave-clements/), [Björn Grüning](/src/people/bjoern-gruening/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 * [Galaxy-compatible Tool for Rapid Aptamer Clustering and HT-SELEX Data Analysis](https://doi.org/10.22377/ajp.v11i02.1265) Nikita A. Skrylnik, *Asian Journal of Pharmaceutics (AJP)*, Vol. 11, No. 02. (2017), doi:10.22377/ajp.v11i02.1265 @@ -56,7 +56,7 @@ Some highlights from the recently added pubs: Chao Zhang, Jochem Bijlard, Christine Staiger, et al. *F1000Research*, Vol. 6 (16 August 2017), 1488, doi:10.12688/f1000research.12168.1 * [The backbone of research reproducibility-sustainable and flexible tool deployment](https://doi.org/10.7490/f1000research.1114482.1) - [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/src/people/john-chilton/), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 + [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/src/people/john-chilton/), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 * [ToolDog-generating tool descriptors from the ELIXIR tool registry](https://doi.org/10.7490/f1000research.1114473.1) Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison, Hervé Ménager. *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114473.1 diff --git a/content/galaxy-updates/2017-10/index.md b/content/galaxy-updates/2017-10/index.md index b740ebdfde..e69d534565 100644 --- a/content/galaxy-updates/2017-10/index.md +++ b/content/galaxy-updates/2017-10/index.md @@ -190,7 +190,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth The Galaxy is expanding! Please help it grow. -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States * [Implémentation d’outils d’analyse et de visualisation de variations structurales et génomes mosaïques](https://www.sfbi.fr/content/impl%C3%A9mentation-d%E2%80%99outils-d%E2%80%99analyse-et-de-visualisation-de-variations-structurales-et-g%C3%A9nomes-), IRD (Institut de Recherche pour le Développement), Montpellier, France * [Metabarcoding, analyses écologiques et statistiques de paleocommunautés de protistes de l’écosystème côtier](https://www.sfbi.fr/content/metabarcoding-analyses-%C3%A9cologiques-et-statistiques-de-paleocommunaut%C3%A9s-de-protistes-de-l%E2%80%99%C3%A9co), IFREMER DYNECO/Pelagos, Brest, France diff --git a/content/galaxy-updates/2017-11/index.md b/content/galaxy-updates/2017-11/index.md index 06eba3ccbe..e2ec09d331 100644 --- a/content/galaxy-updates/2017-11/index.md +++ b/content/galaxy-updates/2017-11/index.md @@ -203,7 +203,7 @@ The Galaxy is expanding! Please help it grow. * [Développeur d’outils MS/MS pour le projet Workflow4Metabolomics sous Galaxy](https://www.sfbi.fr/content/d%C3%A9veloppeur-d%E2%80%99outils-msms-pour-le-projet-workflow4metabolomics-sous-galaxy-0), Station Biologique de Roscoff, France * [Bioinformaticien Gustave Roussy](https://www.sfbi.fr/content/bioinformaticien-gustave-roussy), Villejuif, France -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States * [Implémentation d’outils d’analyse et de visualisation de variations structurales et génomes mosaïques](https://www.sfbi.fr/content/impl%C3%A9mentation-d%E2%80%99outils-d%E2%80%99analyse-et-de-visualisation-de-variations-structurales-et-g%C3%A9nomes-), IRD (Institut de Recherche pour le Développement), Montpellier, France * [Bioinformatics Research Associate](https://academicpositions.harvard.edu/postings/7556), Huttenhower Lab, Harvard School of Public Health, Boston, Massachusetts, United States diff --git a/content/galaxy-updates/2017-12/index.md b/content/galaxy-updates/2017-12/index.md index faaff26b7a..6dce61a8f7 100644 --- a/content/galaxy-updates/2017-12/index.md +++ b/content/galaxy-updates/2017-12/index.md @@ -222,7 +222,7 @@ The Galaxy is expanding! Please help it grow. * [Classification des micropolluants dans l'environnement : amélioration de l'algorithme online TyPol](https://www.sfbi.fr/content/classification-des-micropolluants-dans-lenvironnement-am%C3%A9lioration-de-lalgorithme-online-typ), INRA-LBE, Narbonne, France * [Bioinformaticien immunologie](https://www.sfbi.fr/content/bioinformaticien-immunologie), Gustave Roussy Institute, Villejuif, France * [Bioinformaticien Gustave Roussy](https://www.sfbi.fr/content/bioinformaticien-gustave-roussy), Villejuif, France -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-01/index.md b/content/galaxy-updates/2018-01/index.md index d65ef85fb3..f1dce576ba 100644 --- a/content/galaxy-updates/2018-01/index.md +++ b/content/galaxy-updates/2018-01/index.md @@ -267,7 +267,7 @@ The Galaxy is expanding! Please help it grow. * [Responsable Opérationnel de la Plateforme de Bioinformatique ARTbio](https://www.sfbi.fr/content/responsable-op%C3%A9rationnel-de-la-plateforme-de-bioinformatique-artbio), ARTbio, Institut de Biologie Paris Seine, France * [Classification des micropolluants dans l'environnement : amélioration de l'algorithme online TyPol](https://www.sfbi.fr/content/classification-des-micropolluants-dans-lenvironnement-am%C3%A9lioration-de-lalgorithme-online-typ), INRA-LBE, Narbonne, France -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-02/index.md b/content/galaxy-updates/2018-02/index.md index 381685f5f5..693d10e3ea 100644 --- a/content/galaxy-updates/2018-02/index.md +++ b/content/galaxy-updates/2018-02/index.md @@ -88,7 +88,7 @@ morning session will include presentations on genomic and metagenomic data analy [Galaxy Administrators Course](https://github.com/galaxyproject/dagobah-training)
-A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/people/bjoern-gruening/index.md) and [Enis Afgan](/src/people/enis-afgan/) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. +A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/people/bjoern-gruening/) and [Enis Afgan](/src/people/enis-afgan/) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. Plenty of materials for Galaxy administration are now [up to date and available online](https://github.com/galaxyproject/dagobah-training). The workshop included a sneak [preview of what's coming in the 18.01 release](https://galaxyproject.github.io/dagobah-training/2018-oslo/whatsnew/18.01.html#1) from [Nate Coraor](/people/nate/). @@ -272,7 +272,7 @@ The *Galactic* and *Stellar* publications added in January were: The Galaxy is expanding! Please help it grow. * The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/galaxy-freiburg/people/) is [looking for 2 Postdoctoral researchers](https://usegalaxy-eu.github.io/galaxy-freiburg/2018/01/18/openpositions.html) -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-03/index.md b/content/galaxy-updates/2018-03/index.md index 40a435466f..fcf489aa5e 100644 --- a/content/galaxy-updates/2018-03/index.md +++ b/content/galaxy-updates/2018-03/index.md @@ -286,7 +286,7 @@ The Galaxy is expanding! Please help it grow. * [Développement d'outils bioinformatiques et statistiques pour l'analyse de l'air expiré en médecine par spectrométrie de masse en temps-réel](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA Saclay, France * [Ingénieur en développement de composants Galaxy pour la protéomique](https://www.sfbi.fr/content/ing%C3%A9nieur-en-d%C3%A9veloppement-de-composants-galaxy-pour-la-prot%C3%A9omique-0), MaIAGE , INRA, Jouy-en-Josas, France * The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/galaxy-freiburg/people/) is [looking for 2 Postdoctoral researchers](https://usegalaxy-eu.github.io/galaxy-freiburg/2018/01/18/openpositions.html) -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-04/index.md b/content/galaxy-updates/2018-04/index.md index 892780f283..f5e43141ba 100644 --- a/content/galaxy-updates/2018-04/index.md +++ b/content/galaxy-updates/2018-04/index.md @@ -315,7 +315,7 @@ The Galaxy is expanding! Please help it grow. * [Post-Doc / IR analyse de données miRNA](https://www.sfbi.fr/content/post-doc-ir-analyse-de-donn%C3%A9es-mirna), Unité de Nutrition Humaine, Clermont-Fd, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany * [Development of innovative algorithms to process real-time mass spectrometry data for the clinical analysis of exhaled breath](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA, Saclay, France -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-05/index.md b/content/galaxy-updates/2018-05/index.md index e50ef30c55..665bfbb8c5 100644 --- a/content/galaxy-updates/2018-05/index.md +++ b/content/galaxy-updates/2018-05/index.md @@ -278,7 +278,7 @@ The Galaxy is expanding! Please help it grow. * [Post-Doc / IR analyse de données miRNA](https://www.sfbi.fr/content/post-doc-ir-analyse-de-donn%C3%A9es-mirna), Unité de Nutrition Humaine, Clermont-Fd, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany * [Development of innovative algorithms to process real-time mass spectrometry data for the clinical analysis of exhaled breath](https://www.sfbi.fr/content/d%C3%A9veloppement-doutils-bioinformatiques-et-statistiques-pour-lanalyse-de-lair-expir%C3%A9-en-m%C3%A9dec), CEA, Saclay, France -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/galaxy-updates/2018-08/index.md b/content/galaxy-updates/2018-08/index.md index fa9a4876a0..906319e334 100644 --- a/content/galaxy-updates/2018-08/index.md +++ b/content/galaxy-updates/2018-08/index.md @@ -300,19 +300,19 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t This included a new paper to reference [whenever using, extending, or referencing Galaxy](/src/citing-galaxy/index.md#primary-publication): -* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 A new paper to reference [when discussing Galaxy in the context of reproducibility](/src/citing-galaxy/index.md#reproducibility): -* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/index.md), [John Chilton](/people/john-chilton/index.md), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 +* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 And a new paper to reference [when discussing Galaxy training](/src/citing-galaxy/index.md#training): -* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 And a new paper to cite [when discussing Galaxy in a cloud context](/src/citing-galaxy/index.md#cloud): -* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/people/enis-afgan/index.md), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 +* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 Other highlighted papers include: @@ -351,7 +351,7 @@ Edvard Martins de Oliveira, Júlio Cézar Estrella, Alexandre Cláudio Botazzo D The Galaxy is expanding! Please help it grow. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2012-09-20-distribution-news-brief/index.md b/content/news/2012-09-20-distribution-news-brief/index.md index 08a7b17b3c..797f89a235 100644 --- a/content/news/2012-09-20-distribution-news-brief/index.md +++ b/content/news/2012-09-20-distribution-news-brief/index.md @@ -21,4 +21,4 @@ upgrade: $ hg pull -u -r da9d740fce31 **Thanks for using Galaxy!** -[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) +[Jennifer Jackson](/people/jennifer-jackson/) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-10-05-distribution-news-brief/index.md b/content/news/2012-10-05-distribution-news-brief/index.md index 814bd30f25..5cb0cfd954 100644 --- a/content/news/2012-10-05-distribution-news-brief/index.md +++ b/content/news/2012-10-05-distribution-news-brief/index.md @@ -22,4 +22,4 @@ upgrade: $ hg pull -u -r b5bda7a5c345 **Thanks for using Galaxy!** -[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) +[Jennifer Jackson](/people/jennifer-jackson/) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-10-23-distribution-news-brief/index.md b/content/news/2012-10-23-distribution-news-brief/index.md index 3d8e2b1a94..313066009c 100644 --- a/content/news/2012-10-23-distribution-news-brief/index.md +++ b/content/news/2012-10-23-distribution-news-brief/index.md @@ -23,4 +23,4 @@ upgrade: $ hg pull -u -r 12fcd068b12e **Thanks for using Galaxy!** -[Jennifer Jackson](/people/jennifer-jackson/index.md) & the [Galaxy Team](/src/galaxy-team/) +[Jennifer Jackson](/people/jennifer-jackson/) & the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-11-galaxy-update/index.md b/content/news/2012-11-galaxy-update/index.md index ca1e43b7fb..9f149c37f7 100644 --- a/content/news/2012-11-galaxy-update/index.md +++ b/content/news/2012-11-galaxy-update/index.md @@ -18,4 +18,4 @@ The [November 2012 Galaxy Update is now available](/src/galaxy-updates/2012-11/i If you have anything you would like to see in the December *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2012-12-galaxy-update/index.md b/content/news/2012-12-galaxy-update/index.md index d12a8d578e..fddbb119ab 100644 --- a/content/news/2012-12-galaxy-update/index.md +++ b/content/news/2012-12-galaxy-update/index.md @@ -20,4 +20,4 @@ The [December 2012 Galaxy Update is now available](/src/galaxy-updates/2012-12/i If you have anything you would like to see in the January *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-01-galaxy-update/index.md b/content/news/2013-01-galaxy-update/index.md index 50911c9a18..7e32acc35e 100644 --- a/content/news/2013-01-galaxy-update/index.md +++ b/content/news/2013-01-galaxy-update/index.md @@ -19,4 +19,4 @@ The [January 2013 Galaxy Update is now available](/src/galaxy-updates/2013-01/in If you have anything you would like to see in the Febrarury *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-02-galaxy-update/index.md b/content/news/2013-02-galaxy-update/index.md index 5074f85fff..61cdb49bb8 100644 --- a/content/news/2013-02-galaxy-update/index.md +++ b/content/news/2013-02-galaxy-update/index.md @@ -20,4 +20,4 @@ The [February 2013 Galaxy Update is now available](/src/galaxy-updates/2013-02/i If you have anything you would like to see in the March *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-03-galaxy-admins/index.md b/content/news/2013-03-galaxy-admins/index.md index 63c4a10e12..7bb06f81f3 100644 --- a/content/news/2013-03-galaxy-admins/index.md +++ b/content/news/2013-03-galaxy-admins/index.md @@ -23,7 +23,7 @@ The [next meeting](/src/community/galaxy-admins/meetups/2013-03-20/index.md) of Presenters - Hailiang "Leon" Mei
There will also be a Galaxy Project Update from Dan Blankenberg of the Galaxy Team + Hailiang "Leon" Mei
There will also be a Galaxy Project Update from Dan Blankenberg of the Galaxy Team Links diff --git a/content/news/2013-03-galaxy-update/index.md b/content/news/2013-03-galaxy-update/index.md index aaca2429d8..54d5240a1a 100644 --- a/content/news/2013-03-galaxy-update/index.md +++ b/content/news/2013-03-galaxy-update/index.md @@ -19,4 +19,4 @@ The [March 2013 Galaxy Update is now available](/src/galaxy-updates/2013-03/inde If you have anything you would like to see in the April *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-04-galaxy-update/index.md b/content/news/2013-04-galaxy-update/index.md index 673271ed0d..eda82ae9c9 100644 --- a/content/news/2013-04-galaxy-update/index.md +++ b/content/news/2013-04-galaxy-update/index.md @@ -20,4 +20,4 @@ The [April 2013 Galaxy Update is now available](/src/galaxy-updates/2013-04/inde If you have anything you would like to see in the May *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-05-galaxy-update/index.md b/content/news/2013-05-galaxy-update/index.md index de966ccf74..6aaaa41a35 100644 --- a/content/news/2013-05-galaxy-update/index.md +++ b/content/news/2013-05-galaxy-update/index.md @@ -17,4 +17,4 @@ The [May 2013 Galaxy Update is now available](/src/galaxy-updates/2013-05/index. If you have anything you would like to see in the June *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-06-galaxy-update/index.md b/content/news/2013-06-galaxy-update/index.md index 5dbc138024..2ff3d12e0c 100644 --- a/content/news/2013-06-galaxy-update/index.md +++ b/content/news/2013-06-galaxy-update/index.md @@ -18,4 +18,4 @@ The [June 2013 Galaxy Update is now available](/src/galaxy-updates/2013-06/index If you have anything you would like to see in the July *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-07-galaxy-update/index.md b/content/news/2013-07-galaxy-update/index.md index b470adaad2..5d92880d9f 100644 --- a/content/news/2013-07-galaxy-update/index.md +++ b/content/news/2013-07-galaxy-update/index.md @@ -19,4 +19,4 @@ The [July 2013 Galaxy Update is now available](/src/galaxy-updates/2013-07/index If you have anything you would like to see in the August *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-08-galaxy-update/index.md b/content/news/2013-08-galaxy-update/index.md index 4aa5c697a8..47c5102669 100644 --- a/content/news/2013-08-galaxy-update/index.md +++ b/content/news/2013-08-galaxy-update/index.md @@ -21,4 +21,4 @@ The [August 2013 Galaxy Update is now available](/src/galaxy-updates/2013-08/ind If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-09-galaxy-update/index.md b/content/news/2013-09-galaxy-update/index.md index b36c4b0fb9..3504e2273d 100644 --- a/content/news/2013-09-galaxy-update/index.md +++ b/content/news/2013-09-galaxy-update/index.md @@ -18,4 +18,4 @@ The [September 2013 Galaxy Update is hot off the press](/src/galaxy-updates/2013 If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-10-galaxy-update/index.md b/content/news/2013-10-galaxy-update/index.md index a1fd4f8bdb..14870b9af5 100644 --- a/content/news/2013-10-galaxy-update/index.md +++ b/content/news/2013-10-galaxy-update/index.md @@ -16,4 +16,4 @@ The [October 2013 Galaxy Update is out](/src/galaxy-updates/2013-10/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-11-galaxy-update/index.md b/content/news/2013-11-galaxy-update/index.md index 094ca6a88a..baf1a5e245 100644 --- a/content/news/2013-11-galaxy-update/index.md +++ b/content/news/2013-11-galaxy-update/index.md @@ -19,4 +19,4 @@ The [November 2013 Galaxy Update is out](/src/galaxy-updates/2013-11/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2013-12-galaxy-update/index.md b/content/news/2013-12-galaxy-update/index.md index cf2cb6dfd4..613674b065 100644 --- a/content/news/2013-12-galaxy-update/index.md +++ b/content/news/2013-12-galaxy-update/index.md @@ -20,4 +20,4 @@ The [December 2013 Galaxy Update is out](/src/galaxy-updates/2013-12/index.md): If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-01-galaxy-update/index.md b/content/news/2014-01-galaxy-update/index.md index de896c76a3..e83d099737 100644 --- a/content/news/2014-01-galaxy-update/index.md +++ b/content/news/2014-01-galaxy-update/index.md @@ -32,4 +32,4 @@ If you have anything you would like to see in the next *[Galaxy Update](/src/gal Best wishes to you and yours for a happy and spectacular 2014, -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-02-galaxy-update/index.md b/content/news/2014-02-galaxy-update/index.md index dbaa4bf102..b2a869703e 100644 --- a/content/news/2014-02-galaxy-update/index.md +++ b/content/news/2014-02-galaxy-update/index.md @@ -25,4 +25,4 @@ The [25th Edition of Galaxy Update is out](/src/galaxy-updates/2014-02/index.md) If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-03-galaxy-update/index.md b/content/news/2014-03-galaxy-update/index.md index 92b9df3569..0baf4bba5b 100644 --- a/content/news/2014-03-galaxy-update/index.md +++ b/content/news/2014-03-galaxy-update/index.md @@ -24,4 +24,4 @@ Find out [what's happening in the Galaxy](/src/galaxy-updates/2014-03/index.md). If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-04-galaxy-update/index.md b/content/news/2014-04-galaxy-update/index.md index 89a4ce1970..e174ee6ffb 100644 --- a/content/news/2014-04-galaxy-update/index.md +++ b/content/news/2014-04-galaxy-update/index.md @@ -24,4 +24,4 @@ And as always, there are [new ToolShed contributions](/src/galaxy-updates/2014-0 If you have anything you would like to see in the next *[Galaxy Update](/src/galaxy-updates/index.md)*, please let us know. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-05-galaxy-update/index.md b/content/news/2014-05-galaxy-update/index.md index a43bcf8e6d..4cfe56d206 100644 --- a/content/news/2014-05-galaxy-update/index.md +++ b/content/news/2014-05-galaxy-update/index.md @@ -19,4 +19,4 @@ There's also a [Galaxy UK Tour](/src/galaxy-updates/2014-05/index.md#uk-may-2014 As always, there are [new papers](/src/galaxy-updates/2014-05/index.md#new-papers) (47 of them, including four we highlighted), [new public Galaxy Servers](/src/galaxy-updates/2014-05/index.md#new-public-servers) ([Globus Genomics Proteomics](/src/galaxy-updates/2014-05/index.md#globus-genomics-proteomics) and [SunLab Galaxy](/src/galaxy-updates/2014-05/index.md#sunlab)), [new jobs](/src/galaxy-updates/2014-05/index.md#whos-hiring) (7 postings in 6 countries), [new tools in the project ToolShed](/src/galaxy-updates/2014-05/index.md#galaxy-project-toolshed-new-repositories) (um, *lots*), and a [new public ToolShed](/src/galaxy-updates/2014-05/index.md#new-public-toolsheds) (at the [Dutch Techcentre for Life Sciences (DTL)](http://www.dtls.nl/dtl/). -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-06-galaxy-update/index.md b/content/news/2014-06-galaxy-update/index.md index 098466ef35..4c996a9f35 100644 --- a/content/news/2014-06-galaxy-update/index.md +++ b/content/news/2014-06-galaxy-update/index.md @@ -24,4 +24,4 @@ And, in the past month there were: * [One new Galaxy deployment description (deepTools)](/src/galaxy-updates/2014-06/index.md#galaxy-community-hubs) * and [a stunning number of ToolShed contributions](/src/galaxy-updates/2014-06/index.md#toolshed-contributions) -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-07-galaxy-update/index.md b/content/news/2014-07-galaxy-update/index.md index 2bf45ba1ac..8fc10eaeac 100644 --- a/content/news/2014-07-galaxy-update/index.md +++ b/content/news/2014-07-galaxy-update/index.md @@ -18,4 +18,4 @@ The [July 2014 Galaxy Update Newsletter](/src/galaxy-updates/2014-07/index.md) i * [One new Galaxy Log Board entry](/src/galaxy-updates/2014-07/index.md#galaxy-community-hubs) * and [a stunning number of ToolShed contributions](/src/galaxy-updates/2014-07/index.md#toolshed-contributions) once again. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-08-galaxy-update/index.md b/content/news/2014-08-galaxy-update/index.md index fb9bbf2f42..e9a629182d 100644 --- a/content/news/2014-08-galaxy-update/index.md +++ b/content/news/2014-08-galaxy-update/index.md @@ -15,4 +15,4 @@ The [August 2014 Galaxy Update Newsletter](/src/galaxy-updates/2014-08/index.md) * [One new public server (IM-PET)](/src/galaxy-updates/2014-08/index.md#new-public-servers) * [Who's hiring?](/src/galaxy-updates/2014-08/index.md#whos-hiring) It turns out that lots of places are. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-09-galaxy-update/index.md b/content/news/2014-09-galaxy-update/index.md index 1f4b405897..ab1abfbde4 100644 --- a/content/news/2014-09-galaxy-update/index.md +++ b/content/news/2014-09-galaxy-update/index.md @@ -24,4 +24,4 @@ And, as always, there are [new papers](/src/galaxy-updates/2014-09/index.md#new- Happy September, -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-10-galaxy-update/index.md b/content/news/2014-10-galaxy-update/index.md index 488876669b..e91405a346 100644 --- a/content/news/2014-10-galaxy-update/index.md +++ b/content/news/2014-10-galaxy-update/index.md @@ -20,4 +20,4 @@ A lot is happening in in the Galaxy in October, and a lot of good stuff happened Happy October! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-11-galaxy-update/index.md b/content/news/2014-11-galaxy-update/index.md index 65138cab97..2639c17cf6 100644 --- a/content/news/2014-11-galaxy-update/index.md +++ b/content/news/2014-11-galaxy-update/index.md @@ -20,4 +20,4 @@ A lot is happening in in the Galaxy in November, and a lot of good stuff happene * [35 new ToolShed repos](/src/galaxy-updates/2014-11/index.md#toolshed-contributions) * And a [smattering of other news](/src/galaxy-updates/2014-11/index.md#other-news) too -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2014-12-galaxy-update/index.md b/content/news/2014-12-galaxy-update/index.md index cc37e6b3cd..f540172a4c 100644 --- a/content/news/2014-12-galaxy-update/index.md +++ b/content/news/2014-12-galaxy-update/index.md @@ -18,4 +18,4 @@ As always there's a lot going on in the Galaxy this month. "Like what?" you say * [15 new ToolShed repositories from 10 contributors](/src/galaxy-updates/2014-12/index.md#toolshed-contributions) * And, [10 other juicy](/src/galaxy-updates/2014-12/index.md#other-news) (well maybe not *juicy*, but certainly not *crunchy*) [bits of news](/src/galaxy-updates/2014-12/index.md#other-news) -[Dave Clements](/people/dave-clements/index.md) and the *crisp* [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the *crisp* [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-01-galaxy-update/index.md b/content/news/2015-01-galaxy-update/index.md index 4179b19d46..53f8b2b6ef 100644 --- a/content/news/2015-01-galaxy-update/index.md +++ b/content/news/2015-01-galaxy-update/index.md @@ -21,4 +21,4 @@ Happy New Year from the Galaxy Project! * [Over 30 new and updated ToolShed repositories from 12 contributors](/src/galaxy-updates/2014-12/index.md#toolshed-contributions) * And, [other news](/src/galaxy-updates/2014-12/index.md#other-news) too. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-02-galaxy-update/index.md b/content/news/2015-02-galaxy-update/index.md index f4d870875f..5855b6c626 100644 --- a/content/news/2015-02-galaxy-update/index.md +++ b/content/news/2015-02-galaxy-update/index.md @@ -31,4 +31,4 @@ and *Community News* too: * [Ruđer Bošković Institute joins GTN](/src/galaxy-updates/2015-02/index.md#new-gtn-member-ruđer-bošković-institute) * And, [other news](/src/galaxy-updates/2015-02/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-03-galaxy-update/index.md b/content/news/2015-03-galaxy-update/index.md index 46fb8ef1a3..1c346bc1b1 100644 --- a/content/news/2015-03-galaxy-update/index.md +++ b/content/news/2015-03-galaxy-update/index.md @@ -50,4 +50,4 @@ In addition, there is news on: * **[Galaxy on GitHub!](/src/galaxy-updates/2015-03/index.md#galaxy-github)** Come and join us in developing Galaxy! * And, [other news](/src/galaxy-updates/2015-03/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-04-galaxy-update/index.md b/content/news/2015-04-galaxy-update/index.md index ab3faac231..3548bde558 100644 --- a/content/news/2015-04-galaxy-update/index.md +++ b/content/news/2015-04-galaxy-update/index.md @@ -31,4 +31,4 @@ In addition, there is news on: * [One new Community Log Board entry](/src/galaxy-updates/2015-04/index.md#galaxy-community-hubs) * And, [other news](/src/galaxy-updates/2015-04/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-05-galaxy-update/index.md b/content/news/2015-05-galaxy-update/index.md index b0127169f1..0fecaab926 100644 --- a/content/news/2015-05-galaxy-update/index.md +++ b/content/news/2015-05-galaxy-update/index.md @@ -25,4 +25,4 @@ The **[May Galactic News](/src/galaxy-updates/2015-05/index.md)** brings lots of And, [other news](/src/galaxy-updates/2015-05/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-06-galaxy-update/index.md b/content/news/2015-06-galaxy-update/index.md index df2c4450c4..b52f80c459 100644 --- a/content/news/2015-06-galaxy-update/index.md +++ b/content/news/2015-06-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[June Galactic News](/src/galaxy-updates/2015-06/index.md)** brings this * And, [other news](/src/galaxy-updates/2015-06/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-08-galaxy-update/index.md b/content/news/2015-08-galaxy-update/index.md index e2f7c58f81..a8d0d9af2e 100644 --- a/content/news/2015-08-galaxy-update/index.md +++ b/content/news/2015-08-galaxy-update/index.md @@ -25,7 +25,7 @@ The **[August Galactic News](/src/galaxy-updates/2015-08/index.md)** is out. It * [76 Tool Shed updates and additions from 20+ contributors](/src/toolshed/contributions/2015-07/index.md) * And, of course [other news](/src/galaxy-updates/2015-08/index.md#other-news) as well. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/)
diff --git a/content/news/2015-09-galaxy-update/index.md b/content/news/2015-09-galaxy-update/index.md index 93da3d3434..25aa421853 100644 --- a/content/news/2015-09-galaxy-update/index.md +++ b/content/news/2015-09-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[September Galactic News](/src/galaxy-updates/2015-09/index.md)** is hot o * [Workflow4Metabolomics](/src/galaxy-updates/2015-09/index.md#workflow4metabolomics) and [EpiToolKit](/src/galaxy-updates/2015-09/index.md#epitoolkit) * [Three security advisories](/src/galaxy-updates/2015-09/index.md#security-advisories), [Recent Releases](/src/galaxy-updates/2015-09/index.md#other-releases), and [ToolShed Contributions](/src/galaxy-updates/2015-09/index.md#toolshed-contributions) -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-10-galaxy-update/index.md b/content/news/2015-10-galaxy-update/index.md index 46eb24495f..4e9cbc2d93 100644 --- a/content/news/2015-10-galaxy-update/index.md +++ b/content/news/2015-10-galaxy-update/index.md @@ -28,4 +28,4 @@ The **[October Galactic News](/src/galaxy-updates/2015-10/index.md)** is hot off * [Lots of Tool Shed contributions](/src/toolshed/contributions/2015-09/index.md). * and [lots of other news too](/src/galaxy-updates/2015-10/index.md#other-news), [including a birthday](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) (OK, maybe we are chronologically challenged, but we're young!) -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-11-galaxy-update/index.md b/content/news/2015-11-galaxy-update/index.md index 58eff7d52e..d40e8c566e 100644 --- a/content/news/2015-11-galaxy-update/index.md +++ b/content/news/2015-11-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[November Galactic News](/src/galaxy-updates/2015-11/index.md)** is hot of * [Planemo 0.15.0 - 0.18.1](/src/galaxy-updates/2015-11/index.md#planemo-0150---0181) * and [lots of other news too](/src/galaxy-updates/2015-11/index.md#other-news). -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2015-12-galaxy-update/index.md b/content/news/2015-12-galaxy-update/index.md index bb38d1aefd..8dc2de2185 100644 --- a/content/news/2015-12-galaxy-update/index.md +++ b/content/news/2015-12-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[December Galactic News](/src/galaxy-updates/2015-12/index.md)** is hot of * [ToolShed Contributions in October and November](/src/galaxy-updates/2015-12/index.md#toolshed-contributions) * and [lots of other news too](/src/galaxy-updates/2015-12/index.md#other-news). -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/201502-galaxy-admins/index.md b/content/news/201502-galaxy-admins/index.md index 8fd23b35f4..921fb4715d 100644 --- a/content/news/201502-galaxy-admins/index.md +++ b/content/news/201502-galaxy-admins/index.md @@ -6,10 +6,10 @@ date: "2015-01-28" The first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) will happen online [on Thursday, 19 February](http://bit.ly/1yZJSkN). [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/index.md), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/index.md), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) will lead a short discussion on *GalaxyAdmins direction*. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) will lead a short discussion on *GalaxyAdmins direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. We are looking forward to starting this group again, -[Hans-Rudolf Hotz](/people/hansrudolf-hotz/index.md) and [Dave Clements](/src/people/dave-clements/) +[Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/src/people/dave-clements/) diff --git a/content/news/2016-01-galaxy-update/index.md b/content/news/2016-01-galaxy-update/index.md index eb037dc294..568cf0fbc2 100644 --- a/content/news/2016-01-galaxy-update/index.md +++ b/content/news/2016-01-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[January 2016 Galactic News](/src/galaxy-updates/2016-01/index.md)** is ho * [ToolShed Contributions](/src/galaxy-updates/2016-01/index.md#toolshed-contributions) from December * and [some other news too](/src/galaxy-updates/2016-01/index.md#other-news). -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-02-galaxy-update/index.md b/content/news/2016-02-galaxy-update/index.md index bc32e6eaea..c0cd54d908 100644 --- a/content/news/2016-02-galaxy-update/index.md +++ b/content/news/2016-02-galaxy-update/index.md @@ -30,4 +30,4 @@ The **[February 2016 Galactic News](/src/galaxy-updates/2016-02/index.md)** is h Happy February! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-03-galaxy-update/index.md b/content/news/2016-03-galaxy-update/index.md index 7d61c9a307..148d295fd5 100644 --- a/content/news/2016-03-galaxy-update/index.md +++ b/content/news/2016-03-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[March 2016 Galactic News](/src/galaxy-updates/2016-03/index.md)** is hot * [Three new Galaxy servers](/src/galaxy-updates/2016-03/index.md#new-public-galaxy-servers) * [New ToolShed Contributions](/src/galaxy-updates/2016-03/index.md#toolshed-contributions) -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-04-galaxy-update/index.md b/content/news/2016-04-galaxy-update/index.md index aafd803f9b..e2e948c4d0 100644 --- a/content/news/2016-04-galaxy-update/index.md +++ b/content/news/2016-04-galaxy-update/index.md @@ -42,4 +42,4 @@ And some [other news](/src/galaxy-updates/2016-04/index.md#other-news) too. Happy April, -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-05-galaxy-update/index.md b/content/news/2016-05-galaxy-update/index.md index 6249a3934a..2ea8904d46 100644 --- a/content/news/2016-05-galaxy-update/index.md +++ b/content/news/2016-05-galaxy-update/index.md @@ -30,4 +30,4 @@ Some highlights from the **[May Galaxy News](/src/galaxy-updates/2016-05/index.m Don't miss those deadlines, and [see you in June](https://web.archive.org/web/http://gcc2016.iu.edu/), -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-06-galaxy-update/index.md b/content/news/2016-06-galaxy-update/index.md index 752bf39d07..77203059f4 100644 --- a/content/news/2016-06-galaxy-update/index.md +++ b/content/news/2016-06-galaxy-update/index.md @@ -28,4 +28,4 @@ Some highlights from the **[June Galaxy News](/src/galaxy-updates/2016-06/index. Hope to [see you in Bloomington](https://web.archive.org/web/http://gcc2016.iu.edu/), -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-07-galaxy-update/index.md b/content/news/2016-07-galaxy-update/index.md index 767334483b..1cbe3ede3b 100644 --- a/content/news/2016-07-galaxy-update/index.md +++ b/content/news/2016-07-galaxy-update/index.md @@ -30,4 +30,4 @@ Some highlights from the **[July Galaxy News](/src/galaxy-updates/2016-07/index. Hope to [see you in Montpellier](/src/galaxy-updates/2016-07/index.md#gcc2017-26-30-june-2017-montpellier-france)! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-08-galaxy-update/index.md b/content/news/2016-08-galaxy-update/index.md index 19c2624637..1c38562848 100644 --- a/content/news/2016-08-galaxy-update/index.md +++ b/content/news/2016-08-galaxy-update/index.md @@ -19,4 +19,4 @@ The **[August Galaxy News](/src/galaxy-updates/2016-08/index.md) is out:** * [TooShed Contributions](/src/galaxy-updates/2016-08/index.md#toolshed-contributions) * And [other news](/src/galaxy-updates/2016-08/index.md#other-news) too. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-09-galaxy-update/index.md b/content/news/2016-09-galaxy-update/index.md index 8f1698a05d..1a9df23c94 100644 --- a/content/news/2016-09-galaxy-update/index.md +++ b/content/news/2016-09-galaxy-update/index.md @@ -23,4 +23,4 @@ The **[September Galaxy News](/src/galaxy-updates/2016-09/index.md) is out:** * [TooShed Contributions](/src/galaxy-updates/2016-09/index.md#toolshed-contributions) * And [other news](/src/galaxy-updates/2016-09/index.md#other-news) too. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2016-10-galaxy-update/index.md b/content/news/2016-10-galaxy-update/index.md index f0019a9c13..2bce82e533 100644 --- a/content/news/2016-10-galaxy-update/index.md +++ b/content/news/2016-10-galaxy-update/index.md @@ -25,4 +25,4 @@ There are also [117 new publications](/src/galaxy-updates/2016-10/index.md#new-p We hope to see you in Freiburg, Salt Lake, Melbourne, online, and around the world, -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/2017-11-oslo-admin-reg/index.md b/content/news/2017-11-oslo-admin-reg/index.md index 6c6256c993..7ddc582a4c 100644 --- a/content/news/2017-11-oslo-admin-reg/index.md +++ b/content/news/2017-11-oslo-admin-reg/index.md @@ -24,5 +24,5 @@ Instructors * [Björn Grüning](https://github.com/bgruening) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Elixir Germany](https://www.elixir-europe.org/about-us/who-we-are/nodes/germany), [University of Freiburg](https://www.uni-freiburg.de/?set_language=en)) * [Marius van den Beek](https://github.com/mvdbeek) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Institute Curie](https://science.institut-curie.org/), France) * [Nicola Soranzo](http://www.earlham.ac.uk/nicola-soranzo) ([Elixir Galaxy WG](https://www.elixir-europe.org/about/groups/galaxy-wg), [Earlham Institute](http://www.earlham.ac.uk/), UK) -* [Enis Afgan](/people/enis-afgan/index.md) ([Galaxy Project](/src/), [Johns Hopkins University](https://jhu.edu/), USA) +* [Enis Afgan](/people/enis-afgan/) ([Galaxy Project](/src/), [Johns Hopkins University](https://jhu.edu/), USA) * [Abdulrahman Azab](http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html) ([Elixir Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway), [USIT](http://www.usit.uio.no/), [University of Oslo](http://www.uio.no/), Norway) diff --git a/content/news/2018-05-gccbosc-childcare/index.md b/content/news/2018-05-gccbosc-childcare/index.md index badebf716c..957a517d11 100644 --- a/content/news/2018-05-gccbosc-childcare/index.md +++ b/content/news/2018-05-gccbosc-childcare/index.md @@ -21,4 +21,4 @@ Childcare can be booked in half-day increments and **rates work out to $5.50/hou We hope to see you, and your kids, in Portland, -[Dave Clements](/people/dave-clements/index.md) on behalf of the [GCCBOSC 2018 Organizers](/src/events/gccbosc2018/organizers/) +[Dave Clements](/people/dave-clements/) on behalf of the [GCCBOSC 2018 Organizers](/src/events/gccbosc2018/organizers/) diff --git a/content/news/2018-09-galaxy-update/index.md b/content/news/2018-09-galaxy-update/index.md index cafa7a9cf9..8ff2d4c81e 100644 --- a/content/news/2018-09-galaxy-update/index.md +++ b/content/news/2018-09-galaxy-update/index.md @@ -224,7 +224,7 @@ The Galaxy is expanding! Please help it grow. * [Bioinformaticien/biostatisticien biologiste](http://www.sfbi.fr/content/offre-de-poste-de-bioinformaticienbiostatisticien-biologiste-soci%C3%A9t%C3%A9-phylogene), Phylogene S.A, Bernis, France * [M2 : Diversité bactérienne associée aux microalgues toxiques (metabarcoding)](http://www.sfbi.fr/content/m2-diversit%C3%A9-bact%C3%A9rienne-associ%C3%A9e-aux-microalgues-toxiques-metabarcoding), IFREMER Centre Bretagne, Plouzané, France * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2018-10-galaxy-update/index.md b/content/news/2018-10-galaxy-update/index.md index b000388e57..f9945bf139 100644 --- a/content/news/2018-10-galaxy-update/index.md +++ b/content/news/2018-10-galaxy-update/index.md @@ -281,7 +281,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2018-11-galaxy-update/index.md b/content/news/2018-11-galaxy-update/index.md index 3965ed897b..480b4123f4 100644 --- a/content/news/2018-11-galaxy-update/index.md +++ b/content/news/2018-11-galaxy-update/index.md @@ -267,7 +267,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring software engineers and postdocs at Johns Hopkins](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2018-12-galaxy-admins/index.md b/content/news/2018-12-galaxy-admins/index.md index abeab5a29f..b4b182ef3a 100644 --- a/content/news/2018-12-galaxy-admins/index.md +++ b/content/news/2018-12-galaxy-admins/index.md @@ -13,14 +13,14 @@ Got some ideas? **[Nominate them](https://docs.google.com/forms/d/e/1FAIpQLSfv25 We hope to see you in February, -[Helena Rasche](/people/helena-rasche/index.md) and [Dave Clements](/src/people/dave-clements/) +[Helena Rasche](/people/helena-rasche/) and [Dave Clements](/src/people/dave-clements/)
Q: Why did the bimonthly meetups go away for *two years?*

-A: In early 2017, [Hans-Rudolf](/people/hansrudolf-hotz/index.md) stepped down after several years of leading the group. [Dave C](/people/dave-clements/) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/src/people/helena-rasche/) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.* +A: In early 2017, [Hans-Rudolf](/people/hansrudolf-hotz/) stepped down after several years of leading the group. [Dave C](/people/dave-clements/) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/src/people/helena-rasche/) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.*

diff --git a/content/news/2018-12-galaxy-update/index.md b/content/news/2018-12-galaxy-update/index.md index 65d91aee5a..66d0cd267b 100644 --- a/content/news/2018-12-galaxy-update/index.md +++ b/content/news/2018-12-galaxy-update/index.md @@ -287,7 +287,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Scientist (f/m), NGS bioinformatics core facility](https://bms.candibase.de/atool/helmholtz/frontend.php?view=a32a9d6396d8ca063e28db02ea15e3e3&lang=en), Helmholtz Zentrum München, Germany * [Galaxy Developers](https://twitter.com/GalaxyEnt_Soc/status/1041877925505716225), Intero Life Sciences, United States. * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md): distributed computing engineer and a full stack developer; see [this for more details on the positions](https://jobs.jhu.edu/job/Baltimore-Software-Engineer-MD-21218/442289500/, Baltimore, Maryland, United States). Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2019-01-galaxy-update/index.md b/content/news/2019-01-galaxy-update/index.md index 327f2c4b96..05539a2f14 100644 --- a/content/news/2019-01-galaxy-update/index.md +++ b/content/news/2019-01-galaxy-update/index.md @@ -212,11 +212,11 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications from December: -* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/index.md), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/src/people/bjoern-gruening/), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; +* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/src/people/bjoern-gruening/), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; doi: 10.1101/488643 * **[PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud](https://doi.org/10.1093/gigascience/giy149)**, Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Steffen Neumann, Jon Ander Novella, Claire O'Donovan, Jake T M Pearce, Alina Peluso, Marco Enrico Piras, Luca Pireddu, Michelle A C Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R Viant, Ralf J M Weber, Gianluigi Zanetti, Christoph Steinbeck, *GigaScience*, giy149, doi: 10.1093/gigascience/giy149 -* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/people/vahid-jalili/index.md), [Enis Afgan](/people/enis-afgan/index.md), [James Taylor](/src/people/james-taylor/), [Jeremy Goecks](/src/people/jeremy-goecks/), *bioRxiv* 506238, doi: 10.1101/506238 +* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/people/vahid-jalili/), [Enis Afgan](/people/enis-afgan/), [James Taylor](/src/people/james-taylor/), [Jeremy Goecks](/src/people/jeremy-goecks/), *bioRxiv* 506238, doi: 10.1101/506238 * **[SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data](https://doi.org/10.1093/bioinformatics/bty947 )**, Jamie Soul, Tim E Hardingham, Ray P Boot-Handford, Jean-Marc Schwartz, *Bioinformatics*, bty947, doi: 10.1093/bioinformatics/bty947 @@ -286,7 +286,7 @@ We tag papers that use, mention, implement or extend public Galaxy platforms (se # New Galactic Blog Posts -[Galactic Blog](/src/blog/index.md) +[Galactic Blog](/src/blog/) There is one new *[Galactic Blog](/src/blog/index.md)* entry: @@ -316,7 +316,7 @@ The dark energy* of irreproducible research is threatening the scienc * [Bioinformatics Scientist](https://www.indeed.com/viewjob?jk=5288546935e35605), ResearchDx, Irvine, California, United States * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * [Freiburg Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2018/01/18/openpositions/), Freiburg, Germany -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States). Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2019-02-galaxy-update/index.md b/content/news/2019-02-galaxy-update/index.md index 699fb307b9..f00dd35a06 100644 --- a/content/news/2019-02-galaxy-update/index.md +++ b/content/news/2019-02-galaxy-update/index.md @@ -160,7 +160,7 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t * **[VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes](https://doi.org/10.1101/492074)**, Sara Silva Pereira, John Heap, Andrew R Jones, Andrew P. Jackson. *bioRxiv* 492074; doi: 10.1101/492074 * **[PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting](https://doi.org/10.1101/522458)**, Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau. *bioRxiv* 522458; doi: 10.1101/522458 * **[Enhancing Access to Digital Media: The Language Application Grid in the HTRC Data Capsule](https://doi.org/10.1145/3093338.3104171)**, James Pustejovsky, Marc Verhagen, Keongmin Rim, Yu Ma, Liang Ran, Samitha Liyanage, Jaimie Murdock, Robert H. McDonald, Beth Plale. In PEARC17 Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, Article No. 60. doi: 10.1145/3093338.3104171 -* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/people/nate/index.md), [Anton Nekrutenko](/src/people/anton/). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 +* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/people/nate/), [Anton Nekrutenko](/src/people/anton/). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 * **[Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis](https://link.springer.com/protocol/10.1007%2F978-1-4939-8982-9_8)**, Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer. In: Lai X., Gupta S., Vera J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY * **[QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics](https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727)**, Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda J. Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian A. Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy J. Griffin , and Pratik D. Jagtap. *Journal of Proteome Research*, Article ASAP DOI: 10.1021/acs.jproteome.8b00727 @@ -309,7 +309,7 @@ The *dark energy* of irreproducible research is threatening the science universe * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * The [The European Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2019/01/10/openpositions/), Freiburg, Germany * Software engineer, system analysts/administrators, data analyst, and a comunnity and/or research manager -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States. Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2019-03-galaxy-update/index.md b/content/news/2019-03-galaxy-update/index.md index 60dfaf3694..059a617087 100644 --- a/content/news/2019-03-galaxy-update/index.md +++ b/content/news/2019-03-galaxy-update/index.md @@ -291,7 +291,7 @@ The *dark energy* of irreproducible research is threatening the science universe * [NGS Scientific Applications Specialist](https://careers-idtdna.icims.com/jobs/4112/ngs-scientific-applications-specialist/job), Integrated DNA technologies, Iowa City, Iowa, United States * The [The European Galaxy Team has open positions](https://usegalaxy-eu.github.io/posts/2019/01/10/openpositions/), Freiburg, Germany * Software engineer, system analysts/administrators, data analyst, and a comunnity and/or research manager -* The [Blankenberg](/people/dan/index.md) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). +* The [Blankenberg](/people/dan/) Lab in the [Genomic Medicine Institute](http://www.lerner.ccf.org/gmi/) at the [Cleveland Clinic Lerner Research Institute](https://www.lerner.ccf.org/) is [hiring postdocs](/src/news/2017-09-hiring-at-cc/). * [Galaxy Project is hiring two software engineers at Johns Hopkins University](/src/news/2017-08-hiring-at-hopkins/index.md), Baltimore, Maryland, United States. Have a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it in next month's [update](/src/galaxy-updates/index.md). diff --git a/content/news/2019-06-galaxy-update/index.md b/content/news/2019-06-galaxy-update/index.md index 2495ea4f30..c82e3b1682 100644 --- a/content/news/2019-06-galaxy-update/index.md +++ b/content/news/2019-06-galaxy-update/index.md @@ -177,7 +177,7 @@ There were 10 *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BG * **[NGPhylogeny.fr: new generation phylogenetic services for non-specialists](https://doi.org/10.1093/nar/gkz303)**, Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier Gascuel. *Nucleic Acids Research*, gkz303, doi: 10.1093/nar/gkz303 * **[Rice Galaxy: an open resource for plant science](https://academic.oup.com/gigascience/article/8/5/giz028/5492234)**, Venice Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay Triplett, Jillian Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar and Ramil P. Mauleon. *GigaScience*, 8, 2019, 1–14, doi: 10.1093/gigascience/giz028 * **[The RNA workbench 2.0: next generation RNA data analysis](https://doi.org/10.1093/nar/gkz353)**, Jorg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen and [Björn Grüning](https://github.com/bgruening). *Nucleic Acids Research*, gkz353, doi: 10.1093/nar/gkz353 -* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/people/dan/index.md), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). *bioRxiv* 642280; doi: 10.1101/642280 +* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). *bioRxiv* 642280; doi: 10.1101/642280 * **[Prediction and Characterization of miRNA/Target Pairs in Non‐Model Plants Using RNA‐seq](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cppb.20090)**, Kira C. M. Neller, Alexander Klenov, Katalin A. Hudak. *Current Protocols in Plant Biology*, e20090. doi: 10.1002/cppb.20090 * **[The Repetitive DNA Composition in the Natural Pesticide Producer *Tanacetum cinerariifolium:* Interindividual Variation of Subtelomeric Tandem Repeats](https://doi.org/10.3389/fpls.2019.00613)**, Jelena Mlinarec, Ana Skuhala, Adela Jurković, Nenad Malenica, Jamie McCann, Hanna Weiss-Schneeweiss, Borut Bohanec and Višnja Besendorfer. *Frontiers in Plant Science*, 16 May 2019, doi: 10.3389/fpls.2019.00613 diff --git a/content/news/2019-08-incob-building/index.md b/content/news/2019-08-incob-building/index.md index 8f3323bae2..981c5cd5da 100644 --- a/content/news/2019-08-incob-building/index.md +++ b/content/news/2019-08-incob-building/index.md @@ -16,4 +16,4 @@ Several regional communities and resources already exist in the Galaxy ecosystem Galaxy is a widely used and deployed open-source platform that integrates thousands of analysis tools, and supports data integration and analysis, workflow creation, data visualization, and sharing and publishing your analyses and pipelines. Galaxy is also *a global community* of researchers, programmers, trainers, and users all doing and supporting data intensive research. Interested? Then we hope to see you at INCOB.
-[Dave Clements](/people/dave-clements/index.md), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) +[Dave Clements](/people/dave-clements/), [Gareth Price](https://qfab.org/team-member/dr-gareth-price), [Nuwan Goonesekera](https://www.melbournebioinformatics.org.au/people/nuwan-goonasekera/), and [Simon Gladman](https://galaxyproject.org/blog/2018-12-cotm-simon-gladman/) diff --git a/content/news/2019-10-galaxy-update/index.md b/content/news/2019-10-galaxy-update/index.md index c60710e629..1c165308d4 100644 --- a/content/news/2019-10-galaxy-update/index.md +++ b/content/news/2019-10-galaxy-update/index.md @@ -132,7 +132,7 @@ Ellrott, Kyle, Alex Buchanan, et al. *Genome Biology* 20 (1): 195. doi: 10.1186/
[You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda](http://doi.acm.org/10.1145/3307339.3343178)
-[Daniel Blankenberg](/people/dan/index.md), [Martin Cech](/src/people/marten/). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178 +[Daniel Blankenberg](/people/dan/), [Martin Cech](/src/people/marten/). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178
diff --git a/content/news/2019-10-hacktoberfest/index.md b/content/news/2019-10-hacktoberfest/index.md index 6cf9218ab0..f37864466c 100644 --- a/content/news/2019-10-hacktoberfest/index.md +++ b/content/news/2019-10-hacktoberfest/index.md @@ -15,4 +15,4 @@ Not sure what to contribute? Here are a few suggestions to get you started: * Get your hands dirty with some DevOps topics, check out Galaxy’s incubator project: [CloudVE](https://github.com//cloudve) See you online,
-[Alex Ostrovsky](/people/alex-ostrovsky/index.md) and [Enis Afgan](/src/people/enis-afgan/) +[Alex Ostrovsky](/people/alex-ostrovsky/) and [Enis Afgan](/src/people/enis-afgan/) diff --git a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md index 4332b6bc67..f3e4cd113d 100644 --- a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md +++ b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md @@ -4,4 +4,4 @@ date: "2011-09-01" ---
Concurrency and Computation: Practice & Experience
-A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/src/people/dannon-baker/) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. +A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/src/people/dannon-baker/) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. diff --git a/content/news/baltimore-meetup201501/index.md b/content/news/baltimore-meetup201501/index.md index adff5edd6d..e7277f381a 100644 --- a/content/news/baltimore-meetup201501/index.md +++ b/content/news/baltimore-meetup201501/index.md @@ -16,4 +16,4 @@ We are hoping this will be the first of many meetups, both in the Baltimore area Thanks, -[Enis Afgan](/people/enis-afgan/index.md) and [Nitesh Turaga](/people/nitesh-turaga/), of the [Galaxy Team](/src/galaxy-team/) +[Enis Afgan](/people/enis-afgan/) and [Nitesh Turaga](/people/nitesh-turaga/), of the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/bio-blend-v0.5.2/index.md b/content/news/bio-blend-v0.5.2/index.md index 5da3f5c52e..79cffb96cc 100644 --- a/content/news/bio-blend-v0.5.2/index.md +++ b/content/news/bio-blend-v0.5.2/index.md @@ -22,4 +22,4 @@ See the [commit messages](https://github.com/afgane/bioblend/compare/d8925715a5a Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/) & Simone Leo & Nicola Soranzo & [The Galaxy Team](/src/galaxy-team/) +[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & Simone Leo & Nicola Soranzo & [The Galaxy Team](/src/galaxy-team/) diff --git a/content/news/bio-blend-v0.5.3/index.md b/content/news/bio-blend-v0.5.3/index.md index 61f7aac55f..fad79795c6 100644 --- a/content/news/bio-blend-v0.5.3/index.md +++ b/content/news/bio-blend-v0.5.3/index.md @@ -34,4 +34,4 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/index.md) & [John](/people/john-chilton/index.md) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) +[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) diff --git a/content/news/cloudman-release201401/index.md b/content/news/cloudman-release201401/index.md index ade419305e..a560d10057 100644 --- a/content/news/cloudman-release201401/index.md +++ b/content/news/cloudman-release201401/index.md @@ -32,4 +32,4 @@ For more details on the new features, see the the [CHANGELOG](https://bitbucket. Enjoy and please let us know what you think, -[Enis Afgan](/people/enis-afgan/index.md) and [Dannon Baker](/src/people/dannon-baker/) +[Enis Afgan](/people/enis-afgan/) and [Dannon Baker](/src/people/dannon-baker/) diff --git a/content/news/cloudman-release201408/index.md b/content/news/cloudman-release201408/index.md index df0020de6e..ba8b939d01 100644 --- a/content/news/cloudman-release201408/index.md +++ b/content/news/cloudman-release201408/index.md @@ -26,4 +26,4 @@ For complete details on implemented changes, please see the [source code commits Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/index.md) & [Dannon](/people/dannon-baker/) & [The Galaxy Team](/src/galaxy-team/) +[Enis](/people/enis-afgan/) & [Dannon](/people/dannon-baker/) & [The Galaxy Team](/src/galaxy-team/) diff --git a/content/news/conda-dependency-codefest-report/index.md b/content/news/conda-dependency-codefest-report/index.md index 556477a102..e8e89217fe 100644 --- a/content/news/conda-dependency-codefest-report/index.md +++ b/content/news/conda-dependency-codefest-report/index.md @@ -38,4 +38,4 @@ Infrastructure: Thanks to everyone who participated! -[Rémi Marenco](/people/remi-marenco/index.md). [Nitesh Turaga](/people/nitesh-turaga/), and [Björn Grüning](/src/people/bjoern-gruening/) +[Rémi Marenco](/people/remi-marenco/). [Nitesh Turaga](/people/nitesh-turaga/), and [Björn Grüning](/src/people/bjoern-gruening/) diff --git a/content/news/galaxy-current-protocols/index.md b/content/news/galaxy-current-protocols/index.md index b8829c7ff1..531ed3bbf3 100644 --- a/content/news/galaxy-current-protocols/index.md +++ b/content/news/galaxy-current-protocols/index.md @@ -7,10 +7,10 @@ date: "2012-06-18" Two new Galaxy-related papers are now available in [Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html): **["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html)** - [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/).
+ [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 10.5.

**["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html)** - [Enis Afgan](/people/enis-afgan/index.md), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/).
+ [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 11.9. Both papers feature hands-on, step by step protocols, accompanied by numerous and detailed figures at each step. diff --git a/content/news/galaxy-linked-in-group-created/index.md b/content/news/galaxy-linked-in-group-created/index.md index 05d84bb93a..64c74ecd4f 100644 --- a/content/news/galaxy-linked-in-group-created/index.md +++ b/content/news/galaxy-linked-in-group-created/index.md @@ -10,4 +10,4 @@ A [Galaxy Group now exists on LinkedIn](http://bit.ly/gxyLinkedIn). The group i If you are on LinkedIn, please consider [joining the group](http://bit.ly/gxyLinkedIn) today. -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/galaxy-pag2012/index.md b/content/news/galaxy-pag2012/index.md index a46185681f..7badaa2b28 100644 --- a/content/news/galaxy-pag2012/index.md +++ b/content/news/galaxy-pag2012/index.md @@ -6,7 +6,7 @@ date: "2012-01-06" [Plant and Animal Genome XX (PAG2012)](/src/events/pag2012/index.md) starts in San Diego on January 14. If you are attending PAG then you will have (at least) [a half-dozen opportunities](/src/events/pag2012/index.md) to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the [Galaxy @ PAG2012 page](/src/events/pag2012/index.md) and the [conference website](http://www.intlpag.org/) for more information. -Dannon Baker and [Dave Clements](/people/dave-clements/index.md) from the [Galaxy Team](/src/galaxy-team/) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. +Dannon Baker and [Dave Clements](/people/dave-clements/) from the [Galaxy Team](/src/galaxy-team/) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, diff --git a/content/news/galaxy-project-grant-support/index.md b/content/news/galaxy-project-grant-support/index.md index ab02ebb048..721ff1530f 100644 --- a/content/news/galaxy-project-grant-support/index.md +++ b/content/news/galaxy-project-grant-support/index.md @@ -21,4 +21,4 @@ Any other information you want to provide would be helpful. Not only will this s Many thanks, -[James Taylor](/people/james-taylor/index.md) and [Anton Nekrutenko](/people/anton/), on behalf of the [Galaxy Team](/src/galaxy-team/) +[James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/people/anton/), on behalf of the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/galaxy-tour-de-france2012/index.md b/content/news/galaxy-tour-de-france2012/index.md index 3828bc506f..c799ca32d3 100644 --- a/content/news/galaxy-tour-de-france2012/index.md +++ b/content/news/galaxy-tour-de-france2012/index.md @@ -4,7 +4,7 @@ date: "2012-04-25" ---
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/index.md), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. diff --git a/content/news/gcc2012-registration-is-open/index.md b/content/news/gcc2012-registration-is-open/index.md index e6d04c3c6b..dba6602402 100644 --- a/content/news/gcc2012-registration-is-open/index.md +++ b/content/news/gcc2012-registration-is-open/index.md @@ -17,4 +17,4 @@ There are several [registration levels](/src/events/gcc2012/register/index.md), GCC2012 is hosted by the [University of Illinois at Chicago](http://uic.edu/), the [University of Illinois at Urbana-Champaign](http://illinois.edu/), and the [Computation Institute](http://www.ci.anl.gov/). -[Dave Clements](/people/dave-clements/index.md), on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) +[Dave Clements](/people/dave-clements/), on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) diff --git a/content/news/gcc2012-registration-open/index.md b/content/news/gcc2012-registration-open/index.md index 8103940315..9caa911890 100644 --- a/content/news/gcc2012-registration-open/index.md +++ b/content/news/gcc2012-registration-open/index.md @@ -24,4 +24,4 @@ Finally, [abstract submission](/src/events/gcc2012/abstracts/index.md) is also o Looking forward to seeing you in Chicago! -[Dave Clements](/people/dave-clements/index.md) on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) +[Dave Clements](/people/dave-clements/) on behalf of the [GCC2012 Organizing Committee](/src/events/gcc2012/Organizing Committee/) diff --git a/content/news/gcc2012-scheduled/index.md b/content/news/gcc2012-scheduled/index.md index 536ccfc7b9..17a4f4ca4e 100644 --- a/content/news/gcc2012-scheduled/index.md +++ b/content/news/gcc2012-scheduled/index.md @@ -12,4 +12,4 @@ Some things will be the same as in previous years, but we are also using feedbac Please reserve July 25-27 on your calendars! -[Dave Clements](/people/dave-clements/index.md) and [Neil Bahroos](/src/NeilBahroos/) +[Dave Clements](/people/dave-clements/) and [Neil Bahroos](/src/NeilBahroos/) diff --git a/content/news/gcc2014-hackathon/index.md b/content/news/gcc2014-hackathon/index.md index 5c7c6ad055..7467afb3e9 100644 --- a/content/news/gcc2014-hackathon/index.md +++ b/content/news/gcc2014-hackathon/index.md @@ -16,4 +16,4 @@ Finally, we are very happy to have **[Curoverse](https://curoverse.com/) on boar We hope to see you in June, and can't wait to see what we can accomplish! --[Dannon Baker](/people/dannon-baker/index.md) on behalf of the [GCC2014 Hackathon Organizing Committee](/src/events/gcc2014/organizers/#hackathon-committee) +-[Dannon Baker](/people/dannon-baker/) on behalf of the [GCC2014 Hackathon Organizing Committee](/src/events/gcc2014/organizers/#hackathon-committee) diff --git a/content/news/gcc2016-call-for-host/index.md b/content/news/gcc2016-call-for-host/index.md index 4cc6661c4a..c75a7254b3 100644 --- a/content/news/gcc2016-call-for-host/index.md +++ b/content/news/gcc2016-call-for-host/index.md @@ -36,4 +36,4 @@ Hosts get copious (and enthusiastic) organizational support from Galaxy's Outrea Hoping to work with you in 2016! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/gcc2017-call-for-host/index.md b/content/news/gcc2017-call-for-host/index.md index a688f8c078..9b6a5a8007 100644 --- a/content/news/gcc2017-call-for-host/index.md +++ b/content/news/gcc2017-call-for-host/index.md @@ -45,4 +45,4 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2017! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/gcc2018-call-for-host/index.md b/content/news/gcc2018-call-for-host/index.md index 7c49440df3..0eae7fac09 100644 --- a/content/news/gcc2018-call-for-host/index.md +++ b/content/news/gcc2018-call-for-host/index.md @@ -45,4 +45,4 @@ See the **[full call for host proposals](https://depot.galaxyproject.org/hub/att Hoping to work with you in 2018! -[Dave Clements](/people/dave-clements/index.md) and the [Galaxy Team](/src/galaxy-team/) +[Dave Clements](/people/dave-clements/) and the [Galaxy Team](/src/galaxy-team/) diff --git a/content/news/liste-de-diffusion-galaxy-france/index.md b/content/news/liste-de-diffusion-galaxy-france/index.md index a17f264450..a556ac3829 100644 --- a/content/news/liste-de-diffusion-galaxy-france/index.md +++ b/content/news/liste-de-diffusion-galaxy-france/index.md @@ -28,6 +28,6 @@ Pour vous aider dans votre utilisation de Galaxy, voici une liste de liens utile A très bientôt sur la liste Galaxy France, -Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/people/dave-clements/index.md) & [Jennifer Jackson](/src/people/jennifer-jackson/). +Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/people/dave-clements/) & [Jennifer Jackson](/src/people/jennifer-jackson/). Alban Lermine diff --git a/content/news/s-g2014-report/index.md b/content/news/s-g2014-report/index.md index ee26dff08b..8dc3da5db4 100644 --- a/content/news/s-g2014-report/index.md +++ b/content/news/s-g2014-report/index.md @@ -15,4 +15,4 @@ We would like to thank for the financial support we got from [SystemsX.ch](http: Running the event at two different places caused some logistical problems - some participants even learned about European geography. But the event was again a great success and we got a lot of great feedback. We are looking forward to the next Swiss German Galaxy Tour. -[Björn](/people/bjoern-gruening/index.md) and [Hans-Rudolf](/src/people/hansrudolf-hotz/) +[Björn](/people/bjoern-gruening/) and [Hans-Rudolf](/src/people/hansrudolf-hotz/) diff --git a/content/news/whole-genome-mult-alignments-paper/index.md b/content/news/whole-genome-mult-alignments-paper/index.md index d99582d77e..2f4f78541b 100644 --- a/content/news/whole-genome-mult-alignments-paper/index.md +++ b/content/news/whole-genome-mult-alignments-paper/index.md @@ -5,6 +5,6 @@ date: "2011-07-28"
Bioinformatics Jorunal
-A new paper, "[Making whole genome multiple alignments usable for biologists](http://bioinformatics.oxfordjournals.org/content/early/2011/07/19/bioinformatics.btr398.abstract)," by [Daniel Blankenberg](/people/dan/index.md), *[et al](/src/galaxy-team/).* has been published (early access) in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface." +A new paper, "[Making whole genome multiple alignments usable for biologists](http://bioinformatics.oxfordjournals.org/content/early/2011/07/19/bioinformatics.btr398.abstract)," by [Daniel Blankenberg](/people/dan/), *[et al](/src/galaxy-team/).* has been published (early access) in *[Bioinformatics](http://bioinformatics.oxfordjournals.org/)*. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface." The methods are [described on a Galaxy Page](http://usegalaxy.org/u/dan/p/maf) as well. diff --git a/content/people/dave-clements/index.md b/content/people/dave-clements/index.md index 30b281b3f3..ae3c404e5c 100644 --- a/content/people/dave-clements/index.md +++ b/content/people/dave-clements/index.md @@ -38,10 +38,10 @@ My pre-bioinformatics career included ## Publications -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/index.md), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). -* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/index.md), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) -* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/index.md), [Dave Clements](/people/dave-clements/index.md), [Daniel Blankenberg](/people/dan/index.md), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/) +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). +* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) +* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/) * [The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data](http://database.oxfordjournals.org/content/2011/bar051.full), in *[Database](http://database.oxfordjournals.org/)*, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main * [Organization of the pronephric kidney revealed by large-scale gene expression mapping](http://genomebiology.com/2008/9/5/R84); in *[Genome Biology](http://genomebiology.com/2008/9/5/)*, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli * [A high-resolution anatomical ontology of the developing murine genitourinary tract](https://doi.org/10.1016/j.modgep.2007.03.002); in *[Gene Expression Patterns](http://www.elsevier.com/locate/modgep)*, 7(6), pp. 680-699 (June 2007). Melissa H. Little, Jane Brennan, Kylie Georgas, Jamie A. Davies, Duncan R. Davidson, Richard A. Baldock, Annemiek Beverdam, John F. Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Cullen-McEwen, Jean Fleming, Thierry Gilbert, Doris Herzlinger, Derek Houghton, Matt H. Kaufman, Elena Kleymenova, Peter A. Koopman, Alfor G. Lewis, Andrew P. McMahon, Cathy L. Mendelsohn, Eleanor K. Mitchell, Bree A. Rumballe, Derina E. Sweeney, M. Todd Valerius, Gen Yamada, Yiya Yang and Jing Yu @@ -317,7 +317,7 @@ Are coming, the next time I need to do a biosketch. March 7 - Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam + Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam University of Georgia, Athens, Georgia, United States Slides
diff --git a/content/people/fubar/index.md b/content/people/fubar/index.md index cc20dc9e85..4e626d1ee9 100644 --- a/content/people/fubar/index.md +++ b/content/people/fubar/index.md @@ -2,7 +2,7 @@ Email: [GG ross.lazarus AT gmail DOT com MMM ](mailto:GG ross.lazarus AT gmail DOT com MMM )
![](/src/images/people/team/ross.jpg)
-Ross Lazarus is an Australian medical academic who served as an Associate Professor in Population Medicine at Harvard Medical School and Director of Bioinformatics at the Channing Laboratory for 12 years before returning to take up a position as Head of Computational Biology at the [BakerIDI](http://www.bakeridi.edu.au/) in Melbourne in 2011. While based at HMS, he badgered [Anton](/people/anton/index.md) and [James](/people/james-taylor/) until they let him join the very new [Galaxy Team](/src/galaxy-team/) after he was smitten at first sight of the [source code](https://github.com/galaxyproject/galaxy). He helps take care of Picard and other NGS tool wrappers and is developing a [comprehensive toolkit](https://bitbucket.org/fubar/rgalaxy/src/94584ac7c10f/tools/rgenetics) for digital differential expression, exposing edgeR/DESeq, miRDeep2 and GSEA in a convenient way starting with aligned bam files and an interval file specifying contigs for read counts. For those times when you need a few lines of R or python quickly wrapped into a new Galaxy tool for your local users, you might enjoy a Galaxy tool he recently published that [generates new Galaxy tools from scripts](https://bitbucket.org/fubar/galaxytoolfactory/overview). Ross is often responsible for sending grumpy responses to the lists at times when most other team members are asleep*. In preparing for these roles, he has at various times worked as a public health and family physician, public health informatician, NIH/NSF funded researcher, bioinformatician, genetic epidemiologist and computer wonk. +Ross Lazarus is an Australian medical academic who served as an Associate Professor in Population Medicine at Harvard Medical School and Director of Bioinformatics at the Channing Laboratory for 12 years before returning to take up a position as Head of Computational Biology at the [BakerIDI](http://www.bakeridi.edu.au/) in Melbourne in 2011. While based at HMS, he badgered [Anton](/people/anton/) and [James](/people/james-taylor/) until they let him join the very new [Galaxy Team](/src/galaxy-team/) after he was smitten at first sight of the [source code](https://github.com/galaxyproject/galaxy). He helps take care of Picard and other NGS tool wrappers and is developing a [comprehensive toolkit](https://bitbucket.org/fubar/rgalaxy/src/94584ac7c10f/tools/rgenetics) for digital differential expression, exposing edgeR/DESeq, miRDeep2 and GSEA in a convenient way starting with aligned bam files and an interval file specifying contigs for read counts. For those times when you need a few lines of R or python quickly wrapped into a new Galaxy tool for your local users, you might enjoy a Galaxy tool he recently published that [generates new Galaxy tools from scripts](https://bitbucket.org/fubar/galaxytoolfactory/overview). Ross is often responsible for sending grumpy responses to the lists at times when most other team members are asleep*. In preparing for these roles, he has at various times worked as a public health and family physician, public health informatician, NIH/NSF funded researcher, bioinformatician, genetic epidemiologist and computer wonk. diff --git a/content/use/galaxy-test/index.md b/content/use/galaxy-test/index.md index 598cd0b215..b30f335de8 100644 --- a/content/use/galaxy-test/index.md +++ b/content/use/galaxy-test/index.md @@ -16,7 +16,7 @@ user_support: quotas: - "Storage and computational quotas. See [Test](/src/test/index.md) for details" citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "[Project tagged publications](https://www.zotero.org/groups/1732893/galaxy/tags/%2BProject) in [Galaxy Publication library](/src/publication-library/index.md)." - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: diff --git a/content/use/imaging/index.md b/content/use/imaging/index.md index 6ca7f5da62..d6ff22aac0 100644 --- a/content/use/imaging/index.md +++ b/content/use/imaging/index.md @@ -26,6 +26,6 @@ citations: pub_libraries: - "Imaging EU" sponsors: - - "[Greg von Kuster](/people/greg_vonkuster/index.md), [Björn Grüning](/src/people/bjoern-gruening/) and Thomas Wollmann" + - "[Greg von Kuster](/people/greg_vonkuster/), [Björn Grüning](/src/people/bjoern-gruening/) and Thomas Wollmann" - "The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/freiburg/) but also collectively by groups and individuals from across Europe" --- diff --git a/content/use/usegalaxy-eu/index.md b/content/use/usegalaxy-eu/index.md index 099b43e019..48f022c534 100644 --- a/content/use/usegalaxy-eu/index.md +++ b/content/use/usegalaxy-eu/index.md @@ -18,7 +18,7 @@ user_support: quotas: - "Storage and computational quotas." citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/index.md), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.eu" diff --git a/content/use/usegalaxy-org/index.md b/content/use/usegalaxy-org/index.md index b600bb404c..6737274130 100644 --- a/content/use/usegalaxy-org/index.md +++ b/content/use/usegalaxy-org/index.md @@ -11,7 +11,7 @@ summary: "The [Galaxy Project](/galaxy-project/) free public server; biomedical comments: - "Strong on genomics; good central repository for shared Galaxy objects. See [Main](/main/) for more." citations: - - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/index.md), [Dannon Baker](/people/dannon-baker/index.md), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/index.md), [Martin Čech](/people/marten/index.md), [John Chilton](/people/john-chilton/index.md), [Dave Clements](/people/dave-clements/index.md), [Nate Coraor](/people/nate/index.md), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" + - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.org" From 5246ea0ef204d046a4e3363490fc630324547ba3 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 17:01:58 -0400 Subject: [PATCH 06/24] Fix galaxy-team links --- content/archive/dev-news-briefs/2010-11-24/index.md | 2 +- content/archive/dev-news-briefs/2012-01-27/index.md | 2 +- content/archive/dev-news-briefs/2012-03-12/index.md | 4 ++-- content/archive/dev-news-briefs/2012-07-20/index.md | 2 +- content/archive/dev-news-briefs/2012-09-07/index.md | 2 +- content/archive/dev-news-briefs/2012-09-20/index.md | 2 +- content/archive/dev-news-briefs/2012-10-05/index.md | 2 +- content/archive/dev-news-briefs/2012-10-23/index.md | 2 +- content/archive/dev-news-briefs/2014-08-11/index.md | 2 +- content/archive/dev-news-briefs/2014-10-06/index.md | 2 +- content/archive/dev-news-briefs/2015-01-13/index.md | 2 +- content/archive/dev-news-briefs/2015-03/index.md | 2 +- content/blog/2017-10-5000-pubs/index.md | 2 +- content/blog/2020-08-10k-pubs/index.md | 2 +- content/cloudman/aws/capacity-planning/index.md | 2 +- content/community/galaxy-admins/meetups/2012-07-09/index.md | 2 +- content/community/galaxy-admins/meetups/2016-04-21/index.md | 2 +- content/community/index.md | 2 +- content/datafiles/mouse-chip-seq-data/index.md | 2 +- content/events/admin-training2016/index.md | 2 +- content/events/gcc2012/program/breakouts/end-users/index.md | 2 +- content/events/gcc2012/program/index.md | 2 +- content/events/gcc2013/abstracts/talks/index.md | 2 +- content/events/gcc2013/bof/public-galaxy-servers/index.md | 2 +- content/events/meetups/baltimore/2015-01-22/index.md | 2 +- content/events/meetups/psu/2015-05/index.md | 2 +- content/galaxy-project/index.md | 2 +- content/galaxy-updates/2012-05/index.md | 2 +- content/galaxy-updates/2012-12/index.md | 2 +- content/galaxy-updates/2013-02/index.md | 2 +- content/galaxy-updates/2014-02/index.md | 2 +- content/galaxy-updates/2014-05/index.md | 2 +- content/galaxy-updates/2014-06/index.md | 2 +- content/galaxy-updates/2015-02/index.md | 4 ++-- content/galaxy-updates/2015-04/index.md | 2 +- content/galaxy-updates/2015-06/index.md | 2 +- content/galaxy-updates/2015-09/index.md | 2 +- content/galaxy-updates/2016-06/index.md | 2 +- content/galaxy-updates/2016-07/index.md | 4 ++-- content/galaxy-updates/2016-08/index.md | 4 ++-- content/galaxy-updates/2016-09/index.md | 4 ++-- content/galaxy-updates/2016-10/index.md | 4 ++-- content/get-involved/index.md | 2 +- content/news/2012-11-14-distribution-news-brief/index.md | 2 +- content/news/2012-12-03-distribution-news-brief/index.md | 2 +- content/news/2012-12-20-distribution-news-brief/index.md | 2 +- content/news/2013-01-11-distribution-news-brief/index.md | 2 +- content/news/2013-02-08-galaxy-news-brief/index.md | 2 +- content/news/2013-04-01-galaxy-distribution/index.md | 2 +- content/news/2013-04-08-galaxy-security-release/index.md | 2 +- content/news/2013-06-03-galaxy-distribution/index.md | 2 +- content/news/2013-08-12-galaxy-distribution/index.md | 2 +- content/news/2013-11-04-galaxy-distribution/index.md | 2 +- content/news/2014-02-10-galaxy-distribution/index.md | 2 +- content/news/2014-04-14-galaxy-distribution/index.md | 2 +- content/news/2014-06-02-galaxy-distribution/index.md | 2 +- content/news/2014-08-11-galaxy-distribution/index.md | 2 +- content/news/2014-10-06-galaxy-distribution/index.md | 2 +- content/news/2014-questionnaire/index.md | 2 +- content/news/2015-01-13-galaxy-distribution/index.md | 2 +- content/news/2015-03-galaxy-release/index.md | 2 +- content/news/2015-05-galaxy-release/index.md | 2 +- content/news/2015-07-galaxy-release/index.md | 2 +- content/news/2015-10-galaxy-release/index.md | 2 +- content/news/2017-01-galaxy-update/index.md | 2 +- content/news/2017-09-maintenance/index.md | 2 +- content/news/analysis-by-viz-with-trackster-paper/index.md | 2 +- content/news/aug2011-distribution-news-brief/index.md | 2 +- content/news/duplicate-accounts-on-main/index.md | 2 +- content/news/galaxy-biostar-launch/index.md | 2 +- content/news/galaxy-current-protocols/index.md | 2 +- content/news/galaxy-pag2012/index.md | 2 +- content/news/galaxy-proect-servers-down20130314/index.md | 2 +- content/news/galaxy-project-openings/index.md | 4 ++-- content/news/galaxy-tour-de-france2012/index.md | 2 +- content/news/gat2016-registration-open/index.md | 2 +- content/news/gcc2012-registration-is-open/index.md | 2 +- content/news/gcc2014-hackathon/index.md | 2 +- content/news/irc-public-log-proposal/index.md | 2 +- content/news/jan2012-distribution-news-brief/index.md | 2 +- content/news/jan272012-distribution-news-brief/index.md | 2 +- content/news/jul202012-distribution-news-brief/index.md | 2 +- content/news/mar122012-distribution-news-brief/index.md | 2 +- content/news/may112012-distribution-news-brief/index.md | 2 +- content/news/nov2011-distribution-news-brief/index.md | 2 +- content/news/oct2011-distribution-news-brief/index.md | 2 +- content/news/proteomics-mailing-list/index.md | 2 +- content/news/sep072012-distribution-news-brief/index.md | 2 +- content/people/dannon-baker/index.md | 2 +- content/people/dave-bouvier/index.md | 2 +- content/people/delphine-lariviere/index.md | 2 +- content/people/greg_vonkuster/index.md | 2 +- content/people/guerler/index.md | 2 +- content/people/guru-ananda/index.md | 2 +- content/people/jennifer-jackson/index.md | 2 +- content/people/nate/index.md | 2 +- content/people/sergey/index.md | 2 +- content/publication-library/contribute/index.md | 2 +- content/publication-library/index.md | 2 +- content/support/biostar/index.md | 2 +- 100 files changed, 107 insertions(+), 107 deletions(-) diff --git a/content/archive/dev-news-briefs/2010-11-24/index.md b/content/archive/dev-news-briefs/2010-11-24/index.md index 8db3329109..8a75fad779 100644 --- a/content/archive/dev-news-briefs/2010-11-24/index.md +++ b/content/archive/dev-news-briefs/2010-11-24/index.md @@ -214,7 +214,7 @@ time, especially for data libraries having potentially large menu. **Galaxy** is supported in part by **NSF**, **NHGRI**, the **Huck Institutes of the Life Sciences**, and **The Institute for CyberScience at Penn State**. -[Core Team](/src/galaxy-team/index.md) +[Core Team](/galaxy-team/) [Use Galaxy!](http://usegalaxy.org) diff --git a/content/archive/dev-news-briefs/2012-01-27/index.md b/content/archive/dev-news-briefs/2012-01-27/index.md index b23d9f4b48..3170cc26ca 100644 --- a/content/archive/dev-news-briefs/2012-01-27/index.md +++ b/content/archive/dev-news-briefs/2012-01-27/index.md @@ -103,4 +103,4 @@ The **[GalaxyTeam](http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam/)* Join us at **Twitter [@galaxyproject](http://twitter.com/#galaxyproject)** ---- -Jennifer Jackson, [Galaxy Team](/src/galaxy-team/index.md). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-01-27 +Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-01-27 diff --git a/content/archive/dev-news-briefs/2012-03-12/index.md b/content/archive/dev-news-briefs/2012-03-12/index.md index c5c257f5cf..f70a3712f7 100644 --- a/content/archive/dev-news-briefs/2012-03-12/index.md +++ b/content/archive/dev-news-briefs/2012-03-12/index.md @@ -186,7 +186,7 @@ Trackster visualization of [ENCODE](http://genome.ucsc.edu/ENCODE/) and Composit ## Galaxy is Hiring!
Galaxy wants YOU
-**The [Galaxy Team](/src/galaxy-team/index.md) Wants You!** +**The [Galaxy Team](/galaxy-team/) Wants You!**
Want to work on one of the fastest growing open source bioinformatics projects around? The [Galaxy Project](http://galaxyproject.org/), a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring. [Read more...](/src/galaxy-is-hiring/index.md) @@ -202,4 +202,4 @@ The **[GalaxyTeam](http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam/)* Join us at **Twitter [@galaxyproject](http://twitter.com/#galaxyproject)** or just read our tweets **[Galaxy on Twitter](/src/galaxy-on-twitter/index.md)** ---- -
Jennifer Jackson, [Galaxy Team](/src/galaxy-team/index.md). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-03-12
+
Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-03-12
diff --git a/content/archive/dev-news-briefs/2012-07-20/index.md b/content/archive/dev-news-briefs/2012-07-20/index.md index 098a77b525..8e3346273a 100644 --- a/content/archive/dev-news-briefs/2012-07-20/index.md +++ b/content/archive/dev-news-briefs/2012-07-20/index.md @@ -116,7 +116,7 @@ The [GalaxyCzars group](/src/community/GalaxyCzars/index.md) was launched and ha ## Galaxy is Hiring!
Galaxy wants YOU
-**The [Galaxy Team](/src/galaxy-team/index.md) Wants You!** +**The [Galaxy Team](/galaxy-team/) Wants You!**
Want to work on one of the fastest growing open source bioinformatics projects around? The [Galaxy Project](http://galaxyproject.org/), a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring. [Read more...](/src/galaxy-is-hiring/index.md)
diff --git a/content/archive/dev-news-briefs/2012-09-07/index.md b/content/archive/dev-news-briefs/2012-09-07/index.md index 9acfda53c8..fee5169845 100644 --- a/content/archive/dev-news-briefs/2012-09-07/index.md +++ b/content/archive/dev-news-briefs/2012-09-07/index.md @@ -233,7 +233,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll p **[GalaxyProject.org](http://galaxyproject.org)** -The **[Galaxy Team](/src/galaxy-team/index.md)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). +The **[Galaxy Team](/galaxy-team/)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). **[Galaxy](http://usegalaxy.org )** is supported in part by [NSF](http://www.nsf.gov/), [NHGRI](http://www.genome.gov/), the [Huck Institutes of the Life Sciences](http://www.huck.psu.edu/), and [The Institute for CyberScience at Penn State](http://www.ics.psu.edu/), and [Emory University](http://www.emory.edu/home/index.html). diff --git a/content/archive/dev-news-briefs/2012-09-20/index.md b/content/archive/dev-news-briefs/2012-09-20/index.md index af8eeb5712..78322b73ce 100644 --- a/content/archive/dev-news-briefs/2012-09-20/index.md +++ b/content/archive/dev-news-briefs/2012-09-20/index.md @@ -188,7 +188,7 @@ For example, let's take a look at a Galaxy instance into which 2 revisions of a **[GalaxyProject.org](http://galaxyproject.org)** -The **[Galaxy Team](/src/galaxy-team/index.md)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). +The **[Galaxy Team](/galaxy-team/)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). **[Galaxy](http://usegalaxy.org )** is supported in part by [NSF](http://www.nsf.gov/), [NHGRI](http://www.genome.gov/), the [Huck Institutes of the Life Sciences](http://www.huck.psu.edu/), and [The Institute for CyberScience at Penn State](http://www.ics.psu.edu/), and [Emory University](http://www.emory.edu/home/index.html). diff --git a/content/archive/dev-news-briefs/2012-10-05/index.md b/content/archive/dev-news-briefs/2012-10-05/index.md index d64e0e55ab..011d4fb6a5 100644 --- a/content/archive/dev-news-briefs/2012-10-05/index.md +++ b/content/archive/dev-news-briefs/2012-10-05/index.md @@ -221,7 +221,7 @@ Tool changes that enable clearer experimental tracking and ease reproducibility **[GalaxyProject.org](http://galaxyproject.org)** -The **[Galaxy Team](/src/galaxy-team/index.md)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). +The **[Galaxy Team](/galaxy-team/)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). **[Galaxy](http://usegalaxy.org )** is supported in part by [NSF](http://www.nsf.gov/), [NHGRI](http://www.genome.gov/), the [Huck Institutes of the Life Sciences](http://www.huck.psu.edu/), and [The Institute for CyberScience at Penn State](http://www.ics.psu.edu/), and [Emory University](http://www.emory.edu/home/index.html). diff --git a/content/archive/dev-news-briefs/2012-10-23/index.md b/content/archive/dev-news-briefs/2012-10-23/index.md index 6adfa8b2a6..36c688e9ae 100644 --- a/content/archive/dev-news-briefs/2012-10-23/index.md +++ b/content/archive/dev-news-briefs/2012-10-23/index.md @@ -222,7 +222,7 @@ Detail view of center panel: **[GalaxyProject.org](http://galaxyproject.org)** -The **[Galaxy Team](/src/galaxy-team/index.md)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). +The **[Galaxy Team](/galaxy-team/)** is a part of **[BX](http://www.bx.psu.edu/)** at [Penn State](http://www.psu.edu/), and the **[Biology](http://www.biology.emory.edu/)** and **[Mathematics and Computer Science](http://www.mathcs.emory.edu/)** departments at [Emory University](http://www.emory.edu/home/index.html/). **[Galaxy](http://usegalaxy.org )** is supported in part by [NSF](http://www.nsf.gov/), [NHGRI](http://www.genome.gov/), the [Huck Institutes of the Life Sciences](http://www.huck.psu.edu/), and [The Institute for CyberScience at Penn State](http://www.ics.psu.edu/), and [Emory University](http://www.emory.edu/home/index.html). diff --git a/content/archive/dev-news-briefs/2014-08-11/index.md b/content/archive/dev-news-briefs/2014-08-11/index.md index 6683361dd9..524446b3bc 100644 --- a/content/archive/dev-news-briefs/2014-08-11/index.md +++ b/content/archive/dev-news-briefs/2014-08-11/index.md @@ -159,4 +159,4 @@ Docker integration provides even greater security with [Pulsar](https://github.c # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/src/galaxy-team/index.md) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2014-10-06/index.md b/content/archive/dev-news-briefs/2014-10-06/index.md index 58d09e9f42..f0df75dee5 100644 --- a/content/archive/dev-news-briefs/2014-10-06/index.md +++ b/content/archive/dev-news-briefs/2014-10-06/index.md @@ -142,4 +142,4 @@ Several enhancements and improvements have been made to facilitate easier viewin # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/src/galaxy-team/index.md) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2015-01-13/index.md b/content/archive/dev-news-briefs/2015-01-13/index.md index a86484d943..7ced66777b 100644 --- a/content/archive/dev-news-briefs/2015-01-13/index.md +++ b/content/archive/dev-news-briefs/2015-01-13/index.md @@ -178,4 +178,4 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/src/galaxy-team/index.md) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2015-03/index.md b/content/archive/dev-news-briefs/2015-03/index.md index 7ef54eb416..265577f186 100644 --- a/content/archive/dev-news-briefs/2015-03/index.md +++ b/content/archive/dev-news-briefs/2015-03/index.md @@ -225,4 +225,4 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/src/galaxy-team/index.md) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/blog/2017-10-5000-pubs/index.md b/content/blog/2017-10-5000-pubs/index.md index 57082a985d..81dc3ff1f7 100644 --- a/content/blog/2017-10-5000-pubs/index.md +++ b/content/blog/2017-10-5000-pubs/index.md @@ -461,7 +461,7 @@ Topic tags indicate how the publication relates to Galaxy. Here's the current s | [+IsGalaxy](https://www.zotero.org/groups/galaxy/items/tag/+IsGalaxy/) | Publications about Galaxy itself or installations of Galaxy. | 2011 | | [+Methods](https://www.zotero.org/groups/galaxy/items/tag/+Methods/) | Uses Galaxy in their methods. | 2011 | | [+Other](https://www.zotero.org/groups/galaxy/items/tag/+Other/) | Publications that don't fit well under any other tag. | 2011 | -| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/src/galaxy-team/index.md) member as an author. | 2011 | +| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/galaxy-team/) member as an author. | 2011 | | [+Reproducibility](https://www.zotero.org/groups/galaxy/items/tag/+Reproducibility/) | Reproducibility and persistence in science. | 2011 | | [+Shared](https://www.zotero.org/groups/galaxy/items/tag/+Shared/) | Publications that have published workflows, histories, datasets, pages, or visualizations in a Galaxy instance. | 2011 | | [+Workbench](https://www.zotero.org/groups/galaxy/items/tag/+Workbench/) | Publication mentions Galaxy as a platform. | 2011 | diff --git a/content/blog/2020-08-10k-pubs/index.md b/content/blog/2020-08-10k-pubs/index.md index 1523555516..ff698a0b2c 100644 --- a/content/blog/2020-08-10k-pubs/index.md +++ b/content/blog/2020-08-10k-pubs/index.md @@ -660,7 +660,7 @@ Topic tags indicate how the publication relates to Galaxy. Here's the current s | [+IsGalaxy](https://www.zotero.org/groups/galaxy/items/tag/+IsGalaxy/) | Publications about Galaxy itself or installations of Galaxy. | 2011 | | [+Methods](https://www.zotero.org/groups/galaxy/items/tag/+Methods/) | Uses Galaxy in their methods. | 2011 | | [+Other](https://www.zotero.org/groups/galaxy/items/tag/+Other/) | Publications that don't fit well under any other tag. | 2011 | -| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/src/galaxy-team/index.md) member as an author. | 2011 | +| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/galaxy-team/) member as an author. | 2011 | | [+Reproducibility](https://www.zotero.org/groups/galaxy/items/tag/+Reproducibility/) | Reproducibility and persistence in science. | 2011 | | [+Shared](https://www.zotero.org/groups/galaxy/items/tag/+Shared/) | Publications that have published workflows, histories, datasets, pages, or visualizations in a Galaxy instance. | 2011 | | [+Workbench](https://www.zotero.org/groups/galaxy/items/tag/+Workbench/) | Publication mentions Galaxy as a platform. | 2011 | diff --git a/content/cloudman/aws/capacity-planning/index.md b/content/cloudman/aws/capacity-planning/index.md index 8594c6e2d1..b17e65c28a 100644 --- a/content/cloudman/aws/capacity-planning/index.md +++ b/content/cloudman/aws/capacity-planning/index.md @@ -153,7 +153,7 @@ Which [EC2 instance type(s)](http://aws.amazon.com/ec2/#instance) should you use Y - The Galaxy Team uses this head node in workshops that run TopHat. It can support ~30 concurrent TopHat jobs without significant slowdown, whereas the Double Extra Large option gets bogged down. + The Galaxy Team uses this head node in workshops that run TopHat. It can support ~30 concurrent TopHat jobs without significant slowdown, whereas the Double Extra Large option gets bogged down. Com-
pute diff --git a/content/community/galaxy-admins/meetups/2012-07-09/index.md b/content/community/galaxy-admins/meetups/2012-07-09/index.md index 6ea9573229..00000da0b5 100644 --- a/content/community/galaxy-admins/meetups/2012-07-09/index.md +++ b/content/community/galaxy-admins/meetups/2012-07-09/index.md @@ -30,7 +30,7 @@ Ann proposed this generic agenda for future calls * 20 min: Galaxy in Our Town. Presentation from a local galaxy institution on what they are doing or a problem they are troubleshooting - or have someone walk through their use cases and pain points. * 20 min: Galaxy Today/Tomorrow. - Presentation on a galaxy coding item. Either from [Galaxy Team](/src/galaxy-team/index.md), or from [someone](/src/community/index.md) working on a new feature or customization. + Presentation on a galaxy coding item. Either from [Galaxy Team](/galaxy-team/), or from [someone](/src/community/index.md) working on a new feature or customization. * 20 mins: Open Mic Discussion & make point to point connections. Organize smaller breakouts if someone wants to host a call specific to an issue, ... diff --git a/content/community/galaxy-admins/meetups/2016-04-21/index.md b/content/community/galaxy-admins/meetups/2016-04-21/index.md index 5b3bcfc368..30dc6d281e 100644 --- a/content/community/galaxy-admins/meetups/2016-04-21/index.md +++ b/content/community/galaxy-admins/meetups/2016-04-21/index.md @@ -51,7 +51,7 @@ Galaxy Portal is provided free of charge. ## Tool Development Developments -[Galaxy Team](/src/galaxy-team/index.md) member [John Chilton](/people/john-chilton/) will discuss recent tool development developments including Conda, tool version profiles, and Planemo enhancements. +[Galaxy Team](/galaxy-team/) member [John Chilton](/people/john-chilton/) will discuss recent tool development developments including Conda, tool version profiles, and Planemo enhancements. ## Call Technology diff --git a/content/community/index.md b/content/community/index.md index aca9c9df83..420e71f4a8 100644 --- a/content/community/index.md +++ b/content/community/index.md @@ -1,7 +1,7 @@ --- title: The Galaxy Community --- -A vibrant community of contributors is the reason this project exists. The [Galaxy team](/src/galaxy-team/index.md) alone cannot possibly [maintain enough servers](/src/use/index.md), [wrap enough tools](https://toolshed.g2.bx.psu.edu/), [teach enough workshops](/src/events/index.md), implement [all needed features](https://github.com/galaxyproject), or [answer every question](/src/support/index.md) on its own. This is why community is vital to our core mission - enabling reproducible research in data-rich sciences and beyond. Members within the Galaxy community are located all around the world and often form subgroups that differ in size (small versus large) and degree of privacy (public versus private). This page highlights these groups. +A vibrant community of contributors is the reason this project exists. The [Galaxy team](/galaxy-team/) alone cannot possibly [maintain enough servers](/src/use/index.md), [wrap enough tools](https://toolshed.g2.bx.psu.edu/), [teach enough workshops](/src/events/index.md), implement [all needed features](https://github.com/galaxyproject), or [answer every question](/src/support/index.md) on its own. This is why community is vital to our core mission - enabling reproducible research in data-rich sciences and beyond. Members within the Galaxy community are located all around the world and often form subgroups that differ in size (small versus large) and degree of privacy (public versus private). This page highlights these groups.
diff --git a/content/datafiles/mouse-chip-seq-data/index.md b/content/datafiles/mouse-chip-seq-data/index.md index d9d9329b79..d6939b2520 100644 --- a/content/datafiles/mouse-chip-seq-data/index.md +++ b/content/datafiles/mouse-chip-seq-data/index.md @@ -19,7 +19,7 @@ These data come from the [Mammalian Promoter Database (MPromDB)](http://mpromdb. 1. You must be a registered user to download data files. 1. Downloaded data files may be used only for non-commercial purposes. -The files here are a small subset of the files available for download from MPromDB. We ask you to honor MPromDB's use restrictions. The [Galaxy Team](/src/galaxy-team/index.md) also wishes to thank the [Davuluri Lab](http://bioinformatics.wistar.upenn.edu/davuluri) for allowing us to use this data in the Galaxy project. +The files here are a small subset of the files available for download from MPromDB. We ask you to honor MPromDB's use restrictions. The [Galaxy Team](/galaxy-team/) also wishes to thank the [Davuluri Lab](http://bioinformatics.wistar.upenn.edu/davuluri) for allowing us to use this data in the Galaxy project. ## Data diff --git a/content/events/admin-training2016/index.md b/content/events/admin-training2016/index.md index f2a57c52e8..abcd76a9a3 100644 --- a/content/events/admin-training2016/index.md +++ b/content/events/admin-training2016/index.md @@ -69,7 +69,7 @@ See the [Advanced Session](/src/events/admin-training2016/advanced-session/index # Instructors -Instructors are from the [Galaxy Project Team](/src/galaxy-team/index.md) and the Galaxy Community: +Instructors are from the [Galaxy Project Team](/galaxy-team/) and the Galaxy Community: * [Nate Coraor](/people/nate/), lead sys admin and a software engineer for the Galaxy Project * [Martin Čech](/people/marten/), software engineer and frequent sys admin for the Galaxy Project. * [Simon Gladman](https://www.vlsci.org.au/researcher/sgladman), software engineer and bioinformatician with [VLSCI](https://www.vlsci.org.au/) and has done extensive work with the [Genomics Virtual Lab](https://www.genome.edu.au/). diff --git a/content/events/gcc2012/program/breakouts/end-users/index.md b/content/events/gcc2012/program/breakouts/end-users/index.md index d0b9757699..be98e8f21c 100644 --- a/content/events/gcc2012/program/breakouts/end-users/index.md +++ b/content/events/gcc2012/program/breakouts/end-users/index.md @@ -37,7 +37,7 @@ These are a merged grouping of [Anton's](/people/anton/), [Dan's](/people/dan/), * for storage (S3) * General Comments * The 'Big Plus' for end users: Amazon allows Galaxy to be used in highly controlled IT environments. - * "Galaxy better than commercial software" (the [Galaxy Team](/src/galaxy-team/index.md) says "thank-you"!!) + * "Galaxy better than commercial software" (the [Galaxy Team](/galaxy-team/) says "thank-you"!!) * Trackster/Sweepster amazed everyone (shout-out to Jeremy!) * New end user community to be aware of: Mass spec diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index 68f9da3883..392f7159c5 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -77,7 +77,7 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl ### Day 1: July 26, Thursday -The main meeting started on Thursday, July 26, and featured submitted talks from the Galaxy Community and [Galaxy Team](/src/galaxy-team/index.md). +The main meeting started on Thursday, July 26, and featured submitted talks from the Galaxy Community and [Galaxy Team](/galaxy-team/). | Time | Topic | | ----: | ---- | diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index bee3bf198c..7fc16f69c8 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -470,7 +470,7 @@ In this talk, we describe how to create your own visualization for Galaxy. We pr **[Daniel Blankenberg](/people/dan/)** - [Galaxy Team](/src/galaxy-team/index.md) and Penn State University + [Galaxy Team](/galaxy-team/) and Penn State University *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/BlankenbergBuiltInData.pdf), [Vimeo](https://vimeo.com/74265510)* diff --git a/content/events/gcc2013/bof/public-galaxy-servers/index.md b/content/events/gcc2013/bof/public-galaxy-servers/index.md index 9c6baa518b..20beef036b 100644 --- a/content/events/gcc2013/bof/public-galaxy-servers/index.md +++ b/content/events/gcc2013/bof/public-galaxy-servers/index.md @@ -32,7 +32,7 @@ The [tentative time and location](/src/events/gcc2013/bof/index.md#bof-schedule) If you are interested, please add your name below and/or send an email to [Dave Clements](mailto:clements AT galaxyproject DOT org). * [Dave Clements](/people/dave-clements/), Galaxy Project -* [Dorine Francheteau](/src/galaxy-team/index.md), Galaxy Project +* [Dorine Francheteau](/galaxy-team/), Galaxy Project * Eric Kuyt, Central Veterinary Institute of Wageningen UR (CVI) * Jacqueline Lee, University of Calgary * Ron Horst, University of Queensland, Australia diff --git a/content/events/meetups/baltimore/2015-01-22/index.md b/content/events/meetups/baltimore/2015-01-22/index.md index b45e34b62f..35d2bfcd46 100644 --- a/content/events/meetups/baltimore/2015-01-22/index.md +++ b/content/events/meetups/baltimore/2015-01-22/index.md @@ -9,7 +9,7 @@ title: Jan 22, 2015 Baltimore Area Galaxy Meetup @ Johns Hopkins ## Meetup Report -The first Galaxy meetup or social gathering held in Baltimore was sold out. It was the right mix of current Galaxy users, people who want to learn how to use Galaxy, and students in Biology/Computer science programs. It was good to see academics unwind with a few beers and talk about their ideas to use Galaxy. The idea behind the meetup was to build a local community of Galaxy users, and to get to know one another personally. This would in turn foster collaborations and also bring forward better feedback to the [Galaxy Team](/src/galaxy-team/index.md) as well. +The first Galaxy meetup or social gathering held in Baltimore was sold out. It was the right mix of current Galaxy users, people who want to learn how to use Galaxy, and students in Biology/Computer science programs. It was good to see academics unwind with a few beers and talk about their ideas to use Galaxy. The idea behind the meetup was to build a local community of Galaxy users, and to get to know one another personally. This would in turn foster collaborations and also bring forward better feedback to the [Galaxy Team](/galaxy-team/) as well. The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. diff --git a/content/events/meetups/psu/2015-05/index.md b/content/events/meetups/psu/2015-05/index.md index 72ba6fab00..4d8a4f4f51 100644 --- a/content/events/meetups/psu/2015-05/index.md +++ b/content/events/meetups/psu/2015-05/index.md @@ -14,7 +14,7 @@ Hey Everyone, This meeting is open to anyone interested in RNA-Seq analysis and biology workflows. [Anton Nekrutenko](/people/anton/) of the [Galaxy team](/src/galaxy-team/) will be delivering an introduction to RNA-Seq resources available at Galaxy from a practitioner's viewpoint. -[Galaxy Team members](/src/galaxy-team/index.md) will be available for any additional questions. +[Galaxy Team members](/galaxy-team/) will be available for any additional questions. Thanks and hope to see you there! diff --git a/content/galaxy-project/index.md b/content/galaxy-project/index.md index 7e47f14a55..c9e9c6038b 100644 --- a/content/galaxy-project/index.md +++ b/content/galaxy-project/index.md @@ -8,7 +8,7 @@ Galaxy is an open, web-based platform for accessible, reproducible, and transpar See the [Learn](/src/learn/index.md) page for help on using Galaxy, and the [Admin](/src/admin/index.md) page for help on setting up your own instance. -You can take a look at the current members of the core project [team](/src/galaxy-team/index.md). We are funded by NIH, NSF, Penn State, Johns Hopkins, and the Pennsylvania Department of Public Health. +You can take a look at the current members of the core project [team](/galaxy-team/). We are funded by NIH, NSF, Penn State, Johns Hopkins, and the Pennsylvania Department of Public Health. * [Galaxy Platform Directory](/src/use/index.md) * [Citing Galaxy](/src/citing-galaxy/index.md) diff --git a/content/galaxy-updates/2012-05/index.md b/content/galaxy-updates/2012-05/index.md index ab76ce94a7..bf4cbc8e85 100644 --- a/content/galaxy-updates/2012-05/index.md +++ b/content/galaxy-updates/2012-05/index.md @@ -38,7 +38,7 @@ Also, if you are interested in presenting a topic, especially a "how to use Gala
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See [Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md) for details and links. diff --git a/content/galaxy-updates/2012-12/index.md b/content/galaxy-updates/2012-12/index.md index 6f09003ba5..94cd7e620f 100644 --- a/content/galaxy-updates/2012-12/index.md +++ b/content/galaxy-updates/2012-12/index.md @@ -220,7 +220,7 @@ This update comes as a result of 175 code changesets; for a complete list of cha Several new repositories were added to, and existing repositories updated in the [Galaxy Tool Shed](http://toolshed.g2.bx.psu.edu/) in the past month. * `bsmap`: A short read mapping tool for bisulfite sequencing reads -* `bowtie_wrappers, bowtie_color_wrappers, lastz, lastz_paired_ends`: Wrappers all created by the [Galaxy Team](/src/galaxy-team/index.md) +* `bowtie_wrappers, bowtie_color_wrappers, lastz, lastz_paired_ends`: Wrappers all created by the [Galaxy Team](/galaxy-team/) * `semweb_tools`: A collection of Semantic Web tools, including a (pure python) SPARQL-to-tabular format tool * `ea_utils`: FASTQ processing utilities; sam-stats added * `regex_replace`: Regular expression replacement using the Python diff --git a/content/galaxy-updates/2013-02/index.md b/content/galaxy-updates/2013-02/index.md index 5488f7c4cf..c345df052f 100644 --- a/content/galaxy-updates/2013-02/index.md +++ b/content/galaxy-updates/2013-02/index.md @@ -132,7 +132,7 @@ There are still several [sponsorships](/src/events/gcc2013/sponsorships/index.md
January Galaxy Admins Web Meetup
-A [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) was held on January 16, 2013. [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) presented "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." Greg Von Kuster of the [Galaxy Team](/src/galaxy-team/index.md) gave an update on recent Tool Shed enhancements. Slides and a screencast are now available. +A [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) was held on January 16, 2013. [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) presented "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." Greg Von Kuster of the [Galaxy Team](/galaxy-team/) gave an update on recent Tool Shed enhancements. Slides and a screencast are now available. The next [GalaxyAdmins meetup](/src/community/galaxy-admins/index.md) will be Wednesday, March 20th diff --git a/content/galaxy-updates/2014-02/index.md b/content/galaxy-updates/2014-02/index.md index 9081a5f6db..377f466e72 100644 --- a/content/galaxy-updates/2014-02/index.md +++ b/content/galaxy-updates/2014-02/index.md @@ -381,7 +381,7 @@ bringing the number of log entries to 12. # Galaxy is now at Johns Hopkins and GWU (and Penn State!) -In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/src/galaxy-team/index.md) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. +In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/galaxy-team/) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are [still hiring](/src/galaxy-is-hiring/index.md), but now at three universities instead of two. diff --git a/content/galaxy-updates/2014-05/index.md b/content/galaxy-updates/2014-05/index.md index a616bbf970..c7048add29 100644 --- a/content/galaxy-updates/2014-05/index.md +++ b/content/galaxy-updates/2014-05/index.md @@ -135,7 +135,7 @@ Steve's GCC2014 talk will be on "Transcriptomes and Exomes: Computational Challe The very first [Galaxy Project Hackathon](/src/events/gcc2014/hackathon/index.md) will be a three day event taking place at Johns Hopkins immediately preceding [GCC2014](/src/events/gcc2014/index.md) from June 28th-30th. -Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/src/galaxy-team/index.md) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. +Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/galaxy-team/) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at [EventBrite](http://bit.ly/gcc2014hackreg). diff --git a/content/galaxy-updates/2014-06/index.md b/content/galaxy-updates/2014-06/index.md index aaf710d3ec..c902558d63 100644 --- a/content/galaxy-updates/2014-06/index.md +++ b/content/galaxy-updates/2014-06/index.md @@ -60,7 +60,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon The very first [Galaxy Project Hackathon](/src/events/gcc2014/hackathon/index.md) will take place at Johns Hopkins immediately preceding [GCC2014](/src/events/gcc2014/index.md) from starting June 28th. -Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/src/galaxy-team/index.md) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. +Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/galaxy-team/) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at [EventBrite](http://bit.ly/gcc2014hackreg). **[Register now](http://bit.ly/gcc2014hackreg). As of this writing there are only 11 spots left.** diff --git a/content/galaxy-updates/2015-02/index.md b/content/galaxy-updates/2015-02/index.md index f0ab66fbe0..7459a3ef94 100644 --- a/content/galaxy-updates/2015-02/index.md +++ b/content/galaxy-updates/2015-02/index.md @@ -170,7 +170,7 @@ Thanks to everyone for letting us know what dates and times worked best for you.
January 2015 Galaxy Baltimore Meetup
-The [first Baltimore Area Galaxy meetup](/src/events/meetups/baltimore/2015-01-22/index.md) *was sold out.* It was the right mix of current Galaxy users, people who want to learn how to use Galaxy, and students in Biology/Computer science programs. It was good to see academics unwind with a few beers and talk about their ideas to use Galaxy. The idea behind the meetup was to build a local community of Galaxy users, and to get to know one another personally. This would in turn foster collaborations and also bring forward better feedback to the [Galaxy Team](/src/galaxy-team/index.md) as well. +The [first Baltimore Area Galaxy meetup](/src/events/meetups/baltimore/2015-01-22/index.md) *was sold out.* It was the right mix of current Galaxy users, people who want to learn how to use Galaxy, and students in Biology/Computer science programs. It was good to see academics unwind with a few beers and talk about their ideas to use Galaxy. The idea behind the meetup was to build a local community of Galaxy users, and to get to know one another personally. This would in turn foster collaborations and also bring forward better feedback to the [Galaxy Team](/galaxy-team/) as well. The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. @@ -585,4 +585,4 @@ In no particular order: ## And a Huge Thank You! -The [Galaxy Team](/src/galaxy-team/index.md) would like to thank everyone who took the time to respond to the project's [call for support](/src/news/galaxy-project-grant-support/index.md). These will be extremely helpful with our renewal. +The [Galaxy Team](/galaxy-team/) would like to thank everyone who took the time to respond to the project's [call for support](/src/news/galaxy-project-grant-support/index.md). These will be extremely helpful with our renewal. diff --git a/content/galaxy-updates/2015-04/index.md b/content/galaxy-updates/2015-04/index.md index 09a3d474b0..da9b426960 100644 --- a/content/galaxy-updates/2015-04/index.md +++ b/content/galaxy-updates/2015-04/index.md @@ -457,7 +457,7 @@ One new [Community Log Board](/src/blog/index.md) entry was added in March:

*Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) ## BioBlend v0.5.3 Released diff --git a/content/galaxy-updates/2015-06/index.md b/content/galaxy-updates/2015-06/index.md index e2c1e11821..bdb5230146 100644 --- a/content/galaxy-updates/2015-06/index.md +++ b/content/galaxy-updates/2015-06/index.md @@ -417,7 +417,7 @@ VirAmp includes [Documentation](http://docs.viramp.com/en/latest/) and is suppor The release notes have a new home at **[Read the Docs](http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html)**. We hope that you like the new format as much as we do! *Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) ## Pulsar 0.5.0 diff --git a/content/galaxy-updates/2015-09/index.md b/content/galaxy-updates/2015-09/index.md index 57fa4a18a4..a73f6b7b0e 100644 --- a/content/galaxy-updates/2015-09/index.md +++ b/content/galaxy-updates/2015-09/index.md @@ -101,7 +101,7 @@ The new papers were tagged with: # Galaxy's First 2500 Publications -And in case you missed it, we [reached 2500 publications](/src/news/first2500-papers/index.md) in the [Galaxy CiteULike Library](http://bit.ly/gxyCiteULike). [This writeup](/src/news/first2500-papers/index.md) analyzes the papers by [CiteULike tag](/src/publication-library/index.md#tags) and journal, across the past 11 years, and identifies some trends. Of those 2500 papers, less than 2% have a [Galaxy Team member](/src/galaxy-team/index.md) as a coauthor. +And in case you missed it, we [reached 2500 publications](/src/news/first2500-papers/index.md) in the [Galaxy CiteULike Library](http://bit.ly/gxyCiteULike). [This writeup](/src/news/first2500-papers/index.md) analyzes the papers by [CiteULike tag](/src/publication-library/index.md#tags) and journal, across the past 11 years, and identifies some trends. Of those 2500 papers, less than 2% have a [Galaxy Team member](/galaxy-team/) as a coauthor. ---- diff --git a/content/galaxy-updates/2016-06/index.md b/content/galaxy-updates/2016-06/index.md index 71f0619326..a53a84ca8e 100644 --- a/content/galaxy-updates/2016-06/index.md +++ b/content/galaxy-updates/2016-06/index.md @@ -295,7 +295,7 @@ and ... ## The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update -The [project and the developer community](/src/galaxy-team/index.md) has published a new paper, +The [project and the developer community](/galaxy-team/) has published a new paper, [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](https://doi.org/10.1093/nar/gkw343), *Nucleic Acids Research* (2 May 2016), doi:10.1093/nar/gkw343 diff --git a/content/galaxy-updates/2016-07/index.md b/content/galaxy-updates/2016-07/index.md index a4605f80d2..850654d7e7 100644 --- a/content/galaxy-updates/2016-07/index.md +++ b/content/galaxy-updates/2016-07/index.md @@ -242,13 +242,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 7-8 Galaxy Admin Training: Introduction North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 9-11 Galaxy Admin Training: Advanced North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team 2017 diff --git a/content/galaxy-updates/2016-08/index.md b/content/galaxy-updates/2016-08/index.md index 6ea89953ed..e73576ae6d 100644 --- a/content/galaxy-updates/2016-08/index.md +++ b/content/galaxy-updates/2016-08/index.md @@ -167,13 +167,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 7-8 Galaxy Admin Training: Introduction North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 9-11 Galaxy Admin Training: Advanced North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team 2017 diff --git a/content/galaxy-updates/2016-09/index.md b/content/galaxy-updates/2016-09/index.md index 46204cd05b..ebea1cd662 100644 --- a/content/galaxy-updates/2016-09/index.md +++ b/content/galaxy-updates/2016-09/index.md @@ -169,7 +169,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 7-8 Galaxy Admin Training: Introduction North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 7-9 @@ -187,7 +187,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 9-11 Galaxy Admin Training: Advanced North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 15-16 diff --git a/content/galaxy-updates/2016-10/index.md b/content/galaxy-updates/2016-10/index.md index cca84f9bf7..88294aaf90 100644 --- a/content/galaxy-updates/2016-10/index.md +++ b/content/galaxy-updates/2016-10/index.md @@ -244,7 +244,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 7-8 Galaxy Admin Training: Introduction North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 7-9 @@ -262,7 +262,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md November 9-11 Galaxy Admin Training: Advanced North America Salt Lake City, Utah, United States - Training offered by GTN Member Galaxy Team + Training offered by GTN Member Galaxy Team November 15-16 diff --git a/content/get-involved/index.md b/content/get-involved/index.md index 18328dca64..9b9e54e950 100644 --- a/content/get-involved/index.md +++ b/content/get-involved/index.md @@ -43,7 +43,7 @@ engines](https://galaxyproject.org/search/). # Develop Tools and Tool Definitions
Galaxy Tool Shed
-There are thousands of useful bioinformatics tools in existence and the Galaxy [Main](/src/main/index.md) server (and the [Galaxy Team](/src/galaxy-team/index.md)) cannot possibly support all of them. Only tools that are widely useful in many areas of biomedical research (and meet several other criteria) are available on Main. +There are thousands of useful bioinformatics tools in existence and the Galaxy [Main](/src/main/index.md) server (and the [Galaxy Team](/galaxy-team/)) cannot possibly support all of them. Only tools that are widely useful in many areas of biomedical research (and meet several other criteria) are available on Main. The Galaxy [Tool Shed](/src/toolshed/index.md) is a means to make other tools available for use within local and cloud-based Galaxy instances. You can create tool wrappers (usually a simple file encapsulating how Galaxy should treat the underlying software tool) in order to define tools within Galaxy. In order to share your tool with everyone, you can upload any given wrapper to the [Tool Shed](/src/toolshed/index.md) where it can be downloaded and installed into any Galaxy instance worldwide. To get you started we prepared this [Adding tool tutorial](/src/admin/tools/add-tool-tutorial/index.md) for you. diff --git a/content/news/2012-11-14-distribution-news-brief/index.md b/content/news/2012-11-14-distribution-news-brief/index.md index ee1cb2bf7f..a55184cccf 100644 --- a/content/news/2012-11-14-distribution-news-brief/index.md +++ b/content/news/2012-11-14-distribution-news-brief/index.md @@ -27,4 +27,4 @@ upgrade: $ hg pull -u -r 5dcbbdfe1087 **Thanks for using Galaxy!** -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2012-12-03-distribution-news-brief/index.md b/content/news/2012-12-03-distribution-news-brief/index.md index ec6891047e..86025767a2 100644 --- a/content/news/2012-12-03-distribution-news-brief/index.md +++ b/content/news/2012-12-03-distribution-news-brief/index.md @@ -27,4 +27,4 @@ upgrade: $ hg pull -u -r f364d992270c **Thanks for using Galaxy!** -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2012-12-20-distribution-news-brief/index.md b/content/news/2012-12-20-distribution-news-brief/index.md index b0c84b5ca8..f792199dd5 100644 --- a/content/news/2012-12-20-distribution-news-brief/index.md +++ b/content/news/2012-12-20-distribution-news-brief/index.md @@ -30,4 +30,4 @@ upgrade: $ hg pull -u -r 36ad8aa7b922 **Best wishes for a safe and happy holiday**, -***[The Galaxy Team](/src/galaxy-team/index.md)*** +***[The Galaxy Team](/galaxy-team/)*** diff --git a/content/news/2013-01-11-distribution-news-brief/index.md b/content/news/2013-01-11-distribution-news-brief/index.md index 7b26902575..a3ba4cf841 100644 --- a/content/news/2013-01-11-distribution-news-brief/index.md +++ b/content/news/2013-01-11-distribution-news-brief/index.md @@ -28,4 +28,4 @@ upgrade: $ hg pull -u -r a4113cc1cb5e *Thanks for using Galaxy,* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-02-08-galaxy-news-brief/index.md b/content/news/2013-02-08-galaxy-news-brief/index.md index f26d3683b6..4323f0575d 100644 --- a/content/news/2013-02-08-galaxy-news-brief/index.md +++ b/content/news/2013-02-08-galaxy-news-brief/index.md @@ -33,4 +33,4 @@ upgrade: $ hg pull Thanks for using Galaxy, -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-04-01-galaxy-distribution/index.md b/content/news/2013-04-01-galaxy-distribution/index.md index c71f3517f5..4bfabcf7e3 100644 --- a/content/news/2013-04-01-galaxy-distribution/index.md +++ b/content/news/2013-04-01-galaxy-distribution/index.md @@ -34,4 +34,4 @@ upgrade: $ hg pull *Thanks for using Galaxy,* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-04-08-galaxy-security-release/index.md b/content/news/2013-04-08-galaxy-security-release/index.md index c833fa2819..1487cedc8b 100644 --- a/content/news/2013-04-08-galaxy-security-release/index.md +++ b/content/news/2013-04-08-galaxy-security-release/index.md @@ -16,4 +16,4 @@ Additional details, including workarounds for those who are unable or unwilling *Thanks for using Galaxy,* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-06-03-galaxy-distribution/index.md b/content/news/2013-06-03-galaxy-distribution/index.md index 77104e686e..af5f03c639 100644 --- a/content/news/2013-06-03-galaxy-distribution/index.md +++ b/content/news/2013-06-03-galaxy-distribution/index.md @@ -33,4 +33,4 @@ upgrade: $ hg pull *Thanks for using Galaxy,* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-08-12-galaxy-distribution/index.md b/content/news/2013-08-12-galaxy-distribution/index.md index c2dd3f9d38..c7614a88ca 100644 --- a/content/news/2013-08-12-galaxy-distribution/index.md +++ b/content/news/2013-08-12-galaxy-distribution/index.md @@ -32,4 +32,4 @@ upgrade: $ hg pull *Thanks for using Galaxy,* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2013-11-04-galaxy-distribution/index.md b/content/news/2013-11-04-galaxy-distribution/index.md index b8ab5ca3f0..4343c073b8 100644 --- a/content/news/2013-11-04-galaxy-distribution/index.md +++ b/content/news/2013-11-04-galaxy-distribution/index.md @@ -33,4 +33,4 @@ upgrade: $ hg pull *Thanks for using Galaxy!* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-02-10-galaxy-distribution/index.md b/content/news/2014-02-10-galaxy-distribution/index.md index c2c97e6710..e7503bc56f 100644 --- a/content/news/2014-02-10-galaxy-distribution/index.md +++ b/content/news/2014-02-10-galaxy-distribution/index.md @@ -33,4 +33,4 @@ upgrade: $ hg pull *Thanks for using Galaxy!* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-04-14-galaxy-distribution/index.md b/content/news/2014-04-14-galaxy-distribution/index.md index bce0335058..ab6687ba02 100644 --- a/content/news/2014-04-14-galaxy-distribution/index.md +++ b/content/news/2014-04-14-galaxy-distribution/index.md @@ -50,4 +50,4 @@ date: "2014-04-14"
***Thanks for using Galaxy!*** -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-06-02-galaxy-distribution/index.md b/content/news/2014-06-02-galaxy-distribution/index.md index ec06fb596c..b7a1346835 100644 --- a/content/news/2014-06-02-galaxy-distribution/index.md +++ b/content/news/2014-06-02-galaxy-distribution/index.md @@ -45,4 +45,4 @@ date: "2014-06-02"
*Thanks for using Galaxy!* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-08-11-galaxy-distribution/index.md b/content/news/2014-08-11-galaxy-distribution/index.md index 863207c5b2..dfb12f0eb7 100644 --- a/content/news/2014-08-11-galaxy-distribution/index.md +++ b/content/news/2014-08-11-galaxy-distribution/index.md @@ -44,4 +44,4 @@ date: "2014-08-11"
*Thanks for using Galaxy!* -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-10-06-galaxy-distribution/index.md b/content/news/2014-10-06-galaxy-distribution/index.md index 9e47c39be4..138c6823c5 100644 --- a/content/news/2014-10-06-galaxy-distribution/index.md +++ b/content/news/2014-10-06-galaxy-distribution/index.md @@ -43,4 +43,4 @@ date: "2014-10-06"
*Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2014-questionnaire/index.md b/content/news/2014-questionnaire/index.md index ec96dd469e..39d0aa4799 100644 --- a/content/news/2014-questionnaire/index.md +++ b/content/news/2014-questionnaire/index.md @@ -15,4 +15,4 @@ Please take a few minutes and fill out whichever surveys apply to you. The ques Let your voice be heard! -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2015-01-13-galaxy-distribution/index.md b/content/news/2015-01-13-galaxy-distribution/index.md index 475b693789..1d42c10c12 100644 --- a/content/news/2015-01-13-galaxy-distribution/index.md +++ b/content/news/2015-01-13-galaxy-distribution/index.md @@ -49,4 +49,4 @@ In Galaxy's development branch, the basic tool from has been [redesigned and mod

*Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2015-03-galaxy-release/index.md b/content/news/2015-03-galaxy-release/index.md index 8dffb67669..4c5fd5c1c4 100644 --- a/content/news/2015-03-galaxy-release/index.md +++ b/content/news/2015-03-galaxy-release/index.md @@ -51,4 +51,4 @@ date: "2015-03-16"

*Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2015-05-galaxy-release/index.md b/content/news/2015-05-galaxy-release/index.md index e92eaa313e..3e53dfb6a6 100644 --- a/content/news/2015-05-galaxy-release/index.md +++ b/content/news/2015-05-galaxy-release/index.md @@ -18,4 +18,4 @@ The release notes have a new home at **[Read the Docs](http://galaxy.readthedocs *Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2015-07-galaxy-release/index.md b/content/news/2015-07-galaxy-release/index.md index 8072740028..250dee9b4e 100644 --- a/content/news/2015-07-galaxy-release/index.md +++ b/content/news/2015-07-galaxy-release/index.md @@ -15,4 +15,4 @@ date: "2015-09-03" * And *[much more](http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html)* *Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2015-10-galaxy-release/index.md b/content/news/2015-10-galaxy-release/index.md index 3809cdb2b8..e98f38613b 100644 --- a/content/news/2015-10-galaxy-release/index.md +++ b/content/news/2015-10-galaxy-release/index.md @@ -20,4 +20,4 @@ date: "2016-01-13" * **[Github](https://github.com/galaxyproject)** *Thanks for using Galaxy!*
-[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/2017-01-galaxy-update/index.md b/content/news/2017-01-galaxy-update/index.md index e20a80f115..32e287428c 100644 --- a/content/news/2017-01-galaxy-update/index.md +++ b/content/news/2017-01-galaxy-update/index.md @@ -15,4 +15,4 @@ The **[January Galaxy News](/src/galaxy-updates/2017-01/index.md)** is hot off t * [Galaxy Community Hub Update](/src/galaxy-updates/2017-01/index.md#galaxy-community-hub-update) * And [99 new publications](/src/galaxy-updates/2017-01/index.md#new-publications), [three open positions](/src/galaxy-updates/2017-01/index.md#who-s-hiring), [two new public servers and one new service](/src/galaxy-updates/2017-01/index.md#public-galaxy-server-news), [new releases](/src/galaxy-updates/2017-01/index.md#releases), and new [ToolShed contributions](/src/galaxy-updates/2017-01/index.md#toolshed-contributions) too. -Dave Clements and the [Galaxy Team](/src/galaxy-team/index.md) +Dave Clements and the [Galaxy Team](/galaxy-team/) diff --git a/content/news/2017-09-maintenance/index.md b/content/news/2017-09-maintenance/index.md index 5931a61496..10425c25e9 100644 --- a/content/news/2017-09-maintenance/index.md +++ b/content/news/2017-09-maintenance/index.md @@ -12,4 +12,4 @@ In the meantime, feel free to use the [more than 90 public Galaxy servers](/src/ We apologize for any inconvenience this causes. -The [Galaxy Team](/src/galaxy-team/index.md) +The [Galaxy Team](/galaxy-team/) diff --git a/content/news/analysis-by-viz-with-trackster-paper/index.md b/content/news/analysis-by-viz-with-trackster-paper/index.md index c776d49356..9acf7fa794 100644 --- a/content/news/analysis-by-viz-with-trackster-paper/index.md +++ b/content/news/analysis-by-viz-with-trackster-paper/index.md @@ -6,4 +6,4 @@ date: "2012-11-09" "[NGS analysis by visualization with Trackster](http://bit.ly/VMUz7p)" is a new article in the [November 2012](http://www.nature.com/nbt/journal/v30/n11/index.html) issue of *[Nature Biotechnology](http://www.nature.com/nbt/index.html)*. Trackster is Galaxy's "visual analysis environment for next-generation sequencing data that tightly couples interactive visualization with data analysis." Trackster includes support for "parameter-space visualization and exploration, systematic sweeps of parameter values and dynamic filtering." To learn more read the [article](http://bit.ly/VMUz7p) and give Trackster a spin on a [Galaxy instance near you](/src/use/index.md). -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/aug2011-distribution-news-brief/index.md b/content/news/aug2011-distribution-news-brief/index.md index 8264a98dfb..32595afb48 100644 --- a/content/news/aug2011-distribution-news-brief/index.md +++ b/content/news/aug2011-distribution-news-brief/index.md @@ -24,4 +24,4 @@ upgrade: % hg pull -u -r 949e4f5fa03a [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/duplicate-accounts-on-main/index.md b/content/news/duplicate-accounts-on-main/index.md index f466d33220..5bafbdf457 100644 --- a/content/news/duplicate-accounts-on-main/index.md +++ b/content/news/duplicate-accounts-on-main/index.md @@ -17,4 +17,4 @@ If your account is suspended and you believe that you are not in violation of Ma Thanks, -[The Galaxy Team](/src/galaxy-team/index.md) +[The Galaxy Team](/galaxy-team/) diff --git a/content/news/galaxy-biostar-launch/index.md b/content/news/galaxy-biostar-launch/index.md index af4fa1a1ba..27043fa69c 100644 --- a/content/news/galaxy-biostar-launch/index.md +++ b/content/news/galaxy-biostar-launch/index.md @@ -35,4 +35,4 @@ We hope you will like the change and look forward to any feedback you may have. *Thank you for using Galaxy!* -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/galaxy-current-protocols/index.md b/content/news/galaxy-current-protocols/index.md index 531ed3bbf3..eeeb0ab70b 100644 --- a/content/news/galaxy-current-protocols/index.md +++ b/content/news/galaxy-current-protocols/index.md @@ -17,4 +17,4 @@ Both papers feature hands-on, step by step protocols, accompanied by numerous an We would like to thank [Wiley](http://wiley.com) for making both of these publications be *open access.* -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/galaxy-pag2012/index.md b/content/news/galaxy-pag2012/index.md index 7badaa2b28..ad4d91b4d6 100644 --- a/content/news/galaxy-pag2012/index.md +++ b/content/news/galaxy-pag2012/index.md @@ -11,4 +11,4 @@ Dannon Baker and [Dave Clements](/people/dave-clements/) from the [Galaxy Team]( Hope to see you in San Diego, [Dave Clements](/people/dave-clements/) and Dannon Baker
-[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/galaxy-proect-servers-down20130314/index.md b/content/news/galaxy-proect-servers-down20130314/index.md index 75c37d9bcc..a949890f23 100644 --- a/content/news/galaxy-proect-servers-down20130314/index.md +++ b/content/news/galaxy-proect-servers-down20130314/index.md @@ -14,4 +14,4 @@ The *yellow banner on **Main** and **Test** will provide updates* (when the serv *Thanks for using Galaxy!!* -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/galaxy-project-openings/index.md b/content/news/galaxy-project-openings/index.md index 373cb2077c..08e5d79a67 100644 --- a/content/news/galaxy-project-openings/index.md +++ b/content/news/galaxy-project-openings/index.md @@ -6,8 +6,8 @@ date: "2013-01-25" The [Galaxy Project](http://galaxyproject.org/) is expanding and we are [looking for](/src/galaxy-is-hiring/index.md) highly-motivated, seeking-a-challenge, computationally-savvy, biologically-aware [software engineers](/src/galaxy-is-hiring/index.md#software-engineers) and [post-docs](/src/galaxy-is-hiring/index.md) to work on Galaxy. See the [GalaxyIsHiring](/src/galaxy-is-hiring/index.md) page for details. -Galaxy a great project with a [great community](/src/events/gcc2013/index.md). If you or someone you know would be interested in working with this thriving community on a rapidly evolving high performance platform that is used by thousands of researchers around the world every day, then please consider [joining](/src/galaxy-is-hiring/index.md) the [Galaxy team](/src/galaxy-team/index.md). +Galaxy a great project with a [great community](/src/events/gcc2013/index.md). If you or someone you know would be interested in working with this thriving community on a rapidly evolving high performance platform that is used by thousands of researchers around the world every day, then please consider [joining](/src/galaxy-is-hiring/index.md) the [Galaxy team](/galaxy-team/). -As always, please let me, or [any of us](/src/galaxy-team/index.md), know if you have any questions. +As always, please let me, or [any of us](/galaxy-team/), know if you have any questions. [Dave Clements](/people/dave-clements/) diff --git a/content/news/galaxy-tour-de-france2012/index.md b/content/news/galaxy-tour-de-france2012/index.md index c799ca32d3..0e5b1cfd03 100644 --- a/content/news/galaxy-tour-de-france2012/index.md +++ b/content/news/galaxy-tour-de-france2012/index.md @@ -4,7 +4,7 @@ date: "2012-04-25" ---
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/src/galaxy-team/index.md) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. diff --git a/content/news/gat2016-registration-open/index.md b/content/news/gat2016-registration-open/index.md index 0972cd3f4a..3e14b72457 100644 --- a/content/news/gat2016-registration-open/index.md +++ b/content/news/gat2016-registration-open/index.md @@ -34,4 +34,4 @@ Galaxy Admin Training 2016 is hosted by the [University of Utah Center for High We hope to see you in Salt Lake! -The [Galaxy Team](/src/galaxy-team/index.md) +The [Galaxy Team](/galaxy-team/) diff --git a/content/news/gcc2012-registration-is-open/index.md b/content/news/gcc2012-registration-is-open/index.md index dba6602402..e88867887a 100644 --- a/content/news/gcc2012-registration-is-open/index.md +++ b/content/news/gcc2012-registration-is-open/index.md @@ -8,7 +8,7 @@ date: "2012-03-20" [Registration](/src/events/gcc2012/register/index.md) is now open for the [2012 Galaxy Community Conference (GCC2012)](/src/events/gcc2012/index.md). This annual event will be held [July 25-27](/src/events/gcc2012/program/index.md) in [Chicago, Illinois](/src/events/gcc2012/logistics/index.md). The 2012 conference features [two full days](/src/events/gcc2012/program/index.md) of presentations, breakouts, and lightning talks about extending, developing, deploying, and best practices for Galaxy. A [day long training event](/src/events/gcc2012/training-day/index.md) has also been added, covering 7 different topics in multiple tracks. -The conference will also include talks from the [Galaxy Team](/src/galaxy-team/index.md) on future project direction, and is a chance to *affect and contribute to Galaxy's future direction.* If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, a data and analysis archival specialist, or are otherwise neck-deep in *data-intensive biology* then [GCC2012](/src/events/gcc2012/index.md) is for you. +The conference will also include talks from the [Galaxy Team](/galaxy-team/) on future project direction, and is a chance to *affect and contribute to Galaxy's future direction.* If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, a data and analysis archival specialist, or are otherwise neck-deep in *data-intensive biology* then [GCC2012](/src/events/gcc2012/index.md) is for you.
There are several [registration levels](/src/events/gcc2012/register/index.md), with discounts of over 50% for students and post-docs. Early registration saves an additional 40% and is $95-$195 for the [conference only](/src/events/gcc2012/program/index.md), and $130-$270 for the conference + [Training Day](/src/events/gcc2012/training-day/index.md). [Early registration](/src/events/gcc2012/register/index.md) ends June 11. [Lodging in dorms or a nearby hotel](/src/events/gcc2012/logistics/index.md) can also be booked at registration time. diff --git a/content/news/gcc2014-hackathon/index.md b/content/news/gcc2014-hackathon/index.md index 7467afb3e9..b6df078bcd 100644 --- a/content/news/gcc2014-hackathon/index.md +++ b/content/news/gcc2014-hackathon/index.md @@ -6,7 +6,7 @@ date: "2014-04-18" Galaxy has a fantastic developer community, from the very active [mailing lists](/src/mailing-lists/index.md) and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people involved. To that end, **we’re thrilled to officially announce the very first [Galaxy Project Hackathon](/src/events/gcc2014/hackathon/index.md).** The hackathon will be a three day event taking place at Johns Hopkins immediately preceding [GCC2014](/src/events/gcc2014/index.md) from June 28th-30th. -Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/src/galaxy-team/index.md) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. +Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The [Galaxy Hackathon](/src/events/gcc2014/hackathon/index.md) will be a great opportunity to meet and work closely with other community and [Galaxy Team](/galaxy-team/) members over the course of three days, culminating in some really great improvements and new features to show off at the [Galaxy Community Conference](/src/events/gcc2014/index.md) afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at [EventBrite](http://bit.ly/gcc2014hackreg). diff --git a/content/news/irc-public-log-proposal/index.md b/content/news/irc-public-log-proposal/index.md index 6f2f8585ce..7b1946f998 100644 --- a/content/news/irc-public-log-proposal/index.md +++ b/content/news/irc-public-log-proposal/index.md @@ -27,4 +27,4 @@ Starting sometime after community discussion ends (and assuming that discussion The project's IRC channel came up at the [GalaxyAdmins BoF meetup](/src/events/gcc2014/bofs/galaxy-admins/index.md) at [GCC2014](/src/events/gcc2014/index.md), where it was lauded as both a great resource, *and cursed because it is not archived anywhere.* An action item from that meetup is to propose this change. -The [Galaxy Team](/src/galaxy-team/index.md) +The [Galaxy Team](/galaxy-team/) diff --git a/content/news/jan2012-distribution-news-brief/index.md b/content/news/jan2012-distribution-news-brief/index.md index f9f1386ee9..27659e85f2 100644 --- a/content/news/jan2012-distribution-news-brief/index.md +++ b/content/news/jan2012-distribution-news-brief/index.md @@ -23,4 +23,4 @@ upgrade: % hg pull -u -r 63bc46cc73b7 [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/jan272012-distribution-news-brief/index.md b/content/news/jan272012-distribution-news-brief/index.md index 003b832576..2a4c26a9d9 100644 --- a/content/news/jan272012-distribution-news-brief/index.md +++ b/content/news/jan272012-distribution-news-brief/index.md @@ -26,4 +26,4 @@ upgrade: % hg pull -u -r 26920e20157f [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/jul202012-distribution-news-brief/index.md b/content/news/jul202012-distribution-news-brief/index.md index 7cae4ff88e..bc8d7207b8 100644 --- a/content/news/jul202012-distribution-news-brief/index.md +++ b/content/news/jul202012-distribution-news-brief/index.md @@ -24,4 +24,4 @@ upgrade: % hg pull -u -r ec29ce8e27a1 [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/mar122012-distribution-news-brief/index.md b/content/news/mar122012-distribution-news-brief/index.md index 3e66f19f12..0241fb65fa 100644 --- a/content/news/mar122012-distribution-news-brief/index.md +++ b/content/news/mar122012-distribution-news-brief/index.md @@ -26,4 +26,4 @@ upgrade: % hg pull -u -r 40f1816d6857 [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/may112012-distribution-news-brief/index.md b/content/news/may112012-distribution-news-brief/index.md index 74e1d82661..9e024c589d 100644 --- a/content/news/may112012-distribution-news-brief/index.md +++ b/content/news/may112012-distribution-news-brief/index.md @@ -25,4 +25,4 @@ upgrade: % hg pull -u -r 17d57db9a7c0 [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/nov2011-distribution-news-brief/index.md b/content/news/nov2011-distribution-news-brief/index.md index f68b71764d..6a5103c1f9 100644 --- a/content/news/nov2011-distribution-news-brief/index.md +++ b/content/news/nov2011-distribution-news-brief/index.md @@ -24,4 +24,4 @@ upgrade: % hg pull -u -r b258de1e6cea [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/oct2011-distribution-news-brief/index.md b/content/news/oct2011-distribution-news-brief/index.md index 420940643f..bf03214f99 100644 --- a/content/news/oct2011-distribution-news-brief/index.md +++ b/content/news/oct2011-distribution-news-brief/index.md @@ -24,4 +24,4 @@ upgrade: % hg pull -u -r 338ead4737ba [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/news/proteomics-mailing-list/index.md b/content/news/proteomics-mailing-list/index.md index 11c13c6d7b..2ccaa1a9a4 100644 --- a/content/news/proteomics-mailing-list/index.md +++ b/content/news/proteomics-mailing-list/index.md @@ -11,7 +11,7 @@ To subscribe to the galaxy-proteomics list please add your email address to the See [the complete list of mailing lists](/src/mailing-lists/index.md) for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. -Many thanks to Dave C. and the [Galaxy team](/src/galaxy-team/index.md) for setting this up. +Many thanks to Dave C. and the [Galaxy team](/galaxy-team/) for setting this up. Thanks diff --git a/content/news/sep072012-distribution-news-brief/index.md b/content/news/sep072012-distribution-news-brief/index.md index 5008f95847..6a74f28814 100644 --- a/content/news/sep072012-distribution-news-brief/index.md +++ b/content/news/sep072012-distribution-news-brief/index.md @@ -26,4 +26,4 @@ upgrade: $ hg pull -u -r e6444e7a1685 [Jennifer Jackson](/people/jennifer-jackson/) -[Galaxy Team](/src/galaxy-team/index.md) +[Galaxy Team](/galaxy-team/) diff --git a/content/people/dannon-baker/index.md b/content/people/dannon-baker/index.md index 9314af55ee..1ab5accd7a 100644 --- a/content/people/dannon-baker/index.md +++ b/content/people/dannon-baker/index.md @@ -3,7 +3,7 @@ title: Dannon Baker ---
![](/src/images/people/dannon.jpg)
-Dannon is a software engineer in the [Taylor Lab](http://taylorlab.org/) at [Johns Hopkins University](http://jhu.edu/). He is an active [member of the Galaxy project](/src/galaxy-team/index.md); Galaxy is a web-based platform for doing reproducible and transparent genomic research. Dannon's current efforts include work on a cloud computing deployment of Galaxy, and developing a flexible framework for automatic parallelism of tools within Galaxy. Dannon received his M.S. and B.S. in Computer Science from the Georgia Institute of Technology. +Dannon is a software engineer in the [Taylor Lab](http://taylorlab.org/) at [Johns Hopkins University](http://jhu.edu/). He is an active [member of the Galaxy project](/galaxy-team/); Galaxy is a web-based platform for doing reproducible and transparent genomic research. Dannon's current efforts include work on a cloud computing deployment of Galaxy, and developing a flexible framework for automatic parallelism of tools within Galaxy. Dannon received his M.S. and B.S. in Computer Science from the Georgia Institute of Technology. ## Contact diff --git a/content/people/dave-bouvier/index.md b/content/people/dave-bouvier/index.md index 133887b75c..1a56ebbe39 100644 --- a/content/people/dave-bouvier/index.md +++ b/content/people/dave-bouvier/index.md @@ -2,7 +2,7 @@ # Dave Bouvier -I am a system administrator, programmer, and a part of the [Galaxy Team](/src/galaxy-team/index.md) at [Penn State University](http://www.psu.edu/). I started on the Galaxy Project in March 2012. +I am a system administrator, programmer, and a part of the [Galaxy Team](/galaxy-team/) at [Penn State University](http://www.psu.edu/). I started on the Galaxy Project in March 2012. ## Contact diff --git a/content/people/delphine-lariviere/index.md b/content/people/delphine-lariviere/index.md index 56e3d7c074..71f8fd1030 100644 --- a/content/people/delphine-lariviere/index.md +++ b/content/people/delphine-lariviere/index.md @@ -6,7 +6,7 @@ # Delphine Lariviere -[Galaxy Team](/src/galaxy-team/index.md)
+[Galaxy Team](/galaxy-team/)
[Nekrutenko Lab](http://nekrut.bx.psu.edu/), Penn State University, PA, US
diff --git a/content/people/greg_vonkuster/index.md b/content/people/greg_vonkuster/index.md index f57b38f19a..79bb98d4b4 100644 --- a/content/people/greg_vonkuster/index.md +++ b/content/people/greg_vonkuster/index.md @@ -17,7 +17,7 @@ Greg left HP in early 2000 along with 2 partners and formed a dot-com startup na In 2003 Greg moved to State College, PA, taking a position as VP of Engineering for a Happy Valley startup named Advanced Interfaces, Inc., which eventually became `VideoMining Corporation`. -In 2006 Greg brought his corporate experience to the [Galaxy Team](/src/galaxy-team/index.md) at [Penn State University](http://www.psu.edu/) where he managed the Galaxy development effort and played a key role in landing the 2008 grant that enabled the team to grow to include members at Penn State University, Emory University and beyond. +In 2006 Greg brought his corporate experience to the [Galaxy Team](/galaxy-team/) at [Penn State University](http://www.psu.edu/) where he managed the Galaxy development effort and played a key role in landing the 2008 grant that enabled the team to grow to include members at Penn State University, Emory University and beyond. Greg has been involved at some level in virtually every aspect of Galaxy. He introduced processes early in Galaxy's development lifecycle that enabled its pervasive adoption around the world, and continues to leverage his experience to make Galaxy a useful, high-quality product that fills a unique niche in biological research. diff --git a/content/people/guerler/index.md b/content/people/guerler/index.md index 0a8625a235..eb67ea3895 100644 --- a/content/people/guerler/index.md +++ b/content/people/guerler/index.md @@ -1,7 +1,7 @@
![](/src/galaxy-team/guerler.jpg)
# Aysam Guerler -Aysam is a software engineer in the [Taylor Lab](http://taylorlab.org/) at [Johns Hopkins University](http://jhu.edu/). He is an active [member of the Galaxy project](/src/galaxy-team/index.md). +Aysam is a software engineer in the [Taylor Lab](http://taylorlab.org/) at [Johns Hopkins University](http://jhu.edu/). He is an active [member of the Galaxy project](/galaxy-team/). ## Contact diff --git a/content/people/guru-ananda/index.md b/content/people/guru-ananda/index.md index 51ad34345c..956197cbdf 100644 --- a/content/people/guru-ananda/index.md +++ b/content/people/guru-ananda/index.md @@ -1,7 +1,7 @@
![](/src/galaxy-team/guru.jpg)
# Guru Ananda -Guru is a graduate student in Bioinformatics and Genomics at [Penn State University](http://psu.edu/). Guru is core member of the [Galaxy Team](/src/galaxy-team/index.md). +Guru is a graduate student in Bioinformatics and Genomics at [Penn State University](http://psu.edu/). Guru is core member of the [Galaxy Team](/galaxy-team/). ## Contact diff --git a/content/people/jennifer-jackson/index.md b/content/people/jennifer-jackson/index.md index 489b43fd99..c4a6912079 100644 --- a/content/people/jennifer-jackson/index.md +++ b/content/people/jennifer-jackson/index.md @@ -1,7 +1,7 @@ # Jennifer Hillman-Jackson -[Galaxy Team](/src/galaxy-team/index.md), Application Science +[Galaxy Team](/galaxy-team/), Application Science [Nekrutenko Lab](http://nekrut.bx.psu.edu/), Penn State University, PA, US diff --git a/content/people/nate/index.md b/content/people/nate/index.md index f8116863ff..19912cbcd1 100644 --- a/content/people/nate/index.md +++ b/content/people/nate/index.md @@ -2,7 +2,7 @@ # Nate Coraor -I am a system administrator, programmer, and a part of the [Galaxy Team](/src/galaxy-team/index.md) at [Penn State University](http://www.psu.edu/). My primary contributions to the project are to the infrastructure architecture and maintenance for the [Public Server](/src/main/index.md) and programming related to systems tasks such as running jobs. +I am a system administrator, programmer, and a part of the [Galaxy Team](/galaxy-team/) at [Penn State University](http://www.psu.edu/). My primary contributions to the project are to the infrastructure architecture and maintenance for the [Public Server](/src/main/index.md) and programming related to systems tasks such as running jobs. ## Contact diff --git a/content/people/sergey/index.md b/content/people/sergey/index.md index 689588a76b..98489e3c0e 100644 --- a/content/people/sergey/index.md +++ b/content/people/sergey/index.md @@ -3,7 +3,7 @@ # Sergey Golitsynskiy I am a software engineer in the [Taylor Lab](http://taylorlab.org) at [Johns Hopkins -University](http://www.jhu.edu/) and part of the [Galaxy Team](/src/galaxy-team/index.md). +University](http://www.jhu.edu/) and part of the [Galaxy Team](/galaxy-team/). ## Contact diff --git a/content/publication-library/contribute/index.md b/content/publication-library/contribute/index.md index b01730e0e4..9b6c3c249e 100644 --- a/content/publication-library/contribute/index.md +++ b/content/publication-library/contribute/index.md @@ -9,7 +9,7 @@ title: "Contribute to the Galaxy Publication Library" It takes a fair amount of work to keep track of publications that reference Galaxy in some way: There are now over 1000 papers per year that do so. The bulk of this curation is currently done by [Galaxy -Team](/src/galaxy-team/index.md) members using (quite possibly hundreds) of +Team](/galaxy-team/) members using (quite possibly hundreds) of email alerts and custom software. If you want to help curate papers then here's how you can help. diff --git a/content/publication-library/index.md b/content/publication-library/index.md index 0c99646315..ab0f5f56e5 100644 --- a/content/publication-library/index.md +++ b/content/publication-library/index.md @@ -36,7 +36,7 @@ Galaxy specific tags all start with "+": |   [+UseMain](https://www.zotero.org/groups/galaxy/items/tag/+UseMain/) |   Uses the project's public server, [usegalaxy.org](https://usegalaxy.org/) (a.k.a. [Main](/src/main/index.md), in its methods. | |   [+UsePublic](https://www.zotero.org/groups/galaxy/items/tag/+UsePublic/) |   Uses a [publicly accessible Galaxy platform](/src/use/index.md) in its methods. | | [+Other](https://www.zotero.org/groups/galaxy/items/tag/+Other/) | Publications that don't fit well under any other tag. | -| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/src/galaxy-team/index.md) member as an author. | +| [+Project](https://www.zotero.org/groups/galaxy/items/tag/+Project/) | Publications with a [Galaxy team](/galaxy-team/) member as an author. | | [+RefPublic](https://www.zotero.org/groups/galaxy/items/tag/+RefPublic/) | References a [publicly accessible Galaxy instance](/src/use/index.md) or a [Galaxy service](/src/use/index.md). This is distinct from the *+UsePublic* tag. | | [+Reproducibility](https://www.zotero.org/groups/galaxy/items/tag/+Reproducibility/) | Reproducibility and persistence in science. | | [+Shared](https://www.zotero.org/groups/galaxy/items/tag/+Shared/) | Publications that have published workflows, histories, datasets, pages, or visualizations in a Galaxy instance. | diff --git a/content/support/biostar/index.md b/content/support/biostar/index.md index 24b4002497..6ae78c37f1 100644 --- a/content/support/biostar/index.md +++ b/content/support/biostar/index.md @@ -14,7 +14,7 @@ Galaxy Biostars has been retired and is available as an archived resource at the -As a result of joint efforts of the [Galaxy Team](/src/galaxy-team/index.md) and the [Biostars Team](https://github.com/ialbert/biostar-central/graphs/contributors) a new support platform emerged for the Galaxy community to use: +As a result of joint efforts of the [Galaxy Team](/galaxy-team/) and the [Biostars Team](https://github.com/ialbert/biostar-central/graphs/contributors) a new support platform emerged for the Galaxy community to use: Galaxy Biostars is at **[https://biostar.usegalaxy.org/](https://biostar.usegalaxy.org/)** From 367413361e9e31b7f82095f6696b214f627372c5 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 17:05:15 -0400 Subject: [PATCH 07/24] More people link fixes --- .../index.md | 2 +- content/citing-galaxy/index.md | 16 ++++++++-------- .../galaxy-admins/meetups/2013-11-20/index.md | 2 +- .../galaxy-admins/meetups/2015-02-19/index.md | 2 +- content/develop/gsoc/2015-ideas/index.md | 6 +++--- content/events/archive/wayback/index.md | 12 ++++++------ content/events/caltech2013/index.md | 2 +- .../events/galaxy-tour-de-france2012/index.md | 2 +- content/events/gcc2012/abstracts/index.md | 2 +- content/events/gcc2012/program/index.md | 6 +++--- content/events/gcc2012/training-day/index.md | 6 +++--- content/events/gcc2013/abstracts/talks/index.md | 4 ++-- content/events/gcc2013/program/index.md | 6 +++--- content/events/gcc2013/training-day/index.md | 12 ++++++------ .../events/gcc2014/bofs/heterogeneous/index.md | 2 +- content/events/gcc2014/program/index.md | 4 ++-- content/events/gcc2014/training-day/index.md | 6 +++--- content/galaxy-team/index.md | 2 +- content/galaxy-updates/2012-07/index.md | 2 +- content/galaxy-updates/2012-12/index.md | 2 +- content/galaxy-updates/2013-07/index.md | 4 ++-- content/galaxy-updates/2013-08/index.md | 4 ++-- content/galaxy-updates/2013-09/index.md | 2 +- content/galaxy-updates/2013-10/index.md | 2 +- content/galaxy-updates/2014-03/index.md | 2 +- content/galaxy-updates/2014-04/index.md | 4 ++-- content/galaxy-updates/2015-03/index.md | 2 +- content/galaxy-updates/2015-05/index.md | 4 ++-- content/galaxy-updates/2015-11/index.md | 2 +- content/galaxy-updates/2016-10/index.md | 2 +- content/galaxy-updates/2016-12/index.md | 2 +- content/galaxy-updates/2017-03/index.md | 2 +- content/galaxy-updates/2017-06/index.md | 2 +- content/galaxy-updates/2018-08/index.md | 6 +++--- content/news/2019-02-galaxy-update/index.md | 2 +- content/news/2019-06-galaxy-update/index.md | 2 +- content/news/2019-10-galaxy-update/index.md | 2 +- content/news/galaxy-current-protocols/index.md | 2 +- content/people/dave-clements/index.md | 8 ++++---- content/people/marten/index.md | 2 +- content/use/galaxy-test/index.md | 2 +- content/use/usegalaxy-eu/index.md | 2 +- content/use/usegalaxy-org/index.md | 2 +- 43 files changed, 81 insertions(+), 81 deletions(-) diff --git a/content/admin/tools/external-display-applications-tutorial/index.md b/content/admin/tools/external-display-applications-tutorial/index.md index 52e1f6e700..7a1e44aac6 100644 --- a/content/admin/tools/external-display-applications-tutorial/index.md +++ b/content/admin/tools/external-display-applications-tutorial/index.md @@ -13,7 +13,7 @@ There are many services available that allow users to upload their own data for ## Citation -If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x * * * diff --git a/content/citing-galaxy/index.md b/content/citing-galaxy/index.md index 5afcd73fad..f5d4daba2a 100644 --- a/content/citing-galaxy/index.md +++ b/content/citing-galaxy/index.md @@ -40,7 +40,7 @@ Some excellent examples (*emphasis added*): If you use, extend or reference Galaxy in your published work, please cite this publication: -* [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 This and other references are also [available in GitHub](https://github.com/galaxyproject/galaxy/blob/dev/CITATION) as a [CITATION file](http://software-carpentry.org/blog/2013/09/introducing-citation-files.html). @@ -59,32 +59,32 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## Data Managers -* [Daniel Blankenberg](/people/dan/), James E. Johnson, The [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 +* [Daniel Blankenberg](/people/dan/), James E. Johnson, The [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Wrangling Galaxy's Reference Data](https://academic.oup.com/bioinformatics/article/30/13/1917/205199/Wrangling-Galaxy-s-reference-data)**. *Bioinformatics* (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119 ## DataSource Tools -* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. +* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. ## External Display Applications -* [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x +* [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x ## Interactive Environments -* [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 +* [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 ## Reproducibility -* [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). +* [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/). **[Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014)**, *Cell Systems*, Volume 6, Issue 6, 2018, Pages 631-635, ISSN 2405-4712, doi:10.1016/j.cels.2018.03.014. ## ToolShed -* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/src/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 +* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 ## Training & Education -* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 ### Online Education diff --git a/content/community/galaxy-admins/meetups/2013-11-20/index.md b/content/community/galaxy-admins/meetups/2013-11-20/index.md index dda34ec620..8a632b1615 100644 --- a/content/community/galaxy-admins/meetups/2013-11-20/index.md +++ b/content/community/galaxy-admins/meetups/2013-11-20/index.md @@ -19,7 +19,7 @@ Presentations - GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
+ GalaxyAdmins: GCC2013 Followup
Dave Clements, Srinivas Maddhi
Galaxy Project Update: UseGalaxy.org moves to TACC
Nate Coraor
Links diff --git a/content/community/galaxy-admins/meetups/2015-02-19/index.md b/content/community/galaxy-admins/meetups/2015-02-19/index.md index 35562d277a..39a3630201 100644 --- a/content/community/galaxy-admins/meetups/2015-02-19/index.md +++ b/content/community/galaxy-admins/meetups/2015-02-19/index.md @@ -20,7 +20,7 @@ Topics - GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
+ GalaxyAdmins direction (slides)
Hans-Rudolf Hotz
Results from the 2014 Galaxy Community Questionnaires (Slides)
Dave Clements
Galaxy Project Update: Gravity
Nate Coraor
Links diff --git a/content/develop/gsoc/2015-ideas/index.md b/content/develop/gsoc/2015-ideas/index.md index aa3cf518bd..41e7cde11a 100644 --- a/content/develop/gsoc/2015-ideas/index.md +++ b/content/develop/gsoc/2015-ideas/index.md @@ -53,7 +53,7 @@ The [Global Alliance for Genomics Health](http://genomicsandhealth.org/) (GA4GH) **Potentially Helpful Skills** Familiarity with Galaxy and/or other Workflow Management Systems -**Possible Mentors** [John Chilton](/people/john-chilton/), [Daniel Blankenberg](/src/people/dan/) +**Possible Mentors** [John Chilton](/people/john-chilton/), [Daniel Blankenberg](/people/dan/) ## Docker Swarm and Compose @@ -244,7 +244,7 @@ Once familiar with pages - there are at least two paths this project could diver **Potentially Helpful Skills** Familiarity with Galaxy and IPython -**Possible Mentors** [Carl Eberhard](/people/carl-eberhard/), [Martin Cech](/src/people/marten/) +**Possible Mentors** [Carl Eberhard](/people/carl-eberhard/), [Martin Cech](/people/marten/) ## Easier or More Robust History Imports and Exports @@ -266,7 +266,7 @@ that can be pasted into an import the history from another Galaxy instance. * Split this process in pieces to allow tracking/resuming the transfers. * Rework the API and UI to provide pleasant progress bar tracking progress and estimating time remaining. -**Possible Mentors** [Martin Cech](/people/marten/), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/src/people/dan/) +**Possible Mentors** [Martin Cech](/people/marten/), [Jim Johnson](https://github.com/jj-umn), [Daniel Blankenberg](/people/dan/) **Required Skills** Python programming diff --git a/content/events/archive/wayback/index.md b/content/events/archive/wayback/index.md index 2f8caf67a1..b97bd9fff5 100644 --- a/content/events/archive/wayback/index.md +++ b/content/events/archive/wayback/index.md @@ -1680,7 +1680,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s May 15 RNA-Seq Galaxy Workshop North America Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko Slides @@ -1790,7 +1790,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s April 16 GalaxyAdmins April 2015 Meetup Online - Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler + Hans-Rudolf Hotz, Dave Clements, Carrie Ganote, Aysam Guerler Slides, video @@ -1893,7 +1893,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s March 17 Using Galaxy Workshop Penn State University, State College, Pennsylvania, United States -
Training offered by GTN Member
Martin Cech, Anton Nekrutenko +
Training offered by GTN Member
Martin Cech, Anton Nekrutenko @@ -3165,7 +3165,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November GalaxyAdmins Meetup Online Slides, Screencast - Dave Clements, Srinivas Maddhi, Nate Coraor + Dave Clements, Srinivas Maddhi, Nate Coraor November 19 @@ -3458,7 +3458,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia - Ross Lazarus, Dan Blankenberg + Ross Lazarus, Dan Blankenberg September 27 @@ -4259,7 +4259,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Tour de France 2012 Perpignan, Montpellier, Lyon, Paris - Nate Coraor, Anton Nekrutenko, JamesTaylor + Nate Coraor, Anton Nekrutenko, JamesTaylor May 23-25 diff --git a/content/events/caltech2013/index.md b/content/events/caltech2013/index.md index 3285cf0c15..274be97474 100644 --- a/content/events/caltech2013/index.md +++ b/content/events/caltech2013/index.md @@ -89,7 +89,7 @@ This workshop is generously supported by an [AWS in Education](http://aws.amazon **[Dave Clements](/people/dave-clements/)**
**Emory University**

-This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/people/dannon-baker/) and [Nate Coraor](/src/people/nate/), two members of the [core Galaxy development team](/src/galaxy-team/). +This informal discussion will introduce Galaxy for developers. We will discuss any items of interest to attendees and answer questions relating to, for example, the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment, and anything else about Galaxy. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Dannon Baker](/people/dannon-baker/) and [Nate Coraor](/people/nate/), two members of the [core Galaxy development team](/src/galaxy-team/). *This discussion is open to any member of the Caltech community. It is free, but space is limited and advanced registration is strongly encouraged.*
diff --git a/content/events/galaxy-tour-de-france2012/index.md b/content/events/galaxy-tour-de-france2012/index.md index 85431f43af..6b6d525a1f 100644 --- a/content/events/galaxy-tour-de-france2012/index.md +++ b/content/events/galaxy-tour-de-france2012/index.md @@ -110,7 +110,7 @@ If you attend both workshops and plan to eat in the area, there are many choices ## Meet the Team! -
Nate Coraor!   Anton Nekrutenko!   James Taylor!
+
Nate Coraor!   Anton Nekrutenko!   James Taylor!
* [Nate Coraor](/people/nate/) * [Anton Nekrutenko](/people/anton/) diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index 2b98c3727b..8969e76cac 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -229,7 +229,7 @@ Contact: support@oqtans.org; ratschg@mskcc.org
-**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/people/dan/)2, [Anton Nekrutenko](/src/people/anton/)2 and Oliver Hobert1
+**Gregory Minevich1**, Danny Park1, Richard J. Poole1, [Daniel Blankenberg](/people/dan/)2, [Anton Nekrutenko](/people/anton/)2 and Oliver Hobert1
1 Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
2 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA, USA
diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index 392f7159c5..cc3f5056a3 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -35,7 +35,7 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
@@ -55,9 +55,9 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 diff --git a/content/events/gcc2012/training-day/index.md b/content/events/gcc2012/training-day/index.md index 0c95a11d00..06ae731f01 100644 --- a/content/events/gcc2012/training-day/index.md +++ b/content/events/gcc2012/training-day/index.md @@ -29,7 +29,7 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 9:00 - WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
@@ -49,9 +49,9 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 2:00 - WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
+ WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
- WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
+ WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
3:30 diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index 7fc16f69c8..693773f818 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -430,7 +430,7 @@ We will present an overview of the requirements to move Galaxy into the Clinical
Greg Von Kuster
-**[Greg von Kuster](/people/greg_vonkuster/)**, [Daniel Blankenberg](/src/people/dan/) +**[Greg von Kuster](/people/greg_vonkuster/)**, [Daniel Blankenberg](/people/dan/) Penn State / Galaxy Team *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/VonKusterToolShed.pdf), [Vimeo](https://vimeo.com/74347850)* @@ -451,7 +451,7 @@ To ensure the quality of the Tool Shed and the available contributed Utilities,
-**[Carl Eberhard](/people/carl-eberhard/)**1, [Jeremy Goecks](/people/jeremy-goecks/)1, [The Galaxy Team](/src/galaxy-team/)1,2, [Anton Nekrutenko](/src/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 +**[Carl Eberhard](/people/carl-eberhard/)**1, [Jeremy Goecks](/people/jeremy-goecks/)1, [The Galaxy Team](/src/galaxy-team/)1,2, [Anton Nekrutenko](/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 1 Emory University
2 Penn State University diff --git a/content/events/gcc2013/program/index.md b/content/events/gcc2013/program/index.md index e0a6ac0b08..0dabd91268 100644 --- a/content/events/gcc2013/program/index.md +++ b/content/events/gcc2013/program/index.md @@ -33,7 +33,7 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 9:00 - Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
+ Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
@@ -46,7 +46,7 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 12:30 The Galaxy API
Nate Coraor, Carl Eberhard
- Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
+ Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
@@ -57,7 +57,7 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 15:00 - Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
+ Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
diff --git a/content/events/gcc2013/training-day/index.md b/content/events/gcc2013/training-day/index.md index 7f15b03ea8..ec92e9a70f 100644 --- a/content/events/gcc2013/training-day/index.md +++ b/content/events/gcc2013/training-day/index.md @@ -39,7 +39,7 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and 9:00 - Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
+ Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
@@ -52,7 +52,7 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and 12:30 The Galaxy API
Nate Coraor, Carl Eberhard
- Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
+ Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
@@ -63,7 +63,7 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and 15:00 - Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
+ Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
@@ -336,7 +336,7 @@ See each individual workshop's list of prerequisite for specifics. - + @@ -371,7 +371,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI 		Dan Blankenberg, Penn State University
Ross Lazarus, BakerIDI
Content
- + @@ -480,7 +480,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University 		Ross Lazarus, BakerIDI
Dan Blankenberg, Penn State University
Content
- + diff --git a/content/events/gcc2014/bofs/heterogeneous/index.md b/content/events/gcc2014/bofs/heterogeneous/index.md index 75b8b5073e..c5450b53da 100644 --- a/content/events/gcc2014/bofs/heterogeneous/index.md +++ b/content/events/gcc2014/bofs/heterogeneous/index.md @@ -13,7 +13,7 @@ When: Tuesday, July 1, 5:45pm Where: Salon A -Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Carrie Ganote +Contact: [Philip Blood](mailto:blood AT psc DOT edu), [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Carrie Ganote ## Description diff --git a/content/events/gcc2014/program/index.md b/content/events/gcc2014/program/index.md index ac64f08bb6..fd0c8c61e1 100644 --- a/content/events/gcc2014/program/index.md +++ b/content/events/gcc2014/program/index.md @@ -40,7 +40,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -66,7 +66,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + diff --git a/content/events/gcc2014/training-day/index.md b/content/events/gcc2014/training-day/index.md index e240422651..fdb514bcca 100644 --- a/content/events/gcc2014/training-day/index.md +++ b/content/events/gcc2014/training-day/index.md @@ -36,7 +36,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -62,7 +62,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -212,7 +212,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors James Taylor, Emory University
Nate Coraor, Penn State University 		James Taylor, Emory University
Nate Coraor, Penn State University
Content
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
9:00 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
3:30 RNA-Seq Analysis with Galaxy and Alternative Tools
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
Tool Development from bright idea to toolshed - Data Managers
JJ Johnson & Dan Blankenberg
Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Visualization of NGS data
Jeremy Goecks and Aysam Guerler
 Scriptable Bioinformatics Cloud Infrastructures with Cloud BioLinux, CloudMan & Galaxy
Ntino Krampis, Enis Afgan, Ravi Sanka, Brad Chapman
Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
- + diff --git a/content/galaxy-team/index.md b/content/galaxy-team/index.md index 80120394e5..358ba483b8 100644 --- a/content/galaxy-team/index.md +++ b/content/galaxy-team/index.md @@ -36,7 +36,7 @@ Galaxy is developed by the [Nekrutenko lab](http://nekrut.bx.psu.edu) in the [Ce
-[![Marten Cech](/people/marten/marten.jpg)](/src/people/marten/) +[![Marten Cech](/people/marten/marten.jpg)](/people/marten/) [Martin Cech](/people/marten/) [Penn State](http://www.bx.psu.edu) diff --git a/content/galaxy-updates/2012-07/index.md b/content/galaxy-updates/2012-07/index.md index 2e4fc065f4..0a7efcc0f2 100644 --- a/content/galaxy-updates/2012-07/index.md +++ b/content/galaxy-updates/2012-07/index.md @@ -54,7 +54,7 @@ These papers may be of interest to the Galaxy community: * ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. -* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. +* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. These papers were among [31 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md) (for a total of 348 papers in the last ~16 months). The new papers are spread [across 8 categories](http://www.citeulike.org/group/16008/tags). diff --git a/content/galaxy-updates/2012-12/index.md b/content/galaxy-updates/2012-12/index.md index 94cd7e620f..7aad571f99 100644 --- a/content/galaxy-updates/2012-12/index.md +++ b/content/galaxy-updates/2012-12/index.md @@ -46,7 +46,7 @@ These papers may be of interest to the Galaxy community:
* [Enis Afgan](/people/enis-afgan/), Brad Chapman and [James Taylor](/src/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

-* [Jeremy Goecks](/people/jeremy-goecks/), [Nate Coraor](/people/nate/), [The Galaxy Team](/src/galaxy-team/), [Anton Nekrutenko](/src/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

+* [Jeremy Goecks](/people/jeremy-goecks/), [Nate Coraor](/people/nate/), [The Galaxy Team](/src/galaxy-team/), [Anton Nekrutenko](/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

* Samantha Baldwin, Roopashree Revanna, Susan Thomson, *et al.*, "[A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)](https://doi.org/10.1186/1471-2164-13-637)," *BMC Genomics*, Vol. 13, No. 1. (2012), 637

* Jeremy C. Morgan, Robert W. Chapman, Paul E. Anderson, "[A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources](https://doi.org/10.1145/2382936.2383033). Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

* Bo Liu, Borja Sotomayor, Ravi Madduri, Kyle Chard, "[Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision](http:// bit.ly/UPBbRI)." [Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012)](http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/) diff --git a/content/galaxy-updates/2013-07/index.md b/content/galaxy-updates/2013-07/index.md index 25ca5cd79a..70fe3dba81 100644 --- a/content/galaxy-updates/2013-07/index.md +++ b/content/galaxy-updates/2013-07/index.md @@ -126,7 +126,7 @@ This installation of Galaxy has been configured such that anonymous users can op A record 53 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in June. These papers may be particularly interesting to the Galaxy community -* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/), [Carl Eberhard](/people/carl-eberhard/), Tomithy Too, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 +* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/), [Carl Eberhard](/people/carl-eberhard/), Tomithy Too, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 * "[Detection of non-coding RNA in Bacteria and Archaea using the DETR’PROK Galaxy pipeline](https://doi.org/10.1016/j.ymeth.2013.06.003)" by Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret, *[Methods](http://www.sciencedirect.com/science/journal/10462023)* (June 2013) * "[Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data](https://doi.org/10.1002/gepi.21739)" by Nicholas A. Davis, Caleb A. Lareau, Bill C. White, *et al.* *Genetic Epidemiology* (June 2013) * "[A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America](https://doi.org/10.1093/bib/bbt033)" by Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza, *Briefings in Bioinformatics* (30 May 2013) @@ -356,7 +356,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-08/index.md b/content/galaxy-updates/2013-08/index.md index 05f7be69a6..143893cd23 100644 --- a/content/galaxy-updates/2013-08/index.md +++ b/content/galaxy-updates/2013-08/index.md @@ -103,7 +103,7 @@ The QBRC galaxy server tools are constantly being updated. Please contact author 47 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in July. These papers may be particularly interesting to the Galaxy community -* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Nate Coraor](/src/people/nate/), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) +* "[A sustainable national gateway for biological computation](https://doi.org/10.1145/2484762.2484817)" by [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Nate Coraor](/people/nate/), *et al.* In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery* (2013) * "[Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE](https://doi.org/10.1186/1471-2164-14-494)" by Quang Trinh, Fei Y. Jen, Ziru Zhou, *et al.*, *BMC Genomics,* Vol. 14, No. 1. (2013), 494 * "[The Banana Genome Hub](https://doi.org/10.1093/database/bat035)" by Droc, *et al.*, *Database*, Vol. 2013 (01 January 2013), @@ -193,7 +193,7 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 - + diff --git a/content/galaxy-updates/2013-09/index.md b/content/galaxy-updates/2013-09/index.md index 82513dfd5f..1037fecb94 100644 --- a/content/galaxy-updates/2013-09/index.md +++ b/content/galaxy-updates/2013-09/index.md @@ -180,7 +180,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu - + diff --git a/content/galaxy-updates/2013-10/index.md b/content/galaxy-updates/2013-10/index.md index fbabf49091..904ca63942 100644 --- a/content/galaxy-updates/2013-10/index.md +++ b/content/galaxy-updates/2013-10/index.md @@ -186,7 +186,7 @@ In the next 3 months there are no less than 13 talks and workshops at at least 5 - + diff --git a/content/galaxy-updates/2014-03/index.md b/content/galaxy-updates/2014-03/index.md index ceaa2ba6fd..a4cf546550 100644 --- a/content/galaxy-updates/2014-03/index.md +++ b/content/galaxy-updates/2014-03/index.md @@ -9,7 +9,7 @@ Welcome to the March 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *54 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in Febrary. Some papers that may be particularly interesting to the Galaxy community: -* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/src/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 +* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 * [Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis](https://doi.org/10.1371/journal.pone.0087301), by Khushi, *et al.,* *PLoS ONE*, Vol. 9, No. 2. (12 February 2014), e87301, doi:10.1371/journal.pone.0087301 diff --git a/content/galaxy-updates/2014-04/index.md b/content/galaxy-updates/2014-04/index.md index 462413daf6..a4f4d0ab7d 100644 --- a/content/galaxy-updates/2014-04/index.md +++ b/content/galaxy-updates/2014-04/index.md @@ -9,9 +9,9 @@ Welcome to the April 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *63 papers* (a new monthly record) were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in March. Some papers that may be particularly interesting to the Galaxy community: -* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/people/dan/), James E. Johnson, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 +* "[Wrangling Galaxy's Reference Data](https://doi.org/10.1093/bioinformatics/btu119)," by [Daniel Blankenberg](/people/dan/), James E. Johnson, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/); *Bioinformatics* (28 February 2014), doi:10.1093/bioinformatics/btu119 -* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/people/dan/), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/src/people/anton/), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) +* "[Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach](http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html)," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [Daniel Blankenberg](/people/dan/), Nicholas Stoler, Kateryna D. Makova, [Anton Nekrutenko](/people/anton/), *[BioTechniques](http://www.biotechniques.com/)*, Vol. 56, No. 3. (2014) * "[Orione, a web-based framework for NGS analysis in microbiology](https://doi.org/10.1093/bioinformatics/btu135)," Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia, *Bioinformatics* (Oxford, England) (10 March 2014), doi:10.1093/bioinformatics/btu135 diff --git a/content/galaxy-updates/2015-03/index.md b/content/galaxy-updates/2015-03/index.md index 1e0f8807a0..7511d07256 100644 --- a/content/galaxy-updates/2015-03/index.md +++ b/content/galaxy-updates/2015-03/index.md @@ -22,7 +22,7 @@ Welcome to the March 2015 *[Galaxy Update](/src/galaxy-updates/index.md)*, a sum Jorrit Boeke, [John M Chilton](/people/john-chilton/), Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, *Nature Biotechnology*, Vol. 33, No. 2. (6 February 2015) * [Online Resources for Genomic Analysis Using High-Throughput Sequencing](https://doi.org/10.1101/pdb.top083667) - [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 + [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), *Cold Spring Harbor Protocols* (05 February 2015), doi:10.1101/pdb.top083667 * [Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud](https://doi.org/10.12694/scpe.v16i1.1058) Philip Church, Andrzej Goscinski, *Scalable Computing: Practice and Experience*, Vol. 16, No. 1. (07 February 2015), doi:10.12694/scpe.v16i1.1058 diff --git a/content/galaxy-updates/2015-05/index.md b/content/galaxy-updates/2015-05/index.md index ea0f3d1b63..d7a7159612 100644 --- a/content/galaxy-updates/2015-05/index.md +++ b/content/galaxy-updates/2015-05/index.md @@ -28,7 +28,7 @@ Welcome to the May 2015 *[Galactic News](/src/galaxy-updates/index.md)*, a summa Halfdan Rydbeck, Geir Kjetil K. Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig, *PloS one*, Vol. 10, No. 4. (2015) * [StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo](https://doi.org/10.1093/bioinformatics/btv213) - Yin Tang, [Emil Bouvier](/people/dave-bouvier/), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/src/people/anton/), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 + Yin Tang, [Emil Bouvier](/people/dave-bouvier/), Chun Kit Kwok, Yiliang Ding, [Anton Nekrutenko](/people/anton/), Philip C. Bevilacqua, and Sarah M. Assmann, *Bioinformatics* (16 April 2015), btv213, doi:10.1093/bioinformatics/btv213 The new papers were tagged with: @@ -244,7 +244,7 @@ There are [upcoming events](/src/events/index.md) in 7 countries on 3 continents - + diff --git a/content/galaxy-updates/2015-11/index.md b/content/galaxy-updates/2015-11/index.md index e9d4caf9fb..0424695297 100644 --- a/content/galaxy-updates/2015-11/index.md +++ b/content/galaxy-updates/2015-11/index.md @@ -521,6 +521,6 @@ Ran out of time to compile these. Look for a double batch in December. Galaxy codebase -In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/people/helena-rasche/) originally submitted by team member [Nate Coraor](/src/people/nate/). +In September [Galaxy turned 10 years old](/src/galaxy-updates/2015-10/index.md#galaxy-turns-10) by one important measure. Another milestone was reached in October when the [Galaxy codebase](https://github.com/galaxyproject/galaxy) surpassed of 20000 commits. And appropriately (and if I can count), the 20,000th was a pull request commit from community member [Helena Rasche](/people/helena-rasche/) originally submitted by team member [Nate Coraor](/people/nate/). Our thanks go to the community and the team alike. diff --git a/content/galaxy-updates/2016-10/index.md b/content/galaxy-updates/2016-10/index.md index 88294aaf90..c76932e8f0 100644 --- a/content/galaxy-updates/2016-10/index.md +++ b/content/galaxy-updates/2016-10/index.md @@ -361,7 +361,7 @@ Some highlights from last month: Annette McGrath, Steve McMahon, Sean Li, Joel Ludbey, Tim Ho. *Journal of Grid Computing* (2016), pp. 1-11, doi:10.1007/s10723-016-9379-6 **[Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter](http://biorxiv.org/content/early/2016/09/22/075457)** - [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 + [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 **[Genotyping of evolving prokaryotic populations](https://doi.org/10.7287/peerj.preprints.2449v1)** Markus Zojer, Lisa N. Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei. *PeerJ Preprints* (14 September 2016), doi:10.7287/peerj.preprints.2449v1 diff --git a/content/galaxy-updates/2016-12/index.md b/content/galaxy-updates/2016-12/index.md index ac52cce31f..937d2b2201 100644 --- a/content/galaxy-updates/2016-12/index.md +++ b/content/galaxy-updates/2016-12/index.md @@ -180,7 +180,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth Some highlights from last month: -* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) +* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) * [How Are You – and How’s Your Microbiome?](https://theanalyticalscientist.com/issues/1116/how-are-you-and-hows-your-microbiome/), Pratik Jagtap, *The Analytical Scientist*, November 2016 * [Computational workflow for the fine-grained analysis of metagenomic samples](https://doi.org/10.1186/s12864-016-3063-x), Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles, *BMC Genomics*, Vol. 17, No. S8. (25 October 2016), doi:10.1186/s12864-016-3063-x * [Big Data Smart Socket (BDSS): A System that Abstracts Data Transfer Habits from End Users](https://doi.org/10.1093/bioinformatics/btw679), Nick A. Watts, Frank A. Feltus, *Bioinformatics* (26 October 2016), btw679, doi:10.1093/bioinformatics/btw679 diff --git a/content/galaxy-updates/2017-03/index.md b/content/galaxy-updates/2017-03/index.md index 041e6c9800..15ceb3db95 100644 --- a/content/galaxy-updates/2017-03/index.md +++ b/content/galaxy-updates/2017-03/index.md @@ -260,7 +260,7 @@ Some highlights from the past two months: Connor Wytko, Brian Soto, Stephen P. Ficklin. *Database*, Vol. 2017 (10 January 2017), baw154, doi:10.1093/database/baw154 * [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://doi.org/10.12688/f1000research.9821.1) - [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 + [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/people/anton/), [James Taylor](/src/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 * [MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets](https://doi.org/10.1007/s41048-016-0033-4) Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan. *Biophysics Reports* (2017), pp. 1-10, doi:10.1007/s41048-016-0033-4 diff --git a/content/galaxy-updates/2017-06/index.md b/content/galaxy-updates/2017-06/index.md index 0837d59252..d878e89aba 100644 --- a/content/galaxy-updates/2017-06/index.md +++ b/content/galaxy-updates/2017-06/index.md @@ -211,7 +211,7 @@ Some highlights from the papers added last month: *Nucleic Acids Research* (02 May 2017), doi:10.1093/nar/gkx315 * [Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](https://doi.org/10.1371/journal.pcbi.1005425) - [Björn A. Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/src/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 + [Björn A. Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 * [MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization](https://doi.org/10.1093/bioinformatics/btx320) Katherine M. McCoy, Margaret L. Antonio, Tim van Opijnen. *Bioinformatics* (11 May 2017), doi:10.1093/bioinformatics/btx320 diff --git a/content/galaxy-updates/2018-08/index.md b/content/galaxy-updates/2018-08/index.md index 906319e334..7027a76390 100644 --- a/content/galaxy-updates/2018-08/index.md +++ b/content/galaxy-updates/2018-08/index.md @@ -300,15 +300,15 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t This included a new paper to reference [whenever using, extending, or referencing Galaxy](/src/citing-galaxy/index.md#primary-publication): -* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 A new paper to reference [when discussing Galaxy in the context of reproducibility](/src/citing-galaxy/index.md#reproducibility): -* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 +* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 And a new paper to reference [when discussing Galaxy training](/src/citing-galaxy/index.md#training): -* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 And a new paper to cite [when discussing Galaxy in a cloud context](/src/citing-galaxy/index.md#cloud): diff --git a/content/news/2019-02-galaxy-update/index.md b/content/news/2019-02-galaxy-update/index.md index f00dd35a06..e48ee34833 100644 --- a/content/news/2019-02-galaxy-update/index.md +++ b/content/news/2019-02-galaxy-update/index.md @@ -160,7 +160,7 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t * **[VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes](https://doi.org/10.1101/492074)**, Sara Silva Pereira, John Heap, Andrew R Jones, Andrew P. Jackson. *bioRxiv* 492074; doi: 10.1101/492074 * **[PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting](https://doi.org/10.1101/522458)**, Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau. *bioRxiv* 522458; doi: 10.1101/522458 * **[Enhancing Access to Digital Media: The Language Application Grid in the HTRC Data Capsule](https://doi.org/10.1145/3093338.3104171)**, James Pustejovsky, Marc Verhagen, Keongmin Rim, Yu Ma, Liang Ran, Samitha Liyanage, Jaimie Murdock, Robert H. McDonald, Beth Plale. In PEARC17 Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, Article No. 60. doi: 10.1145/3093338.3104171 -* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/people/nate/), [Anton Nekrutenko](/src/people/anton/). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 +* **[Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage](https://doi.org/10.1093/bioinformatics/btz054)**, Anastasia Tyryshkina, [Nate Coraor](/people/nate/), [Anton Nekrutenko](/people/anton/). *Bioinformatics*, btz054, doi: 10.1093/bioinformatics/btz054 * **[Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis](https://link.springer.com/protocol/10.1007%2F978-1-4939-8982-9_8)**, Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer. In: Lai X., Gupta S., Vera J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY * **[QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics](https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727)**, Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda J. Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian A. Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy J. Griffin , and Pratik D. Jagtap. *Journal of Proteome Research*, Article ASAP DOI: 10.1021/acs.jproteome.8b00727 diff --git a/content/news/2019-06-galaxy-update/index.md b/content/news/2019-06-galaxy-update/index.md index c82e3b1682..49408cd1bb 100644 --- a/content/news/2019-06-galaxy-update/index.md +++ b/content/news/2019-06-galaxy-update/index.md @@ -177,7 +177,7 @@ There were 10 *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BG * **[NGPhylogeny.fr: new generation phylogenetic services for non-specialists](https://doi.org/10.1093/nar/gkz303)**, Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier Gascuel. *Nucleic Acids Research*, gkz303, doi: 10.1093/nar/gkz303 * **[Rice Galaxy: an open resource for plant science](https://academic.oup.com/gigascience/article/8/5/giz028/5492234)**, Venice Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc, Joshua Dizon, John Robert Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay Triplett, Jillian Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar and Ramil P. Mauleon. *GigaScience*, 8, 2019, 1–14, doi: 10.1093/gigascience/giz028 * **[The RNA workbench 2.0: next generation RNA data analysis](https://doi.org/10.1093/nar/gkz353)**, Jorg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen and [Björn Grüning](https://github.com/bgruening). *Nucleic Acids Research*, gkz353, doi: 10.1093/nar/gkz353 -* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/src/people/nate/). *bioRxiv* 642280; doi: 10.1101/642280 +* **[Galaxy External Display Applications: Closing a dataflow interoperability loop](http://dx.doi.org/10.1101/642280)**, [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/people/nate/). *bioRxiv* 642280; doi: 10.1101/642280 * **[Prediction and Characterization of miRNA/Target Pairs in Non‐Model Plants Using RNA‐seq](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cppb.20090)**, Kira C. M. Neller, Alexander Klenov, Katalin A. Hudak. *Current Protocols in Plant Biology*, e20090. doi: 10.1002/cppb.20090 * **[The Repetitive DNA Composition in the Natural Pesticide Producer *Tanacetum cinerariifolium:* Interindividual Variation of Subtelomeric Tandem Repeats](https://doi.org/10.3389/fpls.2019.00613)**, Jelena Mlinarec, Ana Skuhala, Adela Jurković, Nenad Malenica, Jamie McCann, Hanna Weiss-Schneeweiss, Borut Bohanec and Višnja Besendorfer. *Frontiers in Plant Science*, 16 May 2019, doi: 10.3389/fpls.2019.00613 diff --git a/content/news/2019-10-galaxy-update/index.md b/content/news/2019-10-galaxy-update/index.md index 1c165308d4..d78adb656e 100644 --- a/content/news/2019-10-galaxy-update/index.md +++ b/content/news/2019-10-galaxy-update/index.md @@ -132,7 +132,7 @@ Ellrott, Kyle, Alex Buchanan, et al. *Genome Biology* 20 (1): 195. doi: 10.1186/
[You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda](http://doi.acm.org/10.1145/3307339.3343178)
-[Daniel Blankenberg](/people/dan/), [Martin Cech](/src/people/marten/). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178 +[Daniel Blankenberg](/people/dan/), [Martin Cech](/people/marten/). 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178
diff --git a/content/news/galaxy-current-protocols/index.md b/content/news/galaxy-current-protocols/index.md index eeeb0ab70b..e0b14da1eb 100644 --- a/content/news/galaxy-current-protocols/index.md +++ b/content/news/galaxy-current-protocols/index.md @@ -7,7 +7,7 @@ date: "2012-06-18" Two new Galaxy-related papers are now available in [Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html): **["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html)** - [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/).
+ [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 10.5.

**["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html)** [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/).
diff --git a/content/people/dave-clements/index.md b/content/people/dave-clements/index.md index ae3c404e5c..5da14aa0e5 100644 --- a/content/people/dave-clements/index.md +++ b/content/people/dave-clements/index.md @@ -38,10 +38,10 @@ My pre-bioinformatics career included ## Publications -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). -* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/src/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) -* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), [Galaxy Team](/src/galaxy-team/) +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). +* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) +* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/) * [The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data](http://database.oxfordjournals.org/content/2011/bar051.full), in *[Database](http://database.oxfordjournals.org/)*, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main * [Organization of the pronephric kidney revealed by large-scale gene expression mapping](http://genomebiology.com/2008/9/5/R84); in *[Genome Biology](http://genomebiology.com/2008/9/5/)*, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli * [A high-resolution anatomical ontology of the developing murine genitourinary tract](https://doi.org/10.1016/j.modgep.2007.03.002); in *[Gene Expression Patterns](http://www.elsevier.com/locate/modgep)*, 7(6), pp. 680-699 (June 2007). Melissa H. Little, Jane Brennan, Kylie Georgas, Jamie A. Davies, Duncan R. Davidson, Richard A. Baldock, Annemiek Beverdam, John F. Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Cullen-McEwen, Jean Fleming, Thierry Gilbert, Doris Herzlinger, Derek Houghton, Matt H. Kaufman, Elena Kleymenova, Peter A. Koopman, Alfor G. Lewis, Andrew P. McMahon, Cathy L. Mendelsohn, Eleanor K. Mitchell, Bree A. Rumballe, Derina E. Sweeney, M. Todd Valerius, Gen Yamada, Yiya Yang and Jing Yu diff --git a/content/people/marten/index.md b/content/people/marten/index.md index e29c0796d5..e15045ccb2 100644 --- a/content/people/marten/index.md +++ b/content/people/marten/index.md @@ -2,7 +2,7 @@ autotoc: false --- -
Marten
+
Marten
# Martin Cech diff --git a/content/use/galaxy-test/index.md b/content/use/galaxy-test/index.md index b30f335de8..b11dc6c663 100644 --- a/content/use/galaxy-test/index.md +++ b/content/use/galaxy-test/index.md @@ -16,7 +16,7 @@ user_support: quotas: - "Storage and computational quotas. See [Test](/src/test/index.md) for details" citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "[Project tagged publications](https://www.zotero.org/groups/1732893/galaxy/tags/%2BProject) in [Galaxy Publication library](/src/publication-library/index.md)." - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: diff --git a/content/use/usegalaxy-eu/index.md b/content/use/usegalaxy-eu/index.md index 48f022c534..876ab31176 100644 --- a/content/use/usegalaxy-eu/index.md +++ b/content/use/usegalaxy-eu/index.md @@ -18,7 +18,7 @@ user_support: quotas: - "Storage and computational quotas." citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/src/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.eu" diff --git a/content/use/usegalaxy-org/index.md b/content/use/usegalaxy-org/index.md index 6737274130..1511230ad4 100644 --- a/content/use/usegalaxy-org/index.md +++ b/content/use/usegalaxy-org/index.md @@ -11,7 +11,7 @@ summary: "The [Galaxy Project](/galaxy-project/) free public server; biomedical comments: - "Strong on genomics; good central repository for shared Galaxy objects. See [Main](/main/) for more." citations: - - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/src/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/src/people/anton/), and [Daniel Blankenberg](/src/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" + - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.org" From a90c680711e5eeb7c61f4cb238aedbf865aac0e2 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 17:07:03 -0400 Subject: [PATCH 08/24] dos2unix all md content --- content/admin/config/apache-proxy/index.md | 12 +- content/admin/config/nginx-proxy/index.md | 10 +- content/admin/data-integration/index.md | 176 ++--- .../admin/datatypes/adding-datatypes/index.md | 10 +- .../datatypes/composite-datatypes/index.md | 10 +- content/admin/tools/custom-code/index.md | 74 +-- content/admin/tools/data-tables/index.md | 240 +++---- .../index.md | 604 +++++++++--------- 8 files changed, 568 insertions(+), 568 deletions(-) diff --git a/content/admin/config/apache-proxy/index.md b/content/admin/config/apache-proxy/index.md index af1ee3fda8..01cdc61c2b 100644 --- a/content/admin/config/apache-proxy/index.md +++ b/content/admin/config/apache-proxy/index.md @@ -1,6 +1,6 @@ ---- -redirect: "https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html" ---- - -This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html), please check there for up-to-date information. - +--- +redirect: "https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html" +--- + +This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html), please check there for up-to-date information. + diff --git a/content/admin/config/nginx-proxy/index.md b/content/admin/config/nginx-proxy/index.md index 20fd3dea21..2bdffdc71b 100644 --- a/content/admin/config/nginx-proxy/index.md +++ b/content/admin/config/nginx-proxy/index.md @@ -1,5 +1,5 @@ ---- -redirect: "https://docs.galaxyproject.org/en/latest/admin/nginx.html" ---- - -This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/nginx.html), please check there for up-to-date information. +--- +redirect: "https://docs.galaxyproject.org/en/latest/admin/nginx.html" +--- + +This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/nginx.html), please check there for up-to-date information. diff --git a/content/admin/data-integration/index.md b/content/admin/data-integration/index.md index 71102a8634..812cd03abc 100644 --- a/content/admin/data-integration/index.md +++ b/content/admin/data-integration/index.md @@ -1,88 +1,88 @@ - - -## Data Integration for Local Instances - -Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see: **[Data Managers Overview](/src/admin/tools/data-managers/index.md)** and our **[Data Managers Tutorial](https://github.com/galaxyproject/dagobah-training/blob/2017-montpellier/sessions/05-reference-genomes/ex1-reference-genomes.md)**. - -Built-in data files are critical for many Galaxy tools. This page will describe how to get data into your local instance of Galaxy in a general way. For instructions specific for organizing and indexing data for use with tools, see **[Data Preparation](/src/admin/data-preparation/index.md)**. Additional instructions are available for reviewing or retrieving the exact data hosted on the public [Main](/src/main/index.md) instance or for performing more complex data prep used by specific tool groups. - -- Review or retrieve [https://usegalaxy.org](https://usegalaxy.org) reference genomes, indexes, and loc files. All methods are described at http://datacache.galaxyproject.org/, with more rsync server help at **[Usegalaxy.org Rsync](/src/admin/use-galaxy-rsync/index.md)** -- "Fetch Alignment" tools data prep: **[Reference MAFs](/src/admin/reference-mafs/index.md)** - -## How it works - -There are several steps needed for adding a genome to Galaxy. The first is to get the actual data needed and to put it into an appropriate directory accessible to the Galaxy instance. Then you need to establish the particular `.loc` ("location") file. Finally, make sure that the genome is referenced in the `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` file. - -**Note that as of early 2014, more than a builds.txt file change is needed to establish a new reference genome. If not using** [Data Managers](/src/admin/tools/data-managers/index.md) **, you must make the necessary changes/additions to the new [Data Tables](/src/admin/tools/data-tables) or use the alternative configuration file.** - -### Get the data - -First you need to determine what type of data you need. Usually these are `.fasta`, `.nib`, `.2bit`, or special index files, but each tool has a specific need. Open up the XML for the particular tool and identify the `.loc` file referred to in either a validator tag or options tag. Open the `$GALAXYROOT/tool-data/<filename>.loc.sample` file, and read it to discover the type of files necessary. Once you know what you need, you can go acquire it. - -There are several ways to get the data. If you don't already have the right file on your system, you will need to get it from a site such as [UCSC](http://hgdownload.soe.ucsc.edu/downloads.html). - -Or, if you would like to obtain the data as available on the public Galaxy [Main](/src/main/index.md) instance, these can retrieved from the rsync server. Read more here: **[Rsync](/src/admin/use-galaxy-rsync/index.md)** - -### Set up the loc file - -The `.loc.sample` files themselves include instructions for setting them up. In all cases, there is one reference genome per line, with tab-separated information. Create the needed `.loc` files, add your sequence and index data, and place these into the `$GALAXYROOT/tool-data` directory. This can be modified, but is the default location configured in `config/galaxy.ini` and the other configuration files referenced by it, in this section: - -``` -# -- Files and directories - - -# Path where genome builds are stored. This defaults to tool-data/genome -#genome_data_path = tool-data/genome - - -...... - - -# XML config file that contains data table entries for the ToolDataTableManager. This file is manually -# maintained by the Galaxy administrator. -#tool_data_table_config_path = tool_data_table_conf.xml - - -# XML config file that contains additional data table entries for the ToolDataTableManager. This file -# is automatically generated based on the current installed tool shed repositories that contain valid -# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically -# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. -#shed_tool_data_table_config = shed_tool_data_table_conf.xml -``` - -### \*.loc file examples - -With tabs separating the information: - -**alignseq.loc** - -``` -align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1 -align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2 -align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17 -``` - -**bowtie2\_indexes.loc** - -``` -hg38canon hg38 Human (Homo sapiens) (b38): hg38 Canonical /galaxy/data/hg38/hg38canon/bowtie2_index/hg38canon -hg38 hg38 Human (Homo sapiens) (b38): hg38 /galaxy/data/hg38/hg38full/bowtie2_index/hg38full -dipOrd1 dipOrd1 Kangaroo rat (Dipodomys ordii): dipOrd1 /galaxy/data/dipOrd1/bowtie2_index/dipOrd1 -braFlo1 braFlo1 Lancelet (Branchiostoma floridae): braFlo1 /galaxy/data/braFlo1/bowtie2_index/braFlo1 -anoCar1 anoCar1 Lizard (Anolis carolinensis): anoCar1 /galaxy/data/anoCar1/bowtie2_index/anoCar1 -anoCar2 anoCar2 Lizard (Anolis carolinensis): anoCar2 /galaxy/data/anoCar2/bowtie2_index/anoCar2 -``` - -Also see the **[Rsync](/src/admin/use-galaxy-rsync/index.md)** wiki if you want to obtain the exact same location files used on [https://usegalaxy.org](https://usegalaxy.org) for full size examples or for use as base-line files when configuring your own server. - -### Add new genome as Galaxy build - -Final and most important item needed is to include any new reference genomes in the builds.txt file. This is the list of reference genomes appear in the Genome or Database/Build search box when you upload a file or change a file's metadata (Where to find these? See the Rsync link directly above for screenshots). - -To modify the builds.txt file, add a line to `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` for your genome. The format of this line can vary, but should contain enough information to uniquely identify the genome, the source, any external build nomenclature, and the **dbkey** selected for use within your [Galaxy](/src/admin/get-galaxy/index.md) instance. See the public [Main](/src/main/index.md) server for examples: [https://usegalaxy.org](https://usegalaxy.org) - -### Restart the server - -**Any time you change data information, the server has to be restarted!!!** - -* * * + + +## Data Integration for Local Instances + +Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see: **[Data Managers Overview](/src/admin/tools/data-managers/index.md)** and our **[Data Managers Tutorial](https://github.com/galaxyproject/dagobah-training/blob/2017-montpellier/sessions/05-reference-genomes/ex1-reference-genomes.md)**. + +Built-in data files are critical for many Galaxy tools. This page will describe how to get data into your local instance of Galaxy in a general way. For instructions specific for organizing and indexing data for use with tools, see **[Data Preparation](/src/admin/data-preparation/index.md)**. Additional instructions are available for reviewing or retrieving the exact data hosted on the public [Main](/src/main/index.md) instance or for performing more complex data prep used by specific tool groups. + +- Review or retrieve [https://usegalaxy.org](https://usegalaxy.org) reference genomes, indexes, and loc files. All methods are described at http://datacache.galaxyproject.org/, with more rsync server help at **[Usegalaxy.org Rsync](/src/admin/use-galaxy-rsync/index.md)** +- "Fetch Alignment" tools data prep: **[Reference MAFs](/src/admin/reference-mafs/index.md)** + +## How it works + +There are several steps needed for adding a genome to Galaxy. The first is to get the actual data needed and to put it into an appropriate directory accessible to the Galaxy instance. Then you need to establish the particular `.loc` ("location") file. Finally, make sure that the genome is referenced in the `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` file. + +**Note that as of early 2014, more than a builds.txt file change is needed to establish a new reference genome. If not using** [Data Managers](/src/admin/tools/data-managers/index.md) **, you must make the necessary changes/additions to the new [Data Tables](/src/admin/tools/data-tables) or use the alternative configuration file.** + +### Get the data + +First you need to determine what type of data you need. Usually these are `.fasta`, `.nib`, `.2bit`, or special index files, but each tool has a specific need. Open up the XML for the particular tool and identify the `.loc` file referred to in either a validator tag or options tag. Open the `$GALAXYROOT/tool-data/<filename>.loc.sample` file, and read it to discover the type of files necessary. Once you know what you need, you can go acquire it. + +There are several ways to get the data. If you don't already have the right file on your system, you will need to get it from a site such as [UCSC](http://hgdownload.soe.ucsc.edu/downloads.html). + +Or, if you would like to obtain the data as available on the public Galaxy [Main](/src/main/index.md) instance, these can retrieved from the rsync server. Read more here: **[Rsync](/src/admin/use-galaxy-rsync/index.md)** + +### Set up the loc file + +The `.loc.sample` files themselves include instructions for setting them up. In all cases, there is one reference genome per line, with tab-separated information. Create the needed `.loc` files, add your sequence and index data, and place these into the `$GALAXYROOT/tool-data` directory. This can be modified, but is the default location configured in `config/galaxy.ini` and the other configuration files referenced by it, in this section: + +``` +# -- Files and directories + + +# Path where genome builds are stored. This defaults to tool-data/genome +#genome_data_path = tool-data/genome + + +...... + + +# XML config file that contains data table entries for the ToolDataTableManager. This file is manually +# maintained by the Galaxy administrator. +#tool_data_table_config_path = tool_data_table_conf.xml + + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = shed_tool_data_table_conf.xml +``` + +### \*.loc file examples + +With tabs separating the information: + +**alignseq.loc** + +``` +align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1 +align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2 +align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17 +``` + +**bowtie2\_indexes.loc** + +``` +hg38canon hg38 Human (Homo sapiens) (b38): hg38 Canonical /galaxy/data/hg38/hg38canon/bowtie2_index/hg38canon +hg38 hg38 Human (Homo sapiens) (b38): hg38 /galaxy/data/hg38/hg38full/bowtie2_index/hg38full +dipOrd1 dipOrd1 Kangaroo rat (Dipodomys ordii): dipOrd1 /galaxy/data/dipOrd1/bowtie2_index/dipOrd1 +braFlo1 braFlo1 Lancelet (Branchiostoma floridae): braFlo1 /galaxy/data/braFlo1/bowtie2_index/braFlo1 +anoCar1 anoCar1 Lizard (Anolis carolinensis): anoCar1 /galaxy/data/anoCar1/bowtie2_index/anoCar1 +anoCar2 anoCar2 Lizard (Anolis carolinensis): anoCar2 /galaxy/data/anoCar2/bowtie2_index/anoCar2 +``` + +Also see the **[Rsync](/src/admin/use-galaxy-rsync/index.md)** wiki if you want to obtain the exact same location files used on [https://usegalaxy.org](https://usegalaxy.org) for full size examples or for use as base-line files when configuring your own server. + +### Add new genome as Galaxy build + +Final and most important item needed is to include any new reference genomes in the builds.txt file. This is the list of reference genomes appear in the Genome or Database/Build search box when you upload a file or change a file's metadata (Where to find these? See the Rsync link directly above for screenshots). + +To modify the builds.txt file, add a line to `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` for your genome. The format of this line can vary, but should contain enough information to uniquely identify the genome, the source, any external build nomenclature, and the **dbkey** selected for use within your [Galaxy](/src/admin/get-galaxy/index.md) instance. See the public [Main](/src/main/index.md) server for examples: [https://usegalaxy.org](https://usegalaxy.org) + +### Restart the server + +**Any time you change data information, the server has to be restarted!!!** + +* * * diff --git a/content/admin/datatypes/adding-datatypes/index.md b/content/admin/datatypes/adding-datatypes/index.md index 22a8e2b89b..c4726b6cbf 100644 --- a/content/admin/datatypes/adding-datatypes/index.md +++ b/content/admin/datatypes/adding-datatypes/index.md @@ -1,5 +1,5 @@ ---- -redirect: "https://docs.galaxyproject.org/en/latest/dev/data_types.html" ---- - -This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/dev/data_types.html), please check there for up-to-date information. +--- +redirect: "https://docs.galaxyproject.org/en/latest/dev/data_types.html" +--- + +This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/dev/data_types.html), please check there for up-to-date information. diff --git a/content/admin/datatypes/composite-datatypes/index.md b/content/admin/datatypes/composite-datatypes/index.md index 22a8e2b89b..c4726b6cbf 100644 --- a/content/admin/datatypes/composite-datatypes/index.md +++ b/content/admin/datatypes/composite-datatypes/index.md @@ -1,5 +1,5 @@ ---- -redirect: "https://docs.galaxyproject.org/en/latest/dev/data_types.html" ---- - -This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/dev/data_types.html), please check there for up-to-date information. +--- +redirect: "https://docs.galaxyproject.org/en/latest/dev/data_types.html" +--- + +This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/dev/data_types.html), please check there for up-to-date information. diff --git a/content/admin/tools/custom-code/index.md b/content/admin/tools/custom-code/index.md index 8a8004af72..7c1945325b 100644 --- a/content/admin/tools/custom-code/index.md +++ b/content/admin/tools/custom-code/index.md @@ -7,7 +7,7 @@ The purpose of custom code is to provide detailed control on the way the tools are executed. This (optional) code can be deployed in a separate file in the same directory as the tool configuration files (See AddToolTutorial). To enable the code add the ``` -#!highlight xml +#!highlight xml ``` @@ -24,27 +24,27 @@ The principal difference between the executions of steps 1, 2 and 3, 4 is that t This function is called before the tool is executed. If it raises any exceptions the tool execution will be aborted and the exception's value will be displayed in an error message box. Here is an example: ``` -#!highlight python -def validate(incoming): - """Validator for the plotting program""" - - - bins = incoming.get("bins","") - col = incoming.get("col","") - - - if not bins or not col: - raise Exception, "You need to specify a number for bins and columns" - - - try: - bins = int(bins) - col = int(col) - except: - raise Exception, "Parameters are not integers, columns:%s, bins:%s" % (col, bins) - - - if not 1 - - - - - -``` - -The text that is displayed in the browser's dropdown is what's in the `name` column, and the value that would be stored for the parameter is in the `value` column. - -If the loc file looked like this: - -``` -phiX /path/to/phiX -``` - -But more importantly, since the value that was stored for the parameter `index` would be `/path/to/phiX`, the actual path. So if the path to the data changed to `/some/new/path/to/phiX`, any workflows that already used the original value would still have that stored for `index`. And the tool would fail because it wouldn't be able to find the files. Using data tables allows the path to be changed without breaking workflows. - -## How to Use Data Tables - -There are three major components to data tables: -1. An entry in the `tool_data_table_conf.xml` -2. A reference to the relevant data table in the tool XML file -3. An appropriate expression added to the tool XML file to pass the correct value to the supporting script (Python, Perl, etc.). - -The file `tool_data_table_conf.xml.sample` can be used as a source for `tool_data_table_conf.xml`. The `tool_data_table_conf.xml` file looks something like this: - -``` - - -
Instructors Jeremy Goecks, George Washington University
Aysam Guerler, Johns Hopkins University 		Jeremy Goecks, George Washington University
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Content September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia Jennifer Jackson, Ross Lazarus Jennifer Jackson, Ross Lazarus
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- value, dbkey, name, path - -
- -``` - -Note that the `value` is now the first column (index 0). This is what we are calling the "unique ID" because this is now the value that is stored for the index parameter. This approach allows variants of the same build to be listed, since the dbkey is specified for each entry. The `name` is still what is displayed in the browser dropdown. `path` is still the actual path to the data file(s). `value`, `path`, and `name` should all be included. Other columns are possible, but by convention the Unique ID should be in the first column and path in the last. - -The loc file could look like this: - -``` -phiX_ID phiX174 User-friendly phiX174 Description /path/to/phiX -``` - -In the tool XML, there would need to be a parameter such as: - -``` - - - -``` - -This would give the user a dropdown listing all of the values in the name column supplied in the loc file (in our example, "User-friendly phiX174 Description"). The value stored as the value of the parameter `index` would be "phiX\_ID". The script or binary will need the actual path in the command, and since the value returned is a row object from the data table, you can access it like this: `--ref="${index.fields.path}`. Currently, select lists where `multiple=true` are not supported, but you can wrap the single-item select list in a repeat to achieve the same result. The old way of supporting multiple select lists involved using galaxy internals (which is discouraged): `--ref="${ filter( lambda x: str( x[0] ) == str( $index ), $ __app__.tool_data_tables['bowtie_indexes'].get_fields() )[0][-1] }"`, where `str( x[0] )` refers to the unique ID in column 0 and the -1 in `[0][-1]` gets the path in the last column. - -## When Converting from Old-style Approach to Data Tables - -Because the old way of doing things stored the path as the parameter value, when converting to data tables style, that path value needs to be used as the unique ID if backwards compatibility with workflows is to be maintained. For instance, if the original loc file looked like this: - -``` -phiX /path/to/phiX -hg19 /arbitrary/place/to/hg19 -``` - -the new one could look something like: - -``` -/arbitrary/place/to/hg18 hg18 Human (Homo sapiens): hg18 /arbitrary/place/to/hg18 -/path/to/phiX phiX User-friendly phiX174 Description /path/to/phiX -``` - -But if you move the data files to new locations and add some new builds, it could look something like this: - -``` -/arbitrary/place/to/hg18 hg18 Human (Homo sapiens): hg18 /new/path/to/bowtie/hg18 -hg18Haps hg18 Human (Homo sapiens): hg18 Haplotypes /new/path/to/bowtie/hg18 -hg19 hg19 Human (Homo sapiens): hg19 /new/path/to/bowtie/hg19 -hg19Haps hg19 Human (Homo sapiens): hg19 Haplotypes /new/path/to/bowtie/hg19 -/path/to/phiX phiX User-friendly phiX174 Description /new/path/to/bowtie/phiX -mm9 mm9 Mouse (Mus musculus): mm9 /new/path/to/bowtie/mm9 -``` - -### If You Don't Want to Change the Existing loc Files - -The alternative `tool_data_table_conf.xml.oldlocstyle` file can be used as a source for `tool_data_table_conf.xml` instead of `tool_data_table_conf.xml.sample`. + + +# Data Tables + +The data tables approach is an alternative to using raw loc files in tool XML files. + +Using them allows you to change the names or locations of loc files or data files pointed to in loc files, or change aspects of the loc file, without breaking workflows. + +They were originally introduced in commit 4098:2447b9a4dae3: + +``` +Make "loc files" more flexible by adding "tool data tables". These are +configured at the application level. Specific tabular data files are +specified in a application config file and bound to names, the tools +then refer to these names. Thus users can configure where location +files are located without modifying tool configs. + + +Also: + + + - Simpler column name configuration + - Columns can be referred to by name in addition to index in all + dynamic option filters + - A data table can merge multiple files + - Design can support other types of data files +``` + +In commit 4550:535d276c92bc almost all tools using loc files (and TopHat a bit later) were converted to data tables style. This means that they are no longer compatible with existing loc files. See the last section on this page for information on converting. + +## The Pre-data-tables Approach + +The old way of handling this in the loc file looked like this: + +``` + + + + + + +``` + +The text that is displayed in the browser's dropdown is what's in the `name` column, and the value that would be stored for the parameter is in the `value` column. + +If the loc file looked like this: + +``` +phiX /path/to/phiX +``` + +But more importantly, since the value that was stored for the parameter `index` would be `/path/to/phiX`, the actual path. So if the path to the data changed to `/some/new/path/to/phiX`, any workflows that already used the original value would still have that stored for `index`. And the tool would fail because it wouldn't be able to find the files. Using data tables allows the path to be changed without breaking workflows. + +## How to Use Data Tables + +There are three major components to data tables: +1. An entry in the `tool_data_table_conf.xml` +2. A reference to the relevant data table in the tool XML file +3. An appropriate expression added to the tool XML file to pass the correct value to the supporting script (Python, Perl, etc.). + +The file `tool_data_table_conf.xml.sample` can be used as a source for `tool_data_table_conf.xml`. The `tool_data_table_conf.xml` file looks something like this: + +``` + + + + value, dbkey, name, path + +
+ +``` + +Note that the `value` is now the first column (index 0). This is what we are calling the "unique ID" because this is now the value that is stored for the index parameter. This approach allows variants of the same build to be listed, since the dbkey is specified for each entry. The `name` is still what is displayed in the browser dropdown. `path` is still the actual path to the data file(s). `value`, `path`, and `name` should all be included. Other columns are possible, but by convention the Unique ID should be in the first column and path in the last. + +The loc file could look like this: + +``` +phiX_ID phiX174 User-friendly phiX174 Description /path/to/phiX +``` + +In the tool XML, there would need to be a parameter such as: + +``` + + + +``` + +This would give the user a dropdown listing all of the values in the name column supplied in the loc file (in our example, "User-friendly phiX174 Description"). The value stored as the value of the parameter `index` would be "phiX\_ID". The script or binary will need the actual path in the command, and since the value returned is a row object from the data table, you can access it like this: `--ref="${index.fields.path}`. Currently, select lists where `multiple=true` are not supported, but you can wrap the single-item select list in a repeat to achieve the same result. The old way of supporting multiple select lists involved using galaxy internals (which is discouraged): `--ref="${ filter( lambda x: str( x[0] ) == str( $index ), $ __app__.tool_data_tables['bowtie_indexes'].get_fields() )[0][-1] }"`, where `str( x[0] )` refers to the unique ID in column 0 and the -1 in `[0][-1]` gets the path in the last column. + +## When Converting from Old-style Approach to Data Tables + +Because the old way of doing things stored the path as the parameter value, when converting to data tables style, that path value needs to be used as the unique ID if backwards compatibility with workflows is to be maintained. For instance, if the original loc file looked like this: + +``` +phiX /path/to/phiX +hg19 /arbitrary/place/to/hg19 +``` + +the new one could look something like: + +``` +/arbitrary/place/to/hg18 hg18 Human (Homo sapiens): hg18 /arbitrary/place/to/hg18 +/path/to/phiX phiX User-friendly phiX174 Description /path/to/phiX +``` + +But if you move the data files to new locations and add some new builds, it could look something like this: + +``` +/arbitrary/place/to/hg18 hg18 Human (Homo sapiens): hg18 /new/path/to/bowtie/hg18 +hg18Haps hg18 Human (Homo sapiens): hg18 Haplotypes /new/path/to/bowtie/hg18 +hg19 hg19 Human (Homo sapiens): hg19 /new/path/to/bowtie/hg19 +hg19Haps hg19 Human (Homo sapiens): hg19 Haplotypes /new/path/to/bowtie/hg19 +/path/to/phiX phiX User-friendly phiX174 Description /new/path/to/bowtie/phiX +mm9 mm9 Mouse (Mus musculus): mm9 /new/path/to/bowtie/mm9 +``` + +### If You Don't Want to Change the Existing loc Files + +The alternative `tool_data_table_conf.xml.oldlocstyle` file can be used as a source for `tool_data_table_conf.xml` instead of `tool_data_table_conf.xml.sample`. diff --git a/content/admin/tools/external-display-applications-tutorial/index.md b/content/admin/tools/external-display-applications-tutorial/index.md index 7a1e44aac6..6d5b6e5981 100644 --- a/content/admin/tools/external-display-applications-tutorial/index.md +++ b/content/admin/tools/external-display-applications-tutorial/index.md @@ -1,302 +1,302 @@ - - -# Displaying Datasets at External Display Applications / Websites using GEDAs - -## About Display Applications - -There are many services available that allow users to upload their own data for use as viewing as e.g. 'custom tracks' in a genome browser. Examples of these include the UCSC genome browser, GeneTrack and [GBrowse](http://gmod.org/wiki/GBrowse). Adding a new external display applications requires two steps: - -1. define the display application (create a new XML definition file) and -2. instruct Galaxy to load the display application (edit datatypes\_conf.xml with the location of the new XML file). - -* * * - -## Citation - -If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x - -* * * - -## Additional Resources - -* This preprint provides additional information on the structure and configuration of Galaxy External Display Applications (GEDAs): https://www.biorxiv.org/content/10.1101/642280v1.full -* There is also an annotated XML Schema Definition (XSD) available: [geda.xsd](https://raw.githubusercontent.com/galaxyproject/galaxy/a50dcf092a1d33c5b097783131719f3f93616e75/lib/galaxy/datatypes/display_applications/xsd/geda.xsd). - -* * * - -## Topics - -1. Basic Topics - Simple Display Applications -2. Advanced Topics - Dynamic Display Applications - -* * * - -## Basic Topics - -### Simple Display Applications - -Display applications are defined using XML. - -#### Example 1 - -Lets suppose we want to write a display application which displays a BAM file at the UCSC genome browser. After familiarizing ourselves with the UCSC genome browser, we become aware of several pieces of information which are needed to display user data: - -- The data to be displayed is provided by giving a public URL to the UCSC genome browser. -- 3 data files are needed to be provided by URL: 1) a custom track definition, 2) the BAM file and 3) the BAM index. With the following requirement: the index must have the same name as the BAM file, but have the additional suffix of '.bai' -- The url to send data to UCSC is of the form: ` http://genome.ucsc.edu/cgi-bin/hgTracks?db=UCSC_GENOME_BUILD&hgt.customText=URL_OF_CUSTOM_TRACK ` - -This display application will require 3 parameters, corresponding to the 3 data files that are needed. - -1. The custom track file is defined by a dynamically generated template-style parameter. It is referred to as 'track', and is available at [http://some/url/path/track](http://some/url/path/track). The contents of this file are created by replacing the '$' placeholders with the values indicated. -2. The BAM file, the actual dataset being used for the display, is internally referred to as 'bam\_file', but will be available as [http://some/url/path/galaxy.bam](http://some/url/path/galaxy.bam) -3. The index file, which is available as a metadata attribute of the BAM file, is internally referred to as 'bai\_file', but will be available as [http://some/url/path/galaxy.bam.bai](http://some/url/path/galaxy.bam.bai) - -This display application can then be defined like this example (`display_applications/ucsc/bam.xml/`): - -``` - - - http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)} - - - track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey} - - -``` - -To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the BAM datatype: - -``` - - - -``` - -_where our xml file was saved as /display\_applications/ucsc/bam.xml_ - -#### Example 2 - -Now lets create a display application that can view interval (BED-like) files at the UCSC genome browser. The UCSC genome browser natively handles BED files, but Galaxy allows a looser definition for BED files than that accepted at UCSC, so we have defined a new datatype called 'bedstrict' that has data that meets the strict definition of BED. To enable all types of intervals to be viewed at UCSC, we have created an interval to bedstrict datatype converter and defined it in the usual manner (LINK TO THIS DOCUMENTATION). - -Items needed for this display: - -- The data to be displayed is provided by giving a public URL to the UCSC genome browser. -- 1 data file is needed to be provided by URL: 1) the result of converting the interval file to bedstrict -- The url to send data to UCSC is of the form: ` http://genome.ucsc.edu/cgi-bin/hgTracks?db=UCSC_GENOME_BUILD&position=CHR:START-END&hgt.customText=URL_OF_STRICTBED_FILE ` - -This display application requires 2 parameters: - -1. The interval file converted to bestrict, named 'bed\_file', to be availabe as [http://some/url/path/galaxy.bed](http://some/url/path/galaxy.bed) -2. The 'position' (viewport) in the form of CHR:START-END. This is calculated by looking at the first 10 lines of the bed file. This is not available as a URL (viewable is not set to True); but is instead substituted in as part of the URL that users are directed to for display. -``` - - - http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp} - - -#set line_count = 0 -#set chrom = None -#set start = float( 'inf' ) -#set end = 0 -#for $line in open( $bed_file.file_name ): - #if $line_count > 10: ##10 max lines to check for view port - #break - #end if - #if not $line.startswith( "#" ): - #set $fields = $line.split( "\t" ) - #try: - #if len( $fields ) >= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ): - #if $chrom is None or $fields[$bed_file.metadata.chromCol - 1] == $chrom: - #set chrom = $fields[$bed_file.metadata.chromCol - 1] - #set start = min( $start, int( $fields[$bed_file.metadata.startCol - 1] ) ) - #set end = max( $end, int( $fields[$bed_file.metadata.endCol - 1] ) ) - #end if - #end if - #except: - #pass - #end try - #end if - #set line_count += 1 -#end for -#if $chrom is not None: -${chrom}:${start}-${end + 1} -#else: -:- -#end if - - - -``` - -_where the 'strip' attribute of 'position' indicates that whitespace should be removed from around the determined position before being substituted into the URL. This can also be accomplished using ordinary string operations like: `position=${qp(str( position).strip())} `. 'qp' is a shortcut to 'quote\_plus' which escapes text for use as part of a URL_ - -To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the interval datatype: - -``` - - - - -``` - -_where our xml file was saved as /display\_applications/ucsc/interval\_as\_bed.xml and inherit is set to True, so that datatypes subclassing interval (e.g. bed, bedstrict) also have the display application available_ - -#### Example 3 - -Create a display application that can view interval (BED-like) files at GeneTrack. GeneTrack is a browser/peakcalling program that is a server distinct from Galaxy, but which is able to directly access the file system used for storing Galaxy datasets; this direct file system access requires individual Galaxy instances to have a (local) instance of GeneTrack installed. - -Items needed for this display: - -- 1 data file is needed to be provided: 1) A GeneTrack index binary datatype -- The data to be displayed is provided by giving an encoded filename to the GeneTrack server, which has access to the appropriate filesystem. -- A Hashkey, used as an identity check by GeneTrack -- GeneTrack is able to launch peakcalling jobs at Galaxy and so also requires the dataset id and the Galaxy URL used to run jobs -- The url to send data to GeneTrack is of the form: ` http://genetrack.g2.bx.psu.edu/galaxy?filename=ENCODED_FILENAME&hashkey=HASHKEY&input=DATASET_ID&GALAXY_URL=POST_BACK_URL ` - -This display application requires 5 parameters: - -1. The interval file converted to bed or genetrack format, named 'bed\_file' -2. The bed or genetrack file converted to GeneTrack format, named 'genetrack\_file' -3. 'galaxy\_url' containing the url that GeneTrack posts back to for calling peaks. -4. 'hash\_key' used as a verification check by GeneTrack -5. 'encoded\_filename' containing the filesystem location to the 'genetrack\_file', which has been encoded using binascii.hexlify -``` - - - http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}&hashkey=${hash_key.qp}&input=${qp(str($genetrack_file.id))}&GALAXY_URL=${galaxy_url.qp} - - - - ${BASE_URL}/tool_runner?tool_id=predict2genetrack - - - #from galaxy.util.hash_util import hmac_new - ${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )} - - - #import binascii - ${binascii.hexlify( $genetrack_file.file_name )} - - - -``` - -_where 'BASE\_URL', 'APP' and qp are built-in parameters available to display applications_ - -To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the interval datatype: - -``` - - - - -``` - -_where our xml file was saved as /display\_applications/genetrack.xml and inherit is set to True, so that datatypes subclassing interval (e.g. bed, bedstrict) also have the display application available. Note that a BED to GeneTrack Converter has been defined for the BED datatype and is used to create the GeneTrack file to be displayed_ - -* * * - -## Advanced Topics - -### Dynamic Display Applications - -Sometimes it can be desired to have links and parameters for a Display Application to come from an external file. In the following examples we will modify the above examples to be populated using data found in external files. - -The file `tool-data/shared/ucsc/ucsc_build_sites.txt` contains tab delimited data, with one line per display site, consisting of columns: - -1. Site Name -2. Site URL -3. Comma-separated Genome Builds Available at this site - -The display will also be filtered based upon a Galaxy Application configuration variable `ucsc_display_sites` which is used to to restrict available sites to a list specified in universe\_wsgi.ini; alternatively the non-desired sites can be removed by commenting or deleting them out in `tool-data/shared/ucsc/ucsc_build_sites.txt`. - -#### Example 1 Advanced - -Display a BAM file at the UCSC genome browser, dynamically loading sites from a text file (`tool-data/shared/ucsc/ucsc_build_sites.txt`). - -``` - - - - - - - - - - - - - ${site_id in $APP.config.ucsc_display_sites} - ${dataset.dbkey in $builds} - - - - ${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)} - - - track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey} - - - - -``` - -#### Example 2 Advanced - -Display an Interval file at the UCSC genome browser, dynamically loading sites from a text file (`tool-data/shared/ucsc/ucsc_build_sites.txt`). - -``` - - - - - - - - - - - - - ${site_id in $APP.config.ucsc_display_sites} - ${dataset.dbkey in $builds} - - - - ${ucsc_link}db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp} - - -#set line_count = 0 -#set chrom = None -#set start = float( 'inf' ) -#set end = 0 -#for $line in open( $bed_file.file_name ): - #if $line_count > 10: ##10 max lines to check for view port - #break - #end if - #if not $line.startswith( "#" ): - #set $fields = $line.split( "\t" ) - #try: - #if len( $fields ) >= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ): - #if $chrom is None or $fields[$bed_file.metadata.chromCol - 1] == $chrom: - #set chrom = $fields[$bed_file.metadata.chromCol - 1] - #set start = min( $start, int( $fields[$bed_file.metadata.startCol - 1] ) ) - #set end = max( $end, int( $fields[$bed_file.metadata.endCol - 1] ) ) - #end if - #end if - #except: - #pass - #end try - #end if - #set line_count += 1 -#end for -#if $chrom is not None: -${chrom}:${start}-${end + 1} -#else: -:- -#end if - - - -``` + + +# Displaying Datasets at External Display Applications / Websites using GEDAs + +## About Display Applications + +There are many services available that allow users to upload their own data for use as viewing as e.g. 'custom tracks' in a genome browser. Examples of these include the UCSC genome browser, GeneTrack and [GBrowse](http://gmod.org/wiki/GBrowse). Adding a new external display applications requires two steps: + +1. define the display application (create a new XML definition file) and +2. instruct Galaxy to load the display application (edit datatypes\_conf.xml with the location of the new XML file). + +* * * + +## Citation + +If you add a new external display application to Galaxy in your published work, please cite: [Daniel Blankenberg](/people/dan/), [John Chilton](/people/john-chilton/), and [Nate Coraor](/people/nate/). **[Galaxy External Display Applications: Closing a dataflow interoperability loop](https://rdcu.be/b0xnC)**. *Nat Methods* (2020). doi:10.1038/s41592-019-0727-x + +* * * + +## Additional Resources + +* This preprint provides additional information on the structure and configuration of Galaxy External Display Applications (GEDAs): https://www.biorxiv.org/content/10.1101/642280v1.full +* There is also an annotated XML Schema Definition (XSD) available: [geda.xsd](https://raw.githubusercontent.com/galaxyproject/galaxy/a50dcf092a1d33c5b097783131719f3f93616e75/lib/galaxy/datatypes/display_applications/xsd/geda.xsd). + +* * * + +## Topics + +1. Basic Topics - Simple Display Applications +2. Advanced Topics - Dynamic Display Applications + +* * * + +## Basic Topics + +### Simple Display Applications + +Display applications are defined using XML. + +#### Example 1 + +Lets suppose we want to write a display application which displays a BAM file at the UCSC genome browser. After familiarizing ourselves with the UCSC genome browser, we become aware of several pieces of information which are needed to display user data: + +- The data to be displayed is provided by giving a public URL to the UCSC genome browser. +- 3 data files are needed to be provided by URL: 1) a custom track definition, 2) the BAM file and 3) the BAM index. With the following requirement: the index must have the same name as the BAM file, but have the additional suffix of '.bai' +- The url to send data to UCSC is of the form: ` http://genome.ucsc.edu/cgi-bin/hgTracks?db=UCSC_GENOME_BUILD&hgt.customText=URL_OF_CUSTOM_TRACK ` + +This display application will require 3 parameters, corresponding to the 3 data files that are needed. + +1. The custom track file is defined by a dynamically generated template-style parameter. It is referred to as 'track', and is available at [http://some/url/path/track](http://some/url/path/track). The contents of this file are created by replacing the '$' placeholders with the values indicated. +2. The BAM file, the actual dataset being used for the display, is internally referred to as 'bam\_file', but will be available as [http://some/url/path/galaxy.bam](http://some/url/path/galaxy.bam) +3. The index file, which is available as a metadata attribute of the BAM file, is internally referred to as 'bai\_file', but will be available as [http://some/url/path/galaxy.bam.bai](http://some/url/path/galaxy.bam.bai) + +This display application can then be defined like this example (`display_applications/ucsc/bam.xml/`): + +``` + + + http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)} + + + track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey} + + +``` + +To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the BAM datatype: + +``` + + + +``` + +_where our xml file was saved as /display\_applications/ucsc/bam.xml_ + +#### Example 2 + +Now lets create a display application that can view interval (BED-like) files at the UCSC genome browser. The UCSC genome browser natively handles BED files, but Galaxy allows a looser definition for BED files than that accepted at UCSC, so we have defined a new datatype called 'bedstrict' that has data that meets the strict definition of BED. To enable all types of intervals to be viewed at UCSC, we have created an interval to bedstrict datatype converter and defined it in the usual manner (LINK TO THIS DOCUMENTATION). + +Items needed for this display: + +- The data to be displayed is provided by giving a public URL to the UCSC genome browser. +- 1 data file is needed to be provided by URL: 1) the result of converting the interval file to bedstrict +- The url to send data to UCSC is of the form: ` http://genome.ucsc.edu/cgi-bin/hgTracks?db=UCSC_GENOME_BUILD&position=CHR:START-END&hgt.customText=URL_OF_STRICTBED_FILE ` + +This display application requires 2 parameters: + +1. The interval file converted to bestrict, named 'bed\_file', to be availabe as [http://some/url/path/galaxy.bed](http://some/url/path/galaxy.bed) +2. The 'position' (viewport) in the form of CHR:START-END. This is calculated by looking at the first 10 lines of the bed file. This is not available as a URL (viewable is not set to True); but is instead substituted in as part of the URL that users are directed to for display. +``` + + + http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp} + + +#set line_count = 0 +#set chrom = None +#set start = float( 'inf' ) +#set end = 0 +#for $line in open( $bed_file.file_name ): + #if $line_count > 10: ##10 max lines to check for view port + #break + #end if + #if not $line.startswith( "#" ): + #set $fields = $line.split( "\t" ) + #try: + #if len( $fields ) >= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ): + #if $chrom is None or $fields[$bed_file.metadata.chromCol - 1] == $chrom: + #set chrom = $fields[$bed_file.metadata.chromCol - 1] + #set start = min( $start, int( $fields[$bed_file.metadata.startCol - 1] ) ) + #set end = max( $end, int( $fields[$bed_file.metadata.endCol - 1] ) ) + #end if + #end if + #except: + #pass + #end try + #end if + #set line_count += 1 +#end for +#if $chrom is not None: +${chrom}:${start}-${end + 1} +#else: +:- +#end if + + + +``` + +_where the 'strip' attribute of 'position' indicates that whitespace should be removed from around the determined position before being substituted into the URL. This can also be accomplished using ordinary string operations like: `position=${qp(str( position).strip())} `. 'qp' is a shortcut to 'quote\_plus' which escapes text for use as part of a URL_ + +To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the interval datatype: + +``` + + + + +``` + +_where our xml file was saved as /display\_applications/ucsc/interval\_as\_bed.xml and inherit is set to True, so that datatypes subclassing interval (e.g. bed, bedstrict) also have the display application available_ + +#### Example 3 + +Create a display application that can view interval (BED-like) files at GeneTrack. GeneTrack is a browser/peakcalling program that is a server distinct from Galaxy, but which is able to directly access the file system used for storing Galaxy datasets; this direct file system access requires individual Galaxy instances to have a (local) instance of GeneTrack installed. + +Items needed for this display: + +- 1 data file is needed to be provided: 1) A GeneTrack index binary datatype +- The data to be displayed is provided by giving an encoded filename to the GeneTrack server, which has access to the appropriate filesystem. +- A Hashkey, used as an identity check by GeneTrack +- GeneTrack is able to launch peakcalling jobs at Galaxy and so also requires the dataset id and the Galaxy URL used to run jobs +- The url to send data to GeneTrack is of the form: ` http://genetrack.g2.bx.psu.edu/galaxy?filename=ENCODED_FILENAME&hashkey=HASHKEY&input=DATASET_ID&GALAXY_URL=POST_BACK_URL ` + +This display application requires 5 parameters: + +1. The interval file converted to bed or genetrack format, named 'bed\_file' +2. The bed or genetrack file converted to GeneTrack format, named 'genetrack\_file' +3. 'galaxy\_url' containing the url that GeneTrack posts back to for calling peaks. +4. 'hash\_key' used as a verification check by GeneTrack +5. 'encoded\_filename' containing the filesystem location to the 'genetrack\_file', which has been encoded using binascii.hexlify +``` + + + http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}&hashkey=${hash_key.qp}&input=${qp(str($genetrack_file.id))}&GALAXY_URL=${galaxy_url.qp} + + + + ${BASE_URL}/tool_runner?tool_id=predict2genetrack + + + #from galaxy.util.hash_util import hmac_new + ${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )} + + + #import binascii + ${binascii.hexlify( $genetrack_file.file_name )} + + + +``` + +_where 'BASE\_URL', 'APP' and qp are built-in parameters available to display applications_ + +To instruct Galaxy to use this display app, we modify ` datatypes_conf.xml ` and add the following to the interval datatype: + +``` + + + + +``` + +_where our xml file was saved as /display\_applications/genetrack.xml and inherit is set to True, so that datatypes subclassing interval (e.g. bed, bedstrict) also have the display application available. Note that a BED to GeneTrack Converter has been defined for the BED datatype and is used to create the GeneTrack file to be displayed_ + +* * * + +## Advanced Topics + +### Dynamic Display Applications + +Sometimes it can be desired to have links and parameters for a Display Application to come from an external file. In the following examples we will modify the above examples to be populated using data found in external files. + +The file `tool-data/shared/ucsc/ucsc_build_sites.txt` contains tab delimited data, with one line per display site, consisting of columns: + +1. Site Name +2. Site URL +3. Comma-separated Genome Builds Available at this site + +The display will also be filtered based upon a Galaxy Application configuration variable `ucsc_display_sites` which is used to to restrict available sites to a list specified in universe\_wsgi.ini; alternatively the non-desired sites can be removed by commenting or deleting them out in `tool-data/shared/ucsc/ucsc_build_sites.txt`. + +#### Example 1 Advanced + +Display a BAM file at the UCSC genome browser, dynamically loading sites from a text file (`tool-data/shared/ucsc/ucsc_build_sites.txt`). + +``` + + + + + + + + + + + + + ${site_id in $APP.config.ucsc_display_sites} + ${dataset.dbkey in $builds} + + + + ${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)} + + + track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey} + + + + +``` + +#### Example 2 Advanced + +Display an Interval file at the UCSC genome browser, dynamically loading sites from a text file (`tool-data/shared/ucsc/ucsc_build_sites.txt`). + +``` + + + + + + + + + + + + + ${site_id in $APP.config.ucsc_display_sites} + ${dataset.dbkey in $builds} + + + + ${ucsc_link}db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp} + + +#set line_count = 0 +#set chrom = None +#set start = float( 'inf' ) +#set end = 0 +#for $line in open( $bed_file.file_name ): + #if $line_count > 10: ##10 max lines to check for view port + #break + #end if + #if not $line.startswith( "#" ): + #set $fields = $line.split( "\t" ) + #try: + #if len( $fields ) >= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ): + #if $chrom is None or $fields[$bed_file.metadata.chromCol - 1] == $chrom: + #set chrom = $fields[$bed_file.metadata.chromCol - 1] + #set start = min( $start, int( $fields[$bed_file.metadata.startCol - 1] ) ) + #set end = max( $end, int( $fields[$bed_file.metadata.endCol - 1] ) ) + #end if + #end if + #except: + #pass + #end try + #end if + #set line_count += 1 +#end for +#if $chrom is not None: +${chrom}:${start}-${end + 1} +#else: +:- +#end if + + + +``` From ee46bd73d0349f616a6e052665ce4b4a144b2558 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 17:15:23 -0400 Subject: [PATCH 09/24] Global replace - hyphenated name /src/peoples --- .../dev-news-briefs/2015-01-13/index.md | 4 +- content/blog/2019-07-galaxy-twitter/index.md | 2 +- content/citing-galaxy/index.md | 14 ++--- .../galaxy-admins/meetups/2015-06-18/index.md | 2 +- content/develop/gsoc/2015-ideas/index.md | 12 ++--- content/events/2017-ismb-bosc/index.md | 4 +- content/events/2018-europe-dev/index.md | 2 +- content/events/2019-04-bioit/index.md | 2 +- content/events/2019-09-gateways/index.md | 2 +- content/events/2019-admin-training/index.md | 2 +- content/events/2020-abrf/index.md | 2 +- content/events/2020-pag/index.md | 2 +- content/events/archive/wayback/index.md | 52 +++++++++---------- content/events/eccb2014/index.md | 2 +- content/events/gaw2014/index.md | 2 +- content/events/gcc2012/abstracts/index.md | 2 +- .../breakouts/automation-strategies/index.md | 2 +- .../program/breakouts/end-users/index.md | 4 +- .../events/gcc2012/program/breakouts/index.md | 2 +- content/events/gcc2012/program/index.md | 10 ++-- content/events/gcc2012/sponsorships/index.md | 2 +- content/events/gcc2012/training-day/index.md | 6 +-- .../events/gcc2013/abstracts/talks/index.md | 6 +-- content/events/gcc2013/lightning/index.md | 2 +- content/events/gcc2013/program/index.md | 12 ++--- content/events/gcc2013/training-day/index.md | 18 +++---- .../events/gcc2014/abstracts/talks/index.md | 2 +- content/events/gcc2014/program/index.md | 6 +-- .../training-day/admin-walkthrough/index.md | 2 +- content/events/gcc2014/training-day/index.md | 8 +-- .../gcc2015/bofs/galaxy-admins/index.md | 4 +- content/events/germany2014/index.md | 2 +- content/events/germany2016/index.md | 2 +- content/events/indiana-u2012/index.md | 2 +- 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| 2 +- content/galaxy-updates/2013-09/index.md | 2 +- content/galaxy-updates/2013-10/index.md | 4 +- content/galaxy-updates/2013-11/index.md | 2 +- content/galaxy-updates/2014-01/index.md | 2 +- content/galaxy-updates/2014-02/index.md | 4 +- content/galaxy-updates/2014-03/index.md | 6 +-- content/galaxy-updates/2014-05/index.md | 2 +- content/galaxy-updates/2014-07/index.md | 2 +- content/galaxy-updates/2014-08/index.md | 2 +- content/galaxy-updates/2014-09/index.md | 2 +- content/galaxy-updates/2014-10/index.md | 2 +- content/galaxy-updates/2015-02/index.md | 18 +++---- content/galaxy-updates/2015-04/index.md | 4 +- content/galaxy-updates/2015-09/index.md | 2 +- content/galaxy-updates/2015-10/index.md | 6 +-- content/galaxy-updates/2015-11/index.md | 2 +- content/galaxy-updates/2016-02/index.md | 2 +- content/galaxy-updates/2016-04/index.md | 2 +- content/galaxy-updates/2016-05/index.md | 6 +-- content/galaxy-updates/2016-06/index.md | 2 +- content/galaxy-updates/2016-07/index.md | 6 +-- content/galaxy-updates/2016-08/index.md | 6 +-- content/galaxy-updates/2016-09/index.md | 6 +-- content/galaxy-updates/2016-10/index.md | 8 +-- content/galaxy-updates/2016-12/index.md | 6 +-- content/galaxy-updates/2017-06/index.md | 4 +- content/galaxy-updates/2017-09/index.md | 6 +-- content/galaxy-updates/2018-02/index.md | 2 +- content/galaxy-updates/2018-08/index.md | 8 +-- content/news/201502-galaxy-admins/index.md | 4 +- content/news/2018-12-galaxy-admins/index.md | 4 +- content/news/2019-01-galaxy-update/index.md | 4 +- content/news/2019-10-hacktoberfest/index.md | 2 +- .../index.md | 2 +- content/news/bio-blend-v0.5.3/index.md | 2 +- content/news/cloudman-release201401/index.md | 2 +- .../conda-dependency-codefest-report/index.md | 2 +- .../news/galaxy-current-protocols/index.md | 4 +- .../news/galaxy-tour-de-france2012/index.md | 2 +- .../liste-de-diffusion-galaxy-france/index.md | 2 +- content/news/s-g2014-report/index.md | 2 +- content/people/dave-bouvier/index.md | 2 +- content/people/dave-clements/index.md | 10 ++-- content/people/radhika-khetani/index.md | 2 +- content/people/tori-r/index.md | 4 +- content/use/galaxy-test/index.md | 2 +- content/use/imaging/index.md | 2 +- content/use/usegalaxy-eu/index.md | 2 +- content/use/usegalaxy-org/index.md | 2 +- 105 files changed, 226 insertions(+), 226 deletions(-) diff --git a/content/archive/dev-news-briefs/2015-01-13/index.md b/content/archive/dev-news-briefs/2015-01-13/index.md index 7ced66777b..577fbe57dd 100644 --- a/content/archive/dev-news-briefs/2015-01-13/index.md +++ b/content/archive/dev-news-briefs/2015-01-13/index.md @@ -71,7 +71,7 @@ Galaxy’s mobile interface, in addition to being vulnerable to XSS attacks, has ## IPython Integration -Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/) and [Helena Rasche](/src/people/helena-rasche/), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. +Thanks to the awesome work of community members [Björn Grüning](/people/bjoern-gruening/) and [Helena Rasche](/people/helena-rasche/), Galaxy now features integration with the popular IPython project. The [Galaxy-IPython](https://github.com/bgruening/galaxy-ipython) project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found [here](https://www.youtube.com/watch?v=jQDyTuYnn1k). Information on enabling this plugin is linked to via [this Trello card](https://trello.com/c/SE240zCB). [Interactive Environments (IEs)](https://wiki.galaxyproject.org/Admin/IEs) need to be set up. ## Tool Form Upgrade (for Beta Testing) @@ -148,7 +148,7 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Fixed composite Datatypes issue related to renaming individual parts of paired Datasets. [https://trello.com/c/ExOMfxtT](https://trello.com/c/ExOMfxtT) 1. Fixed issue where Dataset download links were being incorrectly populated by regenerating `dataset-model` URLs upon fetching (even when silent). Plus a corrections for cases where the `to_ext` value was missing. [https://trello.com/c/ngLd7M4u](https://trello.com/c/ngLd7M4u) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) [https://trello.com/c/pvdWMBmP](https://trello.com/c/pvdWMBmP) 1. Fix Slurm job post-mortem for »clusters« functionality added to `slurm-drmaa` (and currently in use on [http://usegalaxy.org](http://usegalaxy.org)). [https://trello.com/c/OuNEdZLc](https://trello.com/c/OuNEdZLc) -1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/people/nicola-soranzo/) & [Björn Grüning](/src/people/bjoern-gruening/). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) +1. Fixed datatypes from consuming output extra file paths due to updates in changeset d781366. Resolution aided by James Johnson, [Nicola Soranzo](/people/nicola-soranzo/) & [Björn Grüning](/people/bjoern-gruening/). [https://trello.com/c/gwG6GgW8](https://trello.com/c/gwG6GgW8) 1. Fixed import bug for `run_reports.sh`. Thank you [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/ZmTmQTZl](https://trello.com/c/ZmTmQTZl) 1. Fixed a parameter parsing issue in the Data Libraries API (recently introduced while refactoring Data Managers). [https://trello.com/c/1ZTlAVlT](https://trello.com/c/1ZTlAVlT) 1. Corrected a temporary issue where Import was omitted from the original release of `latest_2014.10.06`. [https://trello.com/c/iJwFduar](https://trello.com/c/iJwFduar) diff --git a/content/blog/2019-07-galaxy-twitter/index.md b/content/blog/2019-07-galaxy-twitter/index.md index 5390b102ad..c6def06b2d 100644 --- a/content/blog/2019-07-galaxy-twitter/index.md +++ b/content/blog/2019-07-galaxy-twitter/index.md @@ -106,4 +106,4 @@ We recommend [TweetDeck](https://tweetdeck.twitter.com/) for using Twitter. Twe See you on Twitter, -[Dave Clements](/people/dave-clements/), [Martin Cech](/people/marten/), [Mo Heydarian](/src/people/mo-heydarian/), [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) and Nicola Soranzo +[Dave Clements](/people/dave-clements/), [Martin Cech](/people/marten/), [Mo Heydarian](/people/mo-heydarian/), [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and Nicola Soranzo diff --git a/content/citing-galaxy/index.md b/content/citing-galaxy/index.md index f5d4daba2a..2e367b054c 100644 --- a/content/citing-galaxy/index.md +++ b/content/citing-galaxy/index.md @@ -40,7 +40,7 @@ Some excellent examples (*emphasis added*): If you use, extend or reference Galaxy in your published work, please cite this publication: -* [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Vahid Jalili](/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/people/jeremy-goecks/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). **[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 This and other references are also [available in GitHub](https://github.com/galaxyproject/galaxy/blob/dev/CITATION) as a [CITATION file](http://software-carpentry.org/blog/2013/09/introducing-citation-files.html). @@ -54,7 +54,7 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## Cloud -* [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. +* [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/people/james-taylor/), Nuwan Goonasekera. **[CloudLaunch: Discover and deploy cloud applications](https://doi.org/10.1016/j.future.2018.04.037)**, *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 ## Data Managers @@ -63,7 +63,7 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## DataSource Tools -* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. +* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. ## External Display Applications @@ -71,20 +71,20 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## Interactive Environments -* [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 +* [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/). **[Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005425)**, *PLOS Computational Biology*, doi:10.1371/journal.pcbi.1005425 ## Reproducibility -* [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/). +* [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/). **[Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014)**, *Cell Systems*, Volume 6, Issue 6, 2018, Pages 631-635, ISSN 2405-4712, doi:10.1016/j.cels.2018.03.014. ## ToolShed -* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/src/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/src/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 +* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 ## Training & Education -* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/people/bjoern-gruening/). **[Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012)**, *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 ### Online Education diff --git a/content/community/galaxy-admins/meetups/2015-06-18/index.md b/content/community/galaxy-admins/meetups/2015-06-18/index.md index 8df6120b78..5a119bd97a 100644 --- a/content/community/galaxy-admins/meetups/2015-06-18/index.md +++ b/content/community/galaxy-admins/meetups/2015-06-18/index.md @@ -20,7 +20,7 @@ Topics - Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
+ Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
Peter Briggs, University of Manchester
Galaxy Project Update: Planemo
John Chilton
GCC2015 GalaxyAdmins Meetup
Hans-Rudolf Hotz
Links diff --git a/content/develop/gsoc/2015-ideas/index.md b/content/develop/gsoc/2015-ideas/index.md index 41e7cde11a..21968aac72 100644 --- a/content/develop/gsoc/2015-ideas/index.md +++ b/content/develop/gsoc/2015-ideas/index.md @@ -32,7 +32,7 @@ Galaxy supports running jobs in Docker containers for running jobs on a single n **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy and/or Kubernetes, bioinformatics knowledge -**Possible Mentors** Kyle Ellrott, [John Chilton](/people/john-chilton/), [Dannon Baker](/src/people/dannon-baker/) +**Possible Mentors** Kyle Ellrott, [John Chilton](/people/john-chilton/), [Dannon Baker](/people/dannon-baker/) ## GA4GH Container and Workflows Integration @@ -75,7 +75,7 @@ By making complex applications easier to deploy and doing so reproducibly, the o **Potentially Helpful Skills** Familiarity with cloud and/or cluster computing, familiarity with Galaxy, Docker, and/or Fig, bioinformatics knowledge -**Possible Mentors** [John Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), [Dannon Baker](/src/people/dannon-baker/) +**Possible Mentors** [John Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), [Dannon Baker](/people/dannon-baker/) ## Fostering Bioconductor Collaborations @@ -92,7 +92,7 @@ The [RGalaxy](http://www.bioconductor.org/packages/release/bioc/html/RGalaxy.htm * Implement automated scripts (for use with cron jobs or CI tools such as Jenkins or Buildbot) to automate the release and publication of such artifacts. * Build and publish workflows demonstrating these tools with actual data. -**Possible Mentors** [Nitesh Turaga](/people/nitesh-turaga/), [Björn Grüning](/src/people/bjoern-gruening/), Daniel Blankenberg +**Possible Mentors** [Nitesh Turaga](/people/nitesh-turaga/), [Björn Grüning](/people/bjoern-gruening/), Daniel Blankenberg **Required Skills** Python programming @@ -303,7 +303,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Convert Galaxy to run on Python 3. * Once all dependencies are upgraded, package Galaxy for [Debian Med](https://www.debian.org/devel/debian-med/). -**Possible Mentors** [Nate Coraor](/people/nate/), [Tim Booth](https://github.com/tbooth), [John Chilton](/src/people/john-chilton/) +**Possible Mentors** [Nate Coraor](/people/nate/), [Tim Booth](https://github.com/tbooth), [John Chilton](/people/john-chilton/) **Required Skills:** * Knowledge of DPKG, BASH scripting, Makefiles, and the layout of files on a standard Linux filesystem (/etc, /var, /usr, ...) @@ -326,7 +326,7 @@ The biggest impediment to the inclusion of Galaxy within Debian is Galaxy's hand * Integrate the authentication mechanism with [Globus Nexus](https://www.globus.org/platform/services). -**Possible Mentors** [Martin Cech](/people/marten/), [Enis Afgan](/people/enis-afgan/), [Nitesh Turaga](/src/people/nitesh-turaga/) +**Possible Mentors** [Martin Cech](/people/marten/), [Enis Afgan](/people/enis-afgan/), [Nitesh Turaga](/people/nitesh-turaga/) **Required Skills** Python Programming @@ -371,7 +371,7 @@ Recently Interactive Environments (IEs) were developed for Galaxy. These consist * Unit test framework for IEs to ensure the proxy works ([some progress](https://github.com/hexylena/vagrant-galaxy-casperjs) exists but it's not very generic). -**Possible Mentors** [Helena Rasche](/people/helena-rasche/), [John Chilton](/src/people/john-chilton/) +**Possible Mentors** [Helena Rasche](/people/helena-rasche/), [John Chilton](/people/john-chilton/) **Required Skills** Docker, NodeJS diff --git a/content/events/2017-ismb-bosc/index.md b/content/events/2017-ismb-bosc/index.md index 43a39305cb..edca1371c1 100644 --- a/content/events/2017-ismb-bosc/index.md +++ b/content/events/2017-ismb-bosc/index.md @@ -19,7 +19,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | -| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | +| 14:30 | [Tutorial PM6: Making Galaxy Work for You](https://www.iscb.org/ismbeccb2017-program/tutorials#p6) (You can still register) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/people/bjoern-gruening/) | North Hall, ISMB/ECCB | [Tutorial](https://github.com/galaxyproject/galaxytutorial-ismb17) | ## 22 July, Saturday @@ -51,7 +51,7 @@ Galaxy has a significant presence at [ISMB/ECCB 2017](https://www.iscb.org/ismbe | Time | Topic | Presenter(s) | Where | Links | | ---- | ---- | ---- | ---- | ---- | -| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/src/people/bjoern-gruening/), [James Taylor](/src/people/james-taylor/) | Meeting Hall V | | +| 12:45 | [BoF B4: What can the Galaxy Project do for you?](https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof) | [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Bjorn Gruning](/people/bjoern-gruening/), [James Taylor](/people/james-taylor/) | Meeting Hall V | | | 18:00 | [B-079: Development of a bioinformatics pipeline for the routine analysis of viral whole genome sequencing data](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=H#B-079) | Qiang Fu | Congress Foyer, Level 2 | [Poster]( https://depot.galaxyproject.org/hub/attachments/documents/posters/2017_ismb_viral_wgs_fu.pdf) | | 18:00 | [B-365: Comparison of open source (galaxy based) and commercial pipelines for RNA-Seq data analysis](https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=P#B-365) | Slave Trajanoski | Congress Foyer, Level 2 | [Poster](https://depot.galaxyproject.org/hub/attachments/documents/posters/ismb2017-trajanoski.pdf) | | 20:00 | [Galaxy Community Dinner](http://bit.ly/gxyismb2017bdinner) | [Martin Čech](/people/marten/) | [VYŠEHRADSKÝ RESTAURANT KANDELÁBR](http://bit.ly/gxyismb2017bdinner) | | diff --git a/content/events/2018-europe-dev/index.md b/content/events/2018-europe-dev/index.md index 06b7d2b59e..abbe43201a 100644 --- a/content/events/2018-europe-dev/index.md +++ b/content/events/2018-europe-dev/index.md @@ -132,5 +132,5 @@ http://www.vag-freiburg.de/fahrplan-linien/netzplaene/liniennetzplan.html ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) (hrh@fmi.ch) or [Björn Grüning](/people/bjoern-gruening/) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/src/people/jeanfrancois-dufayard/) (jean-francois.dufayard@cirad.fr) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) (hrh@fmi.ch) or [Björn Grüning](/people/bjoern-gruening/) (gruening@informatik.uni-freiburg.de) or [Jean-François Dufayard](/people/jeanfrancois-dufayard/) (jean-francois.dufayard@cirad.fr) diff --git a/content/events/2019-04-bioit/index.md b/content/events/2019-04-bioit/index.md index 74102678e8..8609239ec9 100644 --- a/content/events/2019-04-bioit/index.md +++ b/content/events/2019-04-bioit/index.md @@ -21,5 +21,5 @@ Going to [BioIT World 2019](https://www.bio-itworldexpo.com/)? Galaxy is there | Mon 4/15 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 9:00 | [FAIR Data Hackathon](https://www.bio-itworldexpo.com/fair-data-hackathon): Integrating Globus into Galaxy to Enable FAIRifying Data | Cityview 1 | Ben Busby | | Tue 4/16 | 4:15 | Hackathon Report Outs: Integrating Globus into Galaxy to Enable FAIRifying Data | Track 6: FAIR Data | Globus Genomics | -| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/people/enis-afgan/) & [Vahid Jalili](/src/people/vahid-jalili/) | +| Wed 4/17 | 12:00 | [Integrating Google Cloud Platform into the Galaxy data analysis ecosystem](/src/events/2019-04-bioit/bioit-google-galaxy.png) | Google Cloud Booth #400 | [Enis Afgan](/people/enis-afgan/) & [Vahid Jalili](/people/vahid-jalili/) | | Thu 4/18 | 10:40 | [Longitudinal and Context Visualization for Precision Oncology](http://www.giiconference.com/chi653337/data-visualization.shtml) | Track 8: Data Visualization & Exploration Tools | [Jeremy Goecks](/people/jeremy-goecks/) | diff --git a/content/events/2019-09-gateways/index.md b/content/events/2019-09-gateways/index.md index c123ed75d6..41cb878ecc 100644 --- a/content/events/2019-09-gateways/index.md +++ b/content/events/2019-09-gateways/index.md @@ -22,6 +22,6 @@ There are several Galaxy related presentations at [Gateways 2019](https://scienc ## Find out more -Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/people/mo-heydarian/) or [Dave Clements](/src/people/dave-clements/). +Galaxy is also a Gateways 2019 Bronze Sponsor. Please drop by the Galaxy table during [any break](https://gateways2019.sched.com/overview/type/Break) on Tuesday and Wednesday, and during the [Reception and Poster Session](https://sched.co/RaIz) on Tuesday evening. We are also available at other times too. Just ask [Mo Heydarian](/people/mo-heydarian/) or [Dave Clements](/people/dave-clements/). diff --git a/content/events/2019-admin-training/index.md b/content/events/2019-admin-training/index.md index d8205f8213..b023d0f0d0 100644 --- a/content/events/2019-admin-training/index.md +++ b/content/events/2019-admin-training/index.md @@ -76,7 +76,7 @@ We currently have five confirmed (and highly experienced!) instructors: * [Martin Čech](/people/marten/), software engineer for the Galaxy Project and frequent sys admin for usegalaxy.org. * [Nate Coraor](/people/nate/), lead sysadmin of Galaxy Main (https://usegalaxy.org) and a software engineer for the Galaxy Project -* [John Chilton](/src/people/john-chilton/), software engineer for the Galaxy Project working on both the front and back ends, with an emphasis on scalability. +* [John Chilton](/people/john-chilton/), software engineer for the Galaxy Project working on both the front and back ends, with an emphasis on scalability. * [Simon Gladman](https://github.com/Slugger70), administrator of Galaxy Australia (https://usegalaxy.org.au), University of Melbourne * [Helena Rasche](https://github.com/hexylena), lead sysadmin of Galaxy Europe (https://usegalaxy.eu), software engineer and cloud administrator for University of Freiburg/de.NBI Project Freiburg branch diff --git a/content/events/2020-abrf/index.md b/content/events/2020-abrf/index.md index a7b622867e..247f5bd178 100644 --- a/content/events/2020-abrf/index.md +++ b/content/events/2020-abrf/index.md @@ -27,7 +27,7 @@ The day focuses on two topics: # SW4a: Single Cell RNA-Seq and Visualization Using the Galaxy Workbench (AM)
-[](https://www.researchgate.net/profile/Mehmet_Tekman)   [](/src/people/dave-clements/) +[](https://www.researchgate.net/profile/Mehmet_Tekman)   [](/people/dave-clements/)
**Instructors:** diff --git a/content/events/2020-pag/index.md b/content/events/2020-pag/index.md index 37aec4719b..5e5449eeb4 100644 --- a/content/events/2020-pag/index.md +++ b/content/events/2020-pag/index.md @@ -35,4 +35,4 @@ In addition, there was be a [GMOD Codefest](http://gmod.org/wiki/Codefest_2020) | | 7:13-7:25 | [Eukaryotic Pathogen, Vector & Host Informatics Resources (VEuPathDB) - a Merged International Approach Towards Achieving Sustainability](https://plan.core-apps.com/pag_2020/event/06b15a6d8bf3d42e3dbaf3d39ebad5d7) | [Data Resource Sustainability and Funding](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb048f4a), East 1 | | [Jessica Kissinger](http://mango.ctegd.uga.edu/jkissingLab/) | | **Tuesday, January 14** | 4:00-4:20 | **[Introduction to Galaxy and the Galaxy Ecosystem](https://plan.core-apps.com/pag_2020/event/a8f1e9dbae7dc0d6d1e5f05d4657f89d)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-intro-slides.pdf) | [Dave Clements](/people/dave-clements/) | | | 4:20-4:50 | **[Galaxy for Excellence in Breeding](https://plan.core-apps.com/pag_2020/event/0faacece23744ad32bb082ce6b8c5e27)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [Slides](https://depot.galaxyproject.org/hub/attachments/events/2020-pag/pag2020-eib-slides.pdf) | [Star Yanxin Gao](https://twitter.com/stargao3) | -| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/people/mo-heydarian/), [Dave Clements](/src/people/dave-clements/), Umesh Rosyara, Jose Crossa, Mathias Lorieux | +| | 4:50-6:10 | **[Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools](https://plan.core-apps.com/pag_2020/event/959619631bade74d533994f26e218d04)** | **[Galaxy: An Open Platform for Data Analysis and Integration](https://plan.core-apps.com/pag_2020/event/680f532f0a26f8c2f8d1736dbb037b2d)**, California Room | [history](http://galaxy-demo.excellenceinbreeding.org/u/clements/h/pag-2020-3k-rgp) | [Star Yanxin Gao](https://twitter.com/stargao3), [Mo Heydarian](/people/mo-heydarian/), [Dave Clements](/people/dave-clements/), Umesh Rosyara, Jose Crossa, Mathias Lorieux | diff --git a/content/events/archive/wayback/index.md b/content/events/archive/wayback/index.md index b97bd9fff5..8a11f7e0c7 100644 --- a/content/events/archive/wayback/index.md +++ b/content/events/archive/wayback/index.md @@ -90,14 +90,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s December 15 Galaxy Training Materials / The new Galaxy Community Hub: Community creation, curation, and use Online GalaxyAdmins Meetup, Online - Björn Grüning, Bérénice Batut, Dannon Baker + Björn Grüning, Bérénice Batut, Dannon Baker December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online - Dannon Baker, Dave Clements + Dannon Baker, Dave Clements @@ -237,7 +237,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 25-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy - Dannon Baker, Björn Grüning + Dannon Baker, Björn Grüning @@ -258,7 +258,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening @@ -272,7 +272,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening @@ -418,7 +418,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s August 18 GalaxyAdmins Web Meetup Around the World Online - Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements + Nick Hazekamp, Hans-Rudolf Hotz, Dave Clements Slides @@ -564,7 +564,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online - Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Helena Rasche, Hans-Rudolf Hotz, Dave Clements Slides @@ -745,7 +745,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s April 21 The Galaxy Portal: Accessing Galaxy from Mobile Devices and Tool Development Developments Around the World GalaxyAdmins Web Meetup, Online - Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz + Ivar Grytten, Geir Kjetil Sandve, John Chilton, Hans-Rudolf Hotz @@ -787,7 +787,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s April 4 IUC Hackathon - Conda dependencies Around the World Online - Björn Grüning, Rémi Marenco, Nitesh Turaga + Björn Grüning, Rémi Marenco, Nitesh Turaga @@ -872,7 +872,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 18 GalaxyAdmins Web Meetup Around the World Online - Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements + Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements @@ -1126,7 +1126,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States -
Training offered by GTN Member
Dan Blankenberg, John Chilton +
Training offered by GTN Member
Dan Blankenberg, John Chilton @@ -1217,7 +1217,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s October 15 October Galaxy Admins Meetup Around the World Online - David Kovalic, Hans-Rudolf Hotz, Dave Clements + David Kovalic, Hans-Rudolf Hotz, Dave Clements Video, Slides @@ -1556,7 +1556,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester Around the World June 2015 GalaxyAdmins Web Meetup, Online - Peter Briggs, John Chilton, Hans-Rudolf Hotz + Peter Briggs, John Chilton, Hans-Rudolf Hotz Slides @@ -1992,14 +1992,14 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s February 19 February 2015 GalaxyAdmins Web Meetup Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements Slides, Video February 18 Baltimore Area Galaxy Meetup Baltimore, Maryland, United States - Enis Afgan, Nitesh Turaga + Enis Afgan, Nitesh Turaga Slides @@ -2038,7 +2038,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s January 22 Baltimore Area Galaxy Meetup
This meetup is now full.
Baltimore, Maryland, United States - Enis Afgan, Nitesh Turaga + Enis Afgan, Nitesh Turaga Slides @@ -2444,7 +2444,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany Slides - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop @@ -2889,7 +2889,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson March 24-25 @@ -2910,7 +2910,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy Workshop University of Georgia, Athens, Georgia, United States Slides - Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam + Carl Eberhard, Dave Clements, Dannon Baker, Raj Ayyampalayam @@ -2941,7 +2941,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States - Anton Nekrutenko, JamesTaylor + Anton Nekrutenko, JamesTaylor February 10-14 @@ -3298,7 +3298,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
Polymorphism Detection and Visualization - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders @@ -3371,7 +3371,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States Galaxy 101 NGS: Introduction to Polymorphism Detection, Managing a Local Galaxy Instance - Anton Nekrutenko, Jennifer Jackson, Anushka Brownley + Anton Nekrutenko, Jennifer Jackson, Anushka Brownley October 14-18 @@ -3634,7 +3634,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France - Anton Nekrutenko, Enis Afgan + Anton Nekrutenko, Enis Afgan June 6-7 @@ -4008,7 +4008,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Slides
Tutorial - Jeremy Goecks, Jennifer Jackson + Jeremy Goecks, Jennifer Jackson Working with High-Throughput Data and Data Visualization @@ -4040,7 +4040,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Galaxy 101 and RNA-seq Analysis and Visualization QB3 - Computational Genomics Resource Laboratory, Univ of California Berkeley Slides
Tutorials: Galaxy101, RNA-seq - Jeremy Goecks, Jennifer Jackson + Jeremy Goecks, Jennifer Jackson October 28 - November 2 @@ -4634,7 +4634,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s Management and Analysis of Second and Third Generation Sequencing Data with Galaxy
AGBT 2011 Marco Island, Florida, United States Slides - Anton Nekrutenko, James Taylor + Anton Nekrutenko, James Taylor January 15-19 diff --git a/content/events/eccb2014/index.md b/content/events/eccb2014/index.md index 50e0c24cd0..8ca701a251 100644 --- a/content/events/eccb2014/index.md +++ b/content/events/eccb2014/index.md @@ -68,6 +68,6 @@ There were several sessions and posters featuring Galaxy at the [13th European C 14:00-14:30 ID02: A panel of European Public Galaxy Instances
1. Galaxy Project Introduction
2. deepTools: user-friendly tools for data visualization
3. The Nebula ChIP-Seq web service
4. The French Institute of Bioinformatics (IFB) academic cloud infrastructure for life sciences
1. Slides
2. Slides - Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet + Hans-Rudolf Hotz, Björn Grüning, Alban Lermine, Christophe Blanchet diff --git a/content/events/gaw2014/index.md b/content/events/gaw2014/index.md index 2735d363fc..5c5b617780 100644 --- a/content/events/gaw2014/index.md +++ b/content/events/gaw2014/index.md @@ -87,7 +87,7 @@ GAW 2014 also included poster session and keynote speakers. 16:20-17:00 - Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan + Setting up and administering Galaxy - panel discussion
Stephen McMahon, Nate Coraor, Enis Afgan diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index 8969e76cac..88b59d89fc 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -18,7 +18,7 @@ Abstracts for talks that were presented at the [GCC2012 main sessions](/src/even
 
-**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) diff --git a/content/events/gcc2012/program/breakouts/automation-strategies/index.md b/content/events/gcc2012/program/breakouts/automation-strategies/index.md index d3437cf820..cc33a1f065 100644 --- a/content/events/gcc2012/program/breakouts/automation-strategies/index.md +++ b/content/events/gcc2012/program/breakouts/automation-strategies/index.md @@ -7,7 +7,7 @@ title: Automation strategies for Data, Tools, & Config -A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/people/john-chilton/), [Enis Afgan](/people/enis-afgan/), [Dave Bouvier](/src/people/dave-bouvier/) and [Jen Jackson](/src/people/jennifer-jackson/) +A proposed [Breakout Session](/src/events/gcc2012/program/breakouts/automation-strategies//index.md) for [GCC2012](/src/events/gcc2012/index.md), organized by Brad Chapman, [John Chilton](/people/john-chilton/), [Enis Afgan](/people/enis-afgan/), [Dave Bouvier](/people/dave-bouvier/) and [Jen Jackson](/people/jennifer-jackson/) This involves turning the base Galaxy into a production machine: * download of associated genomes and data files, diff --git a/content/events/gcc2012/program/breakouts/end-users/index.md b/content/events/gcc2012/program/breakouts/end-users/index.md index be98e8f21c..b031846504 100644 --- a/content/events/gcc2012/program/breakouts/end-users/index.md +++ b/content/events/gcc2012/program/breakouts/end-users/index.md @@ -15,11 +15,11 @@ title: Galaxy End Users * Karen Reddy * -* [Anton](/people/anton/), [Dan](/people/dan/), Rémi, and [Jen](/src/people/jennifer-jackson/) from [Galaxy Team](/src/galaxy-team/) +* [Anton](/people/anton/), [Dan](/people/dan/), Rémi, and [Jen](/people/jennifer-jackson/) from [Galaxy Team](/src/galaxy-team/) # Notes -These are a merged grouping of [Anton's](/people/anton/), [Dan's](/people/dan/), and [Jen's](/src/people/jennifer-jackson/) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. +These are a merged grouping of [Anton's](/people/anton/), [Dan's](/people/dan/), and [Jen's](/people/jennifer-jackson/) notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session. ## Platforms diff --git a/content/events/gcc2012/program/breakouts/index.md b/content/events/gcc2012/program/breakouts/index.md index 6fc051cf8e..c289ce6587 100644 --- a/content/events/gcc2012/program/breakouts/index.md +++ b/content/events/gcc2012/program/breakouts/index.md @@ -5,7 +5,7 @@ Breakouts are informal, open discussion sessions where participants interested i GalaxyCzars
Ann Black-Ziegelbein - Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson + Automation Strategies for Data, Tools, & Config
Brad Chapman, John Chilton, Enis Afgan, Dave Bouvier and Jen Jackson Bioinformatics Training and Teaching with Galaxy
Dave Clements diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index cc3f5056a3..7f8429b718 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -36,8 +36,8 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 9:00 WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -46,7 +46,7 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl 11:00 WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
WS6: Galaxy API
Dannon Baker
@@ -84,7 +84,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | **8:00-9:00** | Continental Breakfast, Registration Open | | **9:00-9:10** | **Welcome:** [William Hendrickson](http://www.uic.edu/depts/mcmi/faculty/hendrickson/), [University of Illinois at Chicago (UIC)](http://www/uic.edu/) | | **9:10-10:40** | **Session 1:** Moderator: [Tin Lap Lee](http://www.sbs.cuhk.edu.hk/TeachingStaffDetails.asp?TE_NAME=LEE%20Tin%20Lap), [Chinese University of Hong Kong](http://www.cuhk.edu.hk/) | -| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/), Galaxy Project
| +| 9:10 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/State.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 7:10)*
*[State of the Galaxy](/src/events/gcc2012/abstracts/index.md#state-of-the-galaxy)*
[Anton Nekrutenko](/people/anton/) and [James Taylor](/people/james-taylor/), Galaxy Project
| | 9:40 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Luo.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ 31:55)*
*[Integration of S-MART, a toolbox to aid RNA-seq data analysis in Galaxy](/src/events/gcc2012/abstracts/index.md#integration-of-s-mart-a-toolbox-to-aid-rna-seq-data-analysis-in-galaxy)*
Yufei Luo, Unité de recherche en Génomique-Info, INRA
| | 10:00 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Park.pdf), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=abfc6489eb764d4) (start @ xx:yy), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5)*
*[Connecting Galaxy to a Data Repository](/src/events/gcc2012/abstracts/index.md#connecting-galaxy-to-a-data-repository)*
Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School
| | 10:20 |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/MaillolDufayard.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=52bb95ced46c4b5) (starts @ 11:45)*
*[Role of Galaxy in a bioinformatic plant breeding platform](/src/events/gcc2012/abstracts/index.md#role-of-galaxy-in-a-bioinformatic-plant-breeding-platform)*
Vincent Maillol and Jean-Francois Dufayard, INRA and CIRAD
| @@ -142,7 +142,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.ppt), Video*
*Galaxy-P*
Pratik Jagtap, University of Minnesota
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Sandve.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421)*
*The Genomic Hyperbrowser: Prove Your Point*
Geir Kjetil Sandve, University of Oslo
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Gruning.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 6:10)*
*[ChemicalToolBox](/src/chemical-tool-box/index.md)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| -| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/), Penn State University, [James Taylor](/src/people/james-taylor/), Emory University
| +| **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/), Penn State University, [James Taylor](/people/james-taylor/), Emory University
| | **2:55-3:15** | **Break** | | **3:15-5:00** | **Session 8: Breakouts**
Moderator: Dave Clements, [Emory University](http://www.emory.edu/)
[Breakouts](/src/eents/gcc2012/program/breakouts/index.md) | | **5:00** | **[2012 Galaxy Community Conference](/src/events/gcc2012/index.md) ends** | diff --git a/content/events/gcc2012/sponsorships/index.md b/content/events/gcc2012/sponsorships/index.md index a6ba7fbcb1..bbca6bba99 100644 --- a/content/events/gcc2012/sponsorships/index.md +++ b/content/events/gcc2012/sponsorships/index.md @@ -16,7 +16,7 @@ Sponsorships are available at four different levels. Ion Torrent - Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss + Ion Torrent

GCC Representatives:
Mike Lelivelt • Matt Dyer
Mike Hunsicker • Eric Hilligoss diff --git a/content/events/gcc2012/training-day/index.md b/content/events/gcc2012/training-day/index.md index 06ae731f01..ac8b11a16a 100644 --- a/content/events/gcc2012/training-day/index.md +++ b/content/events/gcc2012/training-day/index.md @@ -30,8 +30,8 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 9:00 WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
- WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
- WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
+ WS2: Introduction to Galaxy
Jeremy Goecks, James Taylor & Jennifer Jackson
+ WS3: Galaxy CloudMan
Enis Afgan & Dannon Baker
10:30 @@ -40,7 +40,7 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 11:00 WS4: Galaxy Code Architecture
James Taylor
- WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
+ WS5: Installing Your Own Galaxy
Nate Coraor & Dave Bouvier
WS6: Galaxy API
Dannon Baker
diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index 693773f818..98b239da5a 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -271,7 +271,7 @@ Ion Torrent has invented the first device—a new semiconductor chip—capable o
 
-**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) @@ -451,7 +451,7 @@ To ensure the quality of the Tool Shed and the available contributed Utilities,
-**[Carl Eberhard](/people/carl-eberhard/)**1, [Jeremy Goecks](/people/jeremy-goecks/)1, [The Galaxy Team](/src/galaxy-team/)1,2, [Anton Nekrutenko](/people/anton/)2, and [James Taylor](/src/people/james-taylor/)1 +**[Carl Eberhard](/people/carl-eberhard/)**1, [Jeremy Goecks](/people/jeremy-goecks/)1, [The Galaxy Team](/src/galaxy-team/)1,2, [Anton Nekrutenko](/people/anton/)2, and [James Taylor](/people/james-taylor/)1 1 Emory University
2 Penn State University @@ -486,7 +486,7 @@ Data Managers can be defined locally or installed automatically from a Tool Shed
-**[Dannon Baker](/people/dannon-baker/)**1, [Nate Coraor](/people/nate/)2, [John Chilton](/src/people/john-chilton/)3 +**[Dannon Baker](/people/dannon-baker/)**1, [Nate Coraor](/people/nate/)2, [John Chilton](/people/john-chilton/)3 1 Emory University
2 Penn State
diff --git a/content/events/gcc2013/lightning/index.md b/content/events/gcc2013/lightning/index.md index 3501125bdf..9912822e0a 100644 --- a/content/events/gcc2013/lightning/index.md +++ b/content/events/gcc2013/lightning/index.md @@ -7,7 +7,7 @@ title: Lightning Talks -Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/people/fubar/)) and [Session 8 on Tuesday](/src/events/gcc2013/program/#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/)). **No more than half the lightning talk slots will be allocated before the meeting.** +Lightning talks are a mixture of topics selected in advance and those solicited during the meeting. They will be presented during [Session 4, on Monday](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (moderated by [Ross Lazarus](/people/fubar/)) and [Session 8 on Tuesday](/src/events/gcc2013/program/#day-2-main-meeting-2-july) (moderated by [Hans-Rudolf Hotz](/people/hansrudolf-hotz/)). **No more than half the lightning talk slots will be allocated before the meeting.** If you wish to give a lightning talk, please send an abstract to [GCC2013 Scientific Committee](mailto:gcc2013-sci AT galaxyproject DOT org), either * any time before the start of [Session 2](/src/events/gcc2013/program/index.md#day-1-main-meeting-1-july) (to be considered for Monday or Tuesday slots), or diff --git a/content/events/gcc2013/program/index.md b/content/events/gcc2013/program/index.md index 0dabd91268..e162fc245c 100644 --- a/content/events/gcc2013/program/index.md +++ b/content/events/gcc2013/program/index.md @@ -36,8 +36,8 @@ Workshops will be hands-on and participants will be strongly encouraged to bring Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
- Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00 @@ -45,11 +45,11 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 12:30 - The Galaxy API
Nate Coraor, Carl Eberhard
+ The Galaxy API
Nate Coraor, Carl Eberhard
Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
- Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
+ Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30 @@ -58,7 +58,7 @@ Workshops will be hands-on and participants will be strongly encouraged to bring 15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
- Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
+ Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
@@ -297,7 +297,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - + diff --git a/content/events/gcc2013/training-day/index.md b/content/events/gcc2013/training-day/index.md index ec92e9a70f..47caccc1a2 100644 --- a/content/events/gcc2013/training-day/index.md +++ b/content/events/gcc2013/training-day/index.md @@ -42,8 +42,8 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - - + + @@ -51,11 +51,11 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - + - + @@ -64,7 +64,7 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - + @@ -114,7 +114,7 @@ See each individual workshop's list of prerequisite for specifics.
9:10
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
Slides, Vimeo
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
9:40 Galaxy Code and Storage Architecture
James Taylor, Nate Coraor
 Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Installing and Maintaining a Local Galaxy Server
George Magklaras, Katerina Michalickova, Nikolay Vazov
 Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
Introduction to Galaxy and the Galaxy Ecosystem
Anton Nekrutenko, Jennifer Hillman-Jackson
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
11:00
12:30 The Galaxy API
Nate Coraor, Carl Eberhard
 The Galaxy API
Nate Coraor, Carl Eberhard
 Introduction to Tool and Data Source Configuration
Dan Blankenberg, Ross Lazarus
 RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
Statistical Genome Analysis with Galaxy
Geir Kjetil Sandve, Sveinung Gundersen
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
 Running Galaxy on the Cloud
Enis Afgan, Dannon Baker
14:30
15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
- + @@ -144,7 +144,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University 		Anton Nekrutenko, Penn State University
Jennifer Hillman-Jackson, Penn State University
Content
- + @@ -405,7 +405,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University 		Enis Afgan, Ruđer Bošković Institute (RBI)
Dannon Baker, Emory University
Content
- + @@ -446,7 +446,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University 		Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University
Content
- + diff --git a/content/events/gcc2014/abstracts/talks/index.md b/content/events/gcc2014/abstracts/talks/index.md index cbef643d60..83f0a9b465 100644 --- a/content/events/gcc2014/abstracts/talks/index.md +++ b/content/events/gcc2014/abstracts/talks/index.md @@ -136,7 +136,7 @@ As a trusted industry leader in designing and implementing effective scientific
 
-**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/src/people/james-taylor/)2** +**[Anton Nekrutenko](/people/anton/)1 and [James Taylor](/people/james-taylor/)2** 1 [Penn State University](http://psu.edu/)
2 [Emory University](http://emory.edu/) diff --git a/content/events/gcc2014/program/index.md b/content/events/gcc2014/program/index.md index fd0c8c61e1..0d97a785d9 100644 --- a/content/events/gcc2014/program/index.md +++ b/content/events/gcc2014/program/index.md @@ -43,7 +43,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -53,7 +53,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -197,7 +197,7 @@ Moderator: [Liisa Koski](https://www.linkedin.com/pub/liisa-koski/70/164/b0b), [
Instructors Nate Coraor, Penn State University
Carl Eberhard, Emory University 		Nate Coraor, Penn State University
Carl Eberhard, Emory University
Content Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
- + diff --git a/content/events/gcc2014/training-day/admin-walkthrough/index.md b/content/events/gcc2014/training-day/admin-walkthrough/index.md index d5736ab6a0..891c9224b8 100644 --- a/content/events/gcc2014/training-day/admin-walkthrough/index.md +++ b/content/events/gcc2014/training-day/admin-walkthrough/index.md @@ -9,7 +9,7 @@ title: "Tutorial: Galaxy Installation and Administration"
GCC2014 Training Day
-[Nate Coraor](/people/nate/) and [John Chilton](/src/people/john-chilton/) +[Nate Coraor](/people/nate/) and [John Chilton](/people/john-chilton/)
diff --git a/content/events/gcc2014/training-day/index.md b/content/events/gcc2014/training-day/index.md index fdb514bcca..8e7cec9ee9 100644 --- a/content/events/gcc2014/training-day/index.md +++ b/content/events/gcc2014/training-day/index.md @@ -39,7 +39,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -49,7 +49,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -257,7 +257,7 @@ See each individual workshop's list of prerequisite for specifics.
1:15 State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
1:50 Visualization of NGS data
Jeremy Goecks & Aysam Guerler
 Raisins & Rabbit Turds: NGS Quality Control with Galaxy
Tom Bair & Jennifer Jackson
Galaxy Internals: Flow control within Galaxy
James Taylor
 Galaxy installation and administration
Nate Coraor & John Chilton
Galaxy installation and administration
Nate Coraor & John Chilton
Training with Galaxy: a Genome Assembly Example
Simon Gladman & Andrew Lonie
12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
- + @@ -306,7 +306,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Nate Coraor, Penn State University
John Chilton, Penn State University 		Nate Coraor, Penn State University
John Chilton, Penn State University
Content
- + diff --git a/content/events/gcc2015/bofs/galaxy-admins/index.md b/content/events/gcc2015/bofs/galaxy-admins/index.md index b123adc9e3..8f9cfb33ff 100644 --- a/content/events/gcc2015/bofs/galaxy-admins/index.md +++ b/content/events/gcc2015/bofs/galaxy-admins/index.md @@ -17,7 +17,7 @@ When:: Tuesday, 7 July, 18:20 Where:: Franklin Room, JICCC -Contact:: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Dave Clements](/src/people/dave-clements/) +Contact:: [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Dave Clements](/people/dave-clements/) # Audience @@ -102,4 +102,4 @@ This BoF will meet on **Tuesday, 7 July at 18:20, in the Franklin Room, at the J # Questions? -Send them to [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/src/people/dave-clements/) +Send them to [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/people/dave-clements/) diff --git a/content/events/germany2014/index.md b/content/events/germany2014/index.md index bce3092490..813fe6c0d7 100644 --- a/content/events/germany2014/index.md +++ b/content/events/germany2014/index.md @@ -39,4 +39,4 @@ We have created a [small map of places to find food and drinks](https://mapsengi ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/germany2016/index.md b/content/events/germany2016/index.md index 691a6ef033..5f6b541c30 100644 --- a/content/events/germany2016/index.md +++ b/content/events/germany2016/index.md @@ -39,4 +39,4 @@ Please let us know what you are interesting in. ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/indiana-u2012/index.md b/content/events/indiana-u2012/index.md index cf89d97250..0eb9df88bb 100644 --- a/content/events/indiana-u2012/index.md +++ b/content/events/indiana-u2012/index.md @@ -110,7 +110,7 @@ This is a hands-on workshop. **Please bring a wifi-enabled laptop with a curren **[Dave Clements](/people/dave-clements/)**
**Emory University**

-This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/people/nate/) and [Dannon Baker](/src/people/dannon-baker/) of the Galaxy development team. +This workshop will introduce Galaxy for developers. This includes covering the Galaxy API, Galaxy Architecture, configuring Galaxy for a production environment. This will be more informal than the *Galaxy for Biologists* workshop and will cover topics that are of most interest to attendees. [Dave Clements](/people/dave-clements/) of the Galaxy Project will lead the workshop and we will be joined remotely by [Nate Coraor](/people/nate/) and [Dannon Baker](/people/dannon-baker/) of the Galaxy development team. *Registration is open to any member of the Indiana University community. The workshop is free, but space is limited and advanced registration is required.* diff --git a/content/events/ismb2012/index.md b/content/events/ismb2012/index.md index f34eb29ead..69858800e1 100644 --- a/content/events/ismb2012/index.md +++ b/content/events/ismb2012/index.md @@ -19,7 +19,7 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B - + diff --git a/content/events/meetups/baltimore/2015-01-22/index.md b/content/events/meetups/baltimore/2015-01-22/index.md index 35d2bfcd46..b06a5b30ba 100644 --- a/content/events/meetups/baltimore/2015-01-22/index.md +++ b/content/events/meetups/baltimore/2015-01-22/index.md @@ -13,7 +13,7 @@ The first Galaxy meetup or social gathering held in Baltimore was sold out. It w The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis](/people/enis-afgan/) & [Nitesh](/src/people/nitesh-turaga/) +[Enis](/people/enis-afgan/) & [Nitesh](/people/nitesh-turaga/) ## There's a meetup! diff --git a/content/events/sg2014/index.md b/content/events/sg2014/index.md index 8b33720619..ef453a2893 100644 --- a/content/events/sg2014/index.md +++ b/content/events/sg2014/index.md @@ -10,7 +10,7 @@ title: Swiss German Galaxy Tour 2014 There will be a *Swiss-German Galaxy Tour* this fall featuring a range of events over 3 days in two locations. ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Events @@ -39,4 +39,4 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/sg2016/index.md b/content/events/sg2016/index.md index df03c2fe4a..13fc7fd201 100644 --- a/content/events/sg2016/index.md +++ b/content/events/sg2016/index.md @@ -51,4 +51,4 @@ The [second day](/src/events/germany2016/index.md), October 21st, is ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/switzerland2014/index.md b/content/events/switzerland2014/index.md index 85e18c58c3..95c7bac9a2 100644 --- a/content/events/switzerland2014/index.md +++ b/content/events/switzerland2014/index.md @@ -27,7 +27,7 @@ Following the workshop, we organise a [Developers Day](/src/events/germany2014/i ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. ## Preliminary Schedule @@ -35,7 +35,7 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/welcome_20141001.pdf) | | 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | Status of the Galaxy Project | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/SG2014T__State_of_the_Galaxy.pdf) | | 10:30 - 10:50 | coffee Break | | 10:50 - 11:40 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | Galaxy: putting pieces together | [whiteboard](/src/events/switzerland2014/Bjoern_whiteboard.jpg) | @@ -48,7 +48,7 @@ Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf | 15:00 - 15:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Using Galaxy for NGS analysis in a collaborative environment | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/hrh_20141001.pdf) | | 15:30 - 15:45 | Tim-Christoph Roloff ([FMI](http://www.fmi.ch/)) | Genomics analysis at FMI | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Galaxy_Workshop_Bern_2014_Tim_Roloff.pdf) | | 15:45 - 16:00 | Torsten Houwaart ([University of Freiburg](http://www.uni-freiburg.de/)) | RNA structure visualized in Galaxy | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/Torsten_Bern01.10.2014.pdf) | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | @@ -69,4 +69,4 @@ This workshop is generously supported by [SyBIT](https://wiki.systemsx.ch/displa ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/switzerland2014/trainingday/index.md b/content/events/switzerland2014/trainingday/index.md index 69a52a960f..335544310c 100644 --- a/content/events/switzerland2014/trainingday/index.md +++ b/content/events/switzerland2014/trainingday/index.md @@ -27,7 +27,7 @@ Topics covered: | Time | Speaker | Title | Type | Slides | | ---- | -------- | ------ | ----- | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:40 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | +| 9:30 - 9:40 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/welcome_20140930.pdf) | | 9:40 - 9:50 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | Galaxy Introduction | demo | [pdf](https://depot.galaxyproject.org/hub/attachments/events/switzerland2014/trainingday/intro_20140930.pdf) | | 9:50 - 10:30 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)) | datatypes, histories, datasets, tools, data sharing | hands-on | | | 10:30 - 11:00 | coffee Break | @@ -38,7 +38,7 @@ Topics covered: | 14:40 - 15:00| coffee Break | | 15:00 - 15:30 | [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | NGS-analaysis: a Chip-Seq example | hands-on | | | 15:30 - 16:00 | [Dannon Baker](/people/dannon-baker/) ([Galaxy Project](http://galaxyproject.org)) | visualizations | hands-on | | -| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | +| 16:00 - 16:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | | | | 16:01 - 16:15 | DEPARTURE (....and going to the pub) | This schedule will most likely change. It will be adapted according to the progress we make during the day @@ -50,7 +50,7 @@ The training day will be held in the [UniS-Building (room: A -119) of the Univer ## Registration -Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you. +Registration is now closed. Please contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) if you want your name to be put on the waiting list. There is a good chance, we can still accommodate you.
diff --git a/content/events/switzerland2016/index.md b/content/events/switzerland2016/index.md index d35eaafd77..9847b36ffb 100644 --- a/content/events/switzerland2016/index.md +++ b/content/events/switzerland2016/index.md @@ -20,7 +20,7 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | Time | Speaker | Title | Slides | | ---- | -------- | ------ | ------- | | 9:15 - 9:30 | ARRIVAL | -| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/src/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | +| 9:30 - 9:45 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/people/bjoern-gruening/) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | | | 9:45 - 10:30 | [Dannon Baker](/people/dannon-baker/) | State of the Galaxy Project - priorities, plans, and community | | | 10:30 - 11:00 | Coffee Break | | 11:00 - 11:20 | Nicola Soranzo | News from the [IUC](/src/iuc/index.md) and the Galaxy tool ecosystem | | @@ -35,7 +35,7 @@ This year, the workshop is aimed at Galaxy administrators and will collocate wit | 15:20 - 15:40 | Nikolay Vazov | Customizing Galaxy for Large Institutions | | | 15:40 - 16:00 | TBA | | | | 16:00 - 17:00 | lightening talks | | | -| 17:00 - 17:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Björn Grüning](/src/people/bjoern-gruening/) | concluding remarks | | +| 17:00 - 17:01 | [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), [Björn Grüning](/people/bjoern-gruening/) | concluding remarks | | | 17:01 - 17:15 | ...going to the pub | @@ -45,4 +45,4 @@ The workshop will be held at the Universität of Freiburg in Germany (see the [m ## Questions? -Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/src/people/bjoern-gruening/) +Contact [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) or [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/events/uga2014/index.md b/content/events/uga2014/index.md index 768a2ca9a1..179ad8aeab 100644 --- a/content/events/uga2014/index.md +++ b/content/events/uga2014/index.md @@ -8,7 +8,7 @@
Introduction to Galaxy
March 7, 2014
-**Instructors
[Carl Eberhard](/people/carl-eberhard/), [Dave Clements](/people/dave-clements/), [Dannon Baker](/src/people/dannon-baker/), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) +**Instructors
[Carl Eberhard](/people/carl-eberhard/), [Dave Clements](/people/dave-clements/), [Dannon Baker](/people/dannon-baker/), and [Raj Ayyampalayam](http://plantbio.uga.edu/directory/raj-ayyampalayam)
[Johns Hopkins University](http://www.jhu.edu/) & [University of Georgia](http://www.uga.edu/) 8:30-17:00
[University of Georgia](http://www.uga.edu/), Athens, GA** diff --git a/content/galaxy-updates/2012-05/index.md b/content/galaxy-updates/2012-05/index.md index bf4cbc8e85..236ea9225c 100644 --- a/content/galaxy-updates/2012-05/index.md +++ b/content/galaxy-updates/2012-05/index.md @@ -38,7 +38,7 @@ Also, if you are interested in presenting a topic, especially a "how to use Gala
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See [Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md) for details and links. diff --git a/content/galaxy-updates/2012-07/index.md b/content/galaxy-updates/2012-07/index.md index 0a7efcc0f2..58723db762 100644 --- a/content/galaxy-updates/2012-07/index.md +++ b/content/galaxy-updates/2012-07/index.md @@ -52,9 +52,9 @@ Welcome to the July 2012 edition of *[Galaxy Update](/src/galaxy-updates/index.m These papers may be of interest to the Galaxy community: -* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. +* ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html), by [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/people/james-taylor/), *Current Protocols in Bioinformatics*. 2012 June: Unit 11.9. -* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. +* ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), by [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/), *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. These papers were among [31 papers added to the Galaxy CiteULike group](http://www.citeulike.org/group/16008/library) since the last [Galaxy Update](/src/galaxy-updates/index.md) (for a total of 348 papers in the last ~16 months). The new papers are spread [across 8 categories](http://www.citeulike.org/group/16008/tags). diff --git a/content/galaxy-updates/2012-09/index.md b/content/galaxy-updates/2012-09/index.md index a8061a3667..aed65bf186 100644 --- a/content/galaxy-updates/2012-09/index.md +++ b/content/galaxy-updates/2012-09/index.md @@ -50,7 +50,7 @@ Welcome to the September 2012 edition of *[Galaxy Update](/src/galaxy-updates/in These papers may be of interest to the Galaxy community: -* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/people/anton/) & [Taylor](/src/people/james-taylor/), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) +* "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)", by [Nekrutenko](/people/anton/) & [Taylor](/people/james-taylor/), *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*, 13, 667-672 (September 2012) * "[IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis](https://doi.org/10.1186/1471-2105-13-S14-S5)", by Merelli, Viti, Milanesi, *BMC Bioinformatics*, Vol. 13, No. Suppl 14. (2011), S5 @@ -190,7 +190,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-10/index.md b/content/galaxy-updates/2012-10/index.md index 759c591f8a..2353f308a6 100644 --- a/content/galaxy-updates/2012-10/index.md +++ b/content/galaxy-updates/2012-10/index.md @@ -156,7 +156,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-11/index.md b/content/galaxy-updates/2012-11/index.md index d458317d74..f4b3b23c0f 100644 --- a/content/galaxy-updates/2012-11/index.md +++ b/content/galaxy-updates/2012-11/index.md @@ -137,7 +137,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2012-12/index.md b/content/galaxy-updates/2012-12/index.md index 7aad571f99..13498e0c17 100644 --- a/content/galaxy-updates/2012-12/index.md +++ b/content/galaxy-updates/2012-12/index.md @@ -45,8 +45,8 @@ These papers may be of interest to the Galaxy community: -* [Enis Afgan](/people/enis-afgan/), Brad Chapman and [James Taylor](/src/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

-* [Jeremy Goecks](/people/jeremy-goecks/), [Nate Coraor](/people/nate/), [The Galaxy Team](/src/galaxy-team/), [Anton Nekrutenko](/people/anton/) & [James Taylor](/src/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

+* [Enis Afgan](/people/enis-afgan/), Brad Chapman and [James Taylor](/people/james-taylor/), "[CloudMan as a platform for tool, data, and analysis distribution](http://www.biomedcentral.com/1471-2105/13/315/abstract)." *[BMC Bioinformatics](http://www.biomedcentral.com/bmcbioinformatics/)* 2012, 13:315

+* [Jeremy Goecks](/people/jeremy-goecks/), [Nate Coraor](/people/nate/), [The Galaxy Team](/src/galaxy-team/), [Anton Nekrutenko](/people/anton/) & [James Taylor](/people/james-taylor/), "[NGS analyses by visualization with Trackster](http://bit.ly/VMUz7p)." *[Nature Biotechnology](http://www.nature.com/nbt/index.html)* 30, 1036–1039 (2012)

* Samantha Baldwin, Roopashree Revanna, Susan Thomson, *et al.*, "[A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)](https://doi.org/10.1186/1471-2164-13-637)," *BMC Genomics*, Vol. 13, No. 1. (2012), 637

* Jeremy C. Morgan, Robert W. Chapman, Paul E. Anderson, "[A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources](https://doi.org/10.1145/2382936.2383033). Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

* Bo Liu, Borja Sotomayor, Ravi Madduri, Kyle Chard, "[Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision](http:// bit.ly/UPBbRI)." [Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012)](http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/) diff --git a/content/galaxy-updates/2013-01/index.md b/content/galaxy-updates/2013-01/index.md index 8f15ea3df2..97431bc7d7 100644 --- a/content/galaxy-updates/2013-01/index.md +++ b/content/galaxy-updates/2013-01/index.md @@ -188,7 +188,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-02/index.md b/content/galaxy-updates/2013-02/index.md index c345df052f..f34dd3945a 100644 --- a/content/galaxy-updates/2013-02/index.md +++ b/content/galaxy-updates/2013-02/index.md @@ -204,7 +204,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-03/index.md b/content/galaxy-updates/2013-03/index.md index 8c96ecf84d..9806f3e51f 100644 --- a/content/galaxy-updates/2013-03/index.md +++ b/content/galaxy-updates/2013-03/index.md @@ -200,7 +200,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-04/index.md b/content/galaxy-updates/2013-04/index.md index fdfe520842..a079245c81 100644 --- a/content/galaxy-updates/2013-04/index.md +++ b/content/galaxy-updates/2013-04/index.md @@ -275,7 +275,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-05/index.md b/content/galaxy-updates/2013-05/index.md index 17228d333c..f07a7f3889 100644 --- a/content/galaxy-updates/2013-05/index.md +++ b/content/galaxy-updates/2013-05/index.md @@ -181,7 +181,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-06/index.md b/content/galaxy-updates/2013-06/index.md index f67d4de7e4..40d4f30223 100644 --- a/content/galaxy-updates/2013-06/index.md +++ b/content/galaxy-updates/2013-06/index.md @@ -193,7 +193,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - + diff --git a/content/galaxy-updates/2013-07/index.md b/content/galaxy-updates/2013-07/index.md index 70fe3dba81..bcf04c4488 100644 --- a/content/galaxy-updates/2013-07/index.md +++ b/content/galaxy-updates/2013-07/index.md @@ -126,7 +126,7 @@ This installation of Galaxy has been configured such that anonymous users can op A record 53 new papers were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in June. These papers may be particularly interesting to the Galaxy community -* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/), [Carl Eberhard](/people/carl-eberhard/), Tomithy Too, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 +* "[Web-based visual analysis for high-throughput genomics](https://doi.org/10.1186/1471-2164-14-397)" by [Jeremy Goecks](/people/jeremy-goecks/), [Carl Eberhard](/people/carl-eberhard/), Tomithy Too, [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/), *BMC Genomics*, Vol. 14, No. 1. (2013), 397 * "[Detection of non-coding RNA in Bacteria and Archaea using the DETR’PROK Galaxy pipeline](https://doi.org/10.1016/j.ymeth.2013.06.003)" by Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret, *[Methods](http://www.sciencedirect.com/science/journal/10462023)* (June 2013) * "[Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data](https://doi.org/10.1002/gepi.21739)" by Nicholas A. Davis, Caleb A. Lareau, Bill C. White, *et al.* *Genetic Epidemiology* (June 2013) * "[A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America](https://doi.org/10.1093/bib/bbt033)" by Allan Orozco, Jessica Morera, Sergio Jiménez, Ricardo Boza, *Briefings in Bioinformatics* (30 May 2013) @@ -368,7 +368,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the - +
Instructors Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University 		Dannon Baker, Johns Hopkins University
Carl Eberhard, Johns Hopkins University
Content Wednesday July 11 OpenBio Codefest 2012 All Day Enis Afgan and Dannon Baker of the the Galaxy Team will participate. Enis Afgan and Dannon Baker of the the Galaxy Team will participate. Report
November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization November 6-10 Galaxy 101: Data Integration, Analysis and Sharing American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization November 6-10 Galaxy 101: Data Integration, Analysis and Sharing
Sold out
 American Society of Human Genetics (ASHG), San Francisco, California, United States Jennifer Jackson, Jeremy Goecks Jennifer Jackson, Jeremy Goecks
Working with High-Throughput Data and Data Visualization
Sold out
 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 30 - July 2 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 13-14 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 9-13 June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan Anton Nekrutenko, Enis Afgan
June 9-13 October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States James Taylor, Jennifer Jackson James Taylor, Jennifer Jackson
diff --git a/content/galaxy-updates/2013-08/index.md b/content/galaxy-updates/2013-08/index.md index 143893cd23..e4c71adc71 100644 --- a/content/galaxy-updates/2013-08/index.md +++ b/content/galaxy-updates/2013-08/index.md @@ -233,7 +233,7 @@ Galaxy had a strong presence at [ISMB / ECCB 2013](http://www.iscb.org/ismbeccb2 October 22-26 High Throughput Data Analysis and Visualization with Galaxy ASHG 2013, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson diff --git a/content/galaxy-updates/2013-09/index.md b/content/galaxy-updates/2013-09/index.md index 1037fecb94..47fb6fa479 100644 --- a/content/galaxy-updates/2013-09/index.md +++ b/content/galaxy-updates/2013-09/index.md @@ -224,7 +224,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll pu High Throughput Data Analysis and Visualization with Galaxy' - Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson January 11-15 diff --git a/content/galaxy-updates/2013-10/index.md b/content/galaxy-updates/2013-10/index.md index 904ca63942..4800446485 100644 --- a/content/galaxy-updates/2013-10/index.md +++ b/content/galaxy-updates/2013-10/index.md @@ -327,7 +327,7 @@ And don't worry, you won't have to travel to Australia during its spring just to October 22 Analyzing NGS Data with Galaxy Dana-Farber Cancer Institute, Boston, Massachusetts, United States - Anton Nekrutenko, Jennifer Jackson, Anushka Brownley + Anton Nekrutenko, Jennifer Jackson, Anushka Brownley October 22-26 @@ -337,7 +337,7 @@ And don't worry, you won't have to travel to Australia during its spring just to High Throughput Data Analysis and Visualization with Galaxy
This workshop is sold out.
- Anton Nekrutenko, Jennifer Jackson + Anton Nekrutenko, Jennifer Jackson Poster 1633T: Globus Genomics: Enabling high-throughput analysis and management of NGS data for neurodevelopmental disorders diff --git a/content/galaxy-updates/2013-11/index.md b/content/galaxy-updates/2013-11/index.md index 7dfe3f8bf2..f901656a85 100644 --- a/content/galaxy-updates/2013-11/index.md +++ b/content/galaxy-updates/2013-11/index.md @@ -97,7 +97,7 @@ And ... ## Ten Simple Rules for Reproducible Computational Research -[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October. +[Geir Kjetil Sandve](http://www.mn.uio.no/ifi/english/people/aca/geirksa/), [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/), and [Eivind Hovig](http://www.mn.uio.no/ifi/english/people/aca/ehovig/index.html)'s paper "[Ten Simple Rules for Reproducible Computational Research](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285)" was published in *[PLoS Computational Biology](http://www.ploscompbiol.org/)* in October.
PLoS Computational Biology: Ten Simple Rules for Reproducible Computational Research
diff --git a/content/galaxy-updates/2014-01/index.md b/content/galaxy-updates/2014-01/index.md index 0aaa423eca..0429bc8374 100644 --- a/content/galaxy-updates/2014-01/index.md +++ b/content/galaxy-updates/2014-01/index.md @@ -306,7 +306,7 @@ The [2013 Galaxy Day event](http://wiki.sb-roscoff.fr/ifb/index.php/Accueil) too March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 diff --git a/content/galaxy-updates/2014-02/index.md b/content/galaxy-updates/2014-02/index.md index 377f466e72..ad7ff07f91 100644 --- a/content/galaxy-updates/2014-02/index.md +++ b/content/galaxy-updates/2014-02/index.md @@ -217,7 +217,7 @@ GMOD Malaysia 2014 is made possible by the generous support of the [National Evo March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson May 27 @@ -381,7 +381,7 @@ bringing the number of log entries to 12. # Galaxy is now at Johns Hopkins and GWU (and Penn State!) -In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/galaxy-team/) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/src/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. +In case you haven't heard, the former [Emory University](http://emory.edu) contingent of the [Galaxy Team](/galaxy-team/) went north this month to Baltimore - it's warmer there (at least this week), where [James Taylor](/people/james-taylor/) is now an Associate Professor in the [Johns Hopkins](http://www.johnshopkins.edu/) [Biology](http://www.bio.jhu.edu/) and [Computer Science](http://www.cs.jhu.edu/) Departments. [Jeremy Goecks](/people/jeremy-goecks/), also formerly of the Emory University contingent is now an Assistant Professor of [Computational Biology](http://cbi.gwu.edu/) at [George Washington University](http://www.gwu.edu/) in the Washington DC area. None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are [still hiring](/src/galaxy-is-hiring/index.md), but now at three universities instead of two. diff --git a/content/galaxy-updates/2014-03/index.md b/content/galaxy-updates/2014-03/index.md index a4cf546550..22d5a8717b 100644 --- a/content/galaxy-updates/2014-03/index.md +++ b/content/galaxy-updates/2014-03/index.md @@ -9,7 +9,7 @@ Welcome to the March 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *54 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in Febrary. Some papers that may be particularly interesting to the Galaxy community: -* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/src/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/src/people/james-taylor/) and [Nekrutenko](/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 +* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/people/james-taylor/) and [Nekrutenko](/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 * [Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis](https://doi.org/10.1371/journal.pone.0087301), by Khushi, *et al.,* *PLoS ONE*, Vol. 9, No. 2. (12 February 2014), e87301, doi:10.1371/journal.pone.0087301 @@ -188,7 +188,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States - Anton Nekrutenko, Jen Jackson + Anton Nekrutenko, Jen Jackson April 15-17 @@ -287,7 +287,7 @@ In 2014 we are also adding [non-sponsor exhibit spaces](/src/events/gcc2014/spon September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-05/index.md b/content/galaxy-updates/2014-05/index.md index c7048add29..46c6ae2d0e 100644 --- a/content/galaxy-updates/2014-05/index.md +++ b/content/galaxy-updates/2014-05/index.md @@ -41,7 +41,7 @@ Galaxy Biostar was launched on April 23. We hope you like the change and look f *47 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in April. Some papers that may be particularly interesting to the Galaxy community: -* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/people/dan/) and [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 +* "[Analysis of Next-Generation Sequencing Data Using Galaxy](https://doi.org/10.1007/978-1-4939-0512-6_2)," [Daniel Blankenberg](/people/dan/) and [Jennifer Hillman-Jackson](/people/jennifer-jackson/), *Stem Cell Transcriptional Networks*, Vol. 1150 (2014), pp. 21-43, doi:10.1007/978-1-4939-0512-6_2 * "[Support for data-intensive computing with CloudMan](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6596260)," Yousef Kowsar and [Enis Afgan](/people/enis-afgan/), *[Information & Communication Technology Electronics & Microelectronics (MIPRO), 2013 36th International Convention on](http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6588635),* (May 2013), pp. 243-248 diff --git a/content/galaxy-updates/2014-07/index.md b/content/galaxy-updates/2014-07/index.md index 9b972a1bad..2de91f3e71 100644 --- a/content/galaxy-updates/2014-07/index.md +++ b/content/galaxy-updates/2014-07/index.md @@ -116,7 +116,7 @@ Over the rest of the summer there are other [Galaxy related events](/src/events/ September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-08/index.md b/content/galaxy-updates/2014-08/index.md index 6ef62ad2a0..d8409d677d 100644 --- a/content/galaxy-updates/2014-08/index.md +++ b/content/galaxy-updates/2014-08/index.md @@ -201,7 +201,7 @@ Over the rest of the few months there are many [Galaxy related events](/src/even September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-09/index.md b/content/galaxy-updates/2014-09/index.md index 31b2ced88f..524ae8cd25 100644 --- a/content/galaxy-updates/2014-09/index.md +++ b/content/galaxy-updates/2014-09/index.md @@ -94,7 +94,7 @@ These events are a great way to meet other Galaxy users and developers and learn September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2014-10/index.md b/content/galaxy-updates/2014-10/index.md index a43551a3d3..b006afb928 100644 --- a/content/galaxy-updates/2014-10/index.md +++ b/content/galaxy-updates/2014-10/index.md @@ -61,7 +61,7 @@ There are [upcoming events](/src/events/index.md) in Switzerland, Germany, Austr September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening (second Swiss) Galaxy Workshop diff --git a/content/galaxy-updates/2015-02/index.md b/content/galaxy-updates/2015-02/index.md index 7459a3ef94..e281a44e08 100644 --- a/content/galaxy-updates/2015-02/index.md +++ b/content/galaxy-updates/2015-02/index.md @@ -19,11 +19,11 @@ Welcome to the February *[Galaxy Update](/src/galaxy-updates/index.md)*, a summa 55 new papers referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in January. Some highlights: * [Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines](https://doi.org/10.1002/cam4.360) - [Jeremy Goecks](/people/jeremy-goecks/), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/src/people/james-taylor/), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 + [Jeremy Goecks](/people/jeremy-goecks/), Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, [James Taylor](/people/james-taylor/), Michael R. Rossi, *Cancer Medicine* (December 2014), doi:10.1002/cam4.360 * [Merging OpenLifeData with SADI services using Galaxy and Docker](http://www.biorxiv.org/content/biorxiv/early/2015/01/10/013615) Mikel E. Aranguren, *bioRxiv* * [NCBI BLAST+ integrated into Galaxy](http://www.biorxiv.org/content/early/2015/01/21/014043) - Peter J. A. Cock, [John M. Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), James E. Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/), *bioRxiv* + Peter J. A. Cock, [John M. Chilton](/people/john-chilton/), [Björn Grüning](/people/bjoern-gruening/), James E. Johnson, [Nicola Soranzo](/people/nicola-soranzo/), *bioRxiv* * [SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations](http://www.gigasciencejournal.com/content/4/1/1/abstract) Wilfried M Guiblet, Kai Zhao, Stephen J O'Brien, Steven E Massey, Alfred L Roca and Taras K Oleksyk, *[GigaScience](http://www.gigasciencejournal.com/)* 2015, 4:1
[Supplementary materials](http://gigagalaxy.net/u/gigascience/g/wguiblet2014) (as a Galaxy Page) @@ -174,7 +174,7 @@ The [first Baltimore Area Galaxy meetup](/src/events/meetups/baltimore/2015-01-2 The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore. -[Enis Afgan](/people/enis-afgan/) & [Nitesh Turaga](/src/people/nitesh-turaga/) +[Enis Afgan](/people/enis-afgan/) & [Nitesh Turaga](/people/nitesh-turaga/) ## Other Events @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 5 countries on 4 continents February 19 February 2015 GalaxyAdmins Web Meetup Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements @@ -463,20 +463,20 @@ In no particular order: * [snpsift_dbnsfp_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_datatypes): Galaxy applicable data formats for SnpSift. snpsift_dbnsfp tool Allows for the creation of a snpsift dbnsfp Galaxy dataset from a tabular file that can be used by SnpSift dbnsfp to annotate a vcf formatted file. * [snpeff_datatypes](https://toolshed.g2.bx.psu.edu/view/iuc/snpeff_datatypes): Galaxy applicable data formats for SnpEff tools Galaxy applicable data formats for SnpEff tools. The snpeffdb datatype provides the means to represent a SnpEff genome database in a Galaxy dataset. * [snpsift_dbnsfp](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp): snpEff SnpSift dbnsfp tool from Pablo Cingolani Annotates variants on genes using the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.) http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift): snpEff SnpSift tools from Pablo Cingolani Variant annotation and effect prediction tools. It annotates and predicts the effects of variants on genes. This repository should manage tool dependencies. There are data managers for the Galaxy admin to download genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed /
* [snpsift_genesets](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_genesets): snpEff SnpSift genesets tool from Pablo Cingolani Annotates variants with GeneSets, such as Gene Ontology (GO), KEGG, Reactome, etc.; http://snpeff.sourceforge.net/SnpSift.html#geneSets !SnpEff and !SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * [snpsift_dbnsfp_generic](https://toolshed.g2.bx.psu.edu/view/iuc/snpsift_dbnsfp_generic): snpEff SnpSift dbnsfp tool that can use any dbnsfp-like annotation data Annotates variants on genes using a tabular set of annotation values such as those from the dbNSFP, an integrated database of human functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.)
This tool determines the available annotations from the input, so it can be used for other organisms other than human or other annotation values than available from dbNSFP. http://snpeff.sourceforge.net[/SnpSift](/src/galaxy-updates/2015-02/SnpSift/index.md).html#dbNSFP
SnpEff and SnpSift are developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ * *From [amawla](https://toolshed.g2.bx.psu.edu/view/amawla):* @@ -532,7 +532,7 @@ In no particular order: * *From [iuc](https://toolshed.g2.bx.psu.edu/view/iuc/): * * [data_manager_snpeff](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_snpeff): Manage SnpEff genome reference data Data managers for the Galaxy admin to download SnpEff genome databases. SnpEff is developed by Pablo Cingolani at http://snpeff.sourceforge.net/
- Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/src/people/nicola-soranzo/)
+ Repository-Maintainer: [Björn Grüning](/people/bjoern-gruening/), Jim Johnson, [Nicola Soranzo](/people/nicola-soranzo/)
Repository-Development: https://github.com/galaxy-iuc/tool_shed/ ### Packages / Tool Dependency Definitions diff --git a/content/galaxy-updates/2015-04/index.md b/content/galaxy-updates/2015-04/index.md index da9b426960..a23364c704 100644 --- a/content/galaxy-updates/2015-04/index.md +++ b/content/galaxy-updates/2015-04/index.md @@ -208,7 +208,7 @@ There are [upcoming events](/src/events/index.md) in 8 countries on 4 continents April 16 GalaxyAdmins April 2015 Meetup Online - Hans-Rudolf Hotz, Dave Clements, Carrie Ganote + Hans-Rudolf Hotz, Dave Clements, Carrie Ganote April 20-21 @@ -493,7 +493,7 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) +[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/people/helena-rasche/) ## Planemo 0.6.0 diff --git a/content/galaxy-updates/2015-09/index.md b/content/galaxy-updates/2015-09/index.md index a73f6b7b0e..935294739b 100644 --- a/content/galaxy-updates/2015-09/index.md +++ b/content/galaxy-updates/2015-09/index.md @@ -248,7 +248,7 @@ There are [upcoming events](/src/events/index.md) in five countries on three con october 15 October Galaxy Admins Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements October 19 diff --git a/content/galaxy-updates/2015-10/index.md b/content/galaxy-updates/2015-10/index.md index 73950652ce..ad22fba0b2 100644 --- a/content/galaxy-updates/2015-10/index.md +++ b/content/galaxy-updates/2015-10/index.md @@ -223,7 +223,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents October 15 October Galaxy Admins Meetup Around the World Online - David Kovalic, Hans-Rudolf Hotz, Dave Clements + David Kovalic, Hans-Rudolf Hotz, Dave Clements October 28-29 @@ -245,7 +245,7 @@ There are [upcoming events](/src/events/index.md) in 4 countries on 4 continents November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Anton Nekrutenko, James Taylor + Training offered by GTN Member Anton Nekrutenko, James Taylor Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations Workshop @@ -395,7 +395,7 @@ Thanks to everyone who helped put these together. **Release Highlights ** * **Interactive Environments** - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by [Helena Rasche](/people/helena-rasche/). * **Workflow Editor Enhancements** - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections. -* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/people/bjoern-gruening/), [Nicola Soranzo](/people/nicola-soranzo/), and [Helena Rasche](/src/people/helena-rasche/). +* **Policies for Committers and Pull Requests** - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - [Björn Grüning](/people/bjoern-gruening/), [Nicola Soranzo](/people/nicola-soranzo/), and [Helena Rasche](/people/helena-rasche/). * And *[much more](http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html)* ## Mid 2015 Galaxy CloudMan Release diff --git a/content/galaxy-updates/2015-11/index.md b/content/galaxy-updates/2015-11/index.md index 0424695297..eafe99e546 100644 --- a/content/galaxy-updates/2015-11/index.md +++ b/content/galaxy-updates/2015-11/index.md @@ -205,7 +205,7 @@ There are [upcoming events](/src/events/index.md) on 3 continents in 4 countries November 3 Galaxy for the Analysis of Very Large Biomedical Data Workshop North America Festival of Genomics California, San Mateo, California, United States - Training offered by GTN Member Dan Blankenberg, John Chilton + Training offered by GTN Member Dan Blankenberg, John Chilton Common Workflow Language on Galaxy
Part of Portable Bioinformatics Workshop diff --git a/content/galaxy-updates/2016-02/index.md b/content/galaxy-updates/2016-02/index.md index c25c2002c7..a36af6e5ec 100644 --- a/content/galaxy-updates/2016-02/index.md +++ b/content/galaxy-updates/2016-02/index.md @@ -215,7 +215,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. February 18 GalaxyAdmins Web Meetup Around the World Online - Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements + Marius van den Beek, Nate Coraor,Hans-Rudolf Hotz, Dave Clements February 20-23 diff --git a/content/galaxy-updates/2016-04/index.md b/content/galaxy-updates/2016-04/index.md index e79790c38c..f39a724da8 100644 --- a/content/galaxy-updates/2016-04/index.md +++ b/content/galaxy-updates/2016-04/index.md @@ -175,7 +175,7 @@ There are [many upcoming events](/src/events/index.md) in the next few months. April 21 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements April 22-26 diff --git a/content/galaxy-updates/2016-05/index.md b/content/galaxy-updates/2016-05/index.md index 0bdf3cf0cc..da9a083074 100644 --- a/content/galaxy-updates/2016-05/index.md +++ b/content/galaxy-updates/2016-05/index.md @@ -262,7 +262,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth June 16 GalaxyAdmins Web Meetup Around the World Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 25-29 @@ -464,11 +464,11 @@ Variant calling is a complex field that was significantly propelled by advances
Reference based RNA seq
-Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). +Much of Galaxy-related features described in this tutorial have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Reference based RNA seq -**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/src/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). +**[This tutorial](https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq)** is inspired by an [exceptional RNAseq course](http://chagall.med.cornell.edu/RNASEQcourse/) at the Weill Cornell Medical College compiled by Friederike Dündar, Luce Skrabanek, and Paul Zumbo and by tutorials produced by Björn Grüning (@bgruening) for Freiburg Galaxy instance. Much of Galaxy-related features described in this section have been developed by [Björn Grüning](/people/bjoern-gruening/) ([@bgruening](https://github.com/bgruening)) and configured by [Dave Bouvier](/people/dave-bouvier/) ([@davebx](https://github.com/davebx)). ## Dataset Collections diff --git a/content/galaxy-updates/2016-06/index.md b/content/galaxy-updates/2016-06/index.md index a53a84ca8e..8e179e97c3 100644 --- a/content/galaxy-updates/2016-06/index.md +++ b/content/galaxy-updates/2016-06/index.md @@ -175,7 +175,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md June 16 Galaxy in Production at the University of Minnesota Around the World GalaxyAdmins Web Meetup, Online - Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements + Evan Bollig, JJ Johnson, Hans-Rudolf Hotz, Dave Clements June 20 diff --git a/content/galaxy-updates/2016-07/index.md b/content/galaxy-updates/2016-07/index.md index 850654d7e7..58f5cafc30 100644 --- a/content/galaxy-updates/2016-07/index.md +++ b/content/galaxy-updates/2016-07/index.md @@ -185,7 +185,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -227,13 +227,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-08/index.md b/content/galaxy-updates/2016-08/index.md index e73576ae6d..ae16b1c7dc 100644 --- a/content/galaxy-updates/2016-08/index.md +++ b/content/galaxy-updates/2016-08/index.md @@ -92,7 +92,7 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md August 18 GalaxyAdmins Web Meetup Around the World Online - Hans-Rudolf Hotz, Dave Clements + Hans-Rudolf Hotz, Dave Clements August 29 - September 2 @@ -152,13 +152,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening diff --git a/content/galaxy-updates/2016-09/index.md b/content/galaxy-updates/2016-09/index.md index ebea1cd662..8b587e2540 100644 --- a/content/galaxy-updates/2016-09/index.md +++ b/content/galaxy-updates/2016-09/index.md @@ -154,13 +154,13 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Tour in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening @@ -266,7 +266,7 @@ Some highlights from last month: Matt Chambers. * **[CloudBridge: a Simple Cross-Cloud Python Library](https://s3.amazonaws.com/cloudbridgelib/CloudBridge.pdf)** - Nuwan Goonasekera, Andrew Lonie, [James Taylor](/people/james-taylor/), [Enis Afgan](/src/people/enis-afgan/). XSEDE16. + Nuwan Goonasekera, Andrew Lonie, [James Taylor](/people/james-taylor/), [Enis Afgan](/people/enis-afgan/). XSEDE16. * **[DISMISS: detection of stranded methylation in MeDIP-Seq data](http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1158-7)** Umar Niazi, Kathrin K Geyer, Martin J Vickers, Karl F Hoffmann, Martin T Swain. *BMC Bioinformatics*, Vol. 17, No. 1. (2016), pp. 1-12, doi:10.1186/s12859-016-1158-7 diff --git a/content/galaxy-updates/2016-10/index.md b/content/galaxy-updates/2016-10/index.md index c76932e8f0..d5f44383aa 100644 --- a/content/galaxy-updates/2016-10/index.md +++ b/content/galaxy-updates/2016-10/index.md @@ -217,19 +217,19 @@ There are [a plentitude of Galaxy related events coming up](/src/events/index.md October 20 (third Swiss) Galaxy Workshop Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 21 (second German) Galaxy Developers Day Europe 2016 Swiss-German Galaxy Days in Freiburg, Germany - Hans-Rudolf Hotz and Bjoern Gruening + Hans-Rudolf Hotz and Bjoern Gruening October 24-27 The Galaxy tool lifecycle supporting reproducibility in scientific research Europe NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics, Rome, Italy - Dannon Baker, Björn Grüning + Dannon Baker, Björn Grüning @@ -361,7 +361,7 @@ Some highlights from last month: Annette McGrath, Steve McMahon, Sean Li, Joel Ludbey, Tim Ho. *Journal of Grid Computing* (2016), pp. 1-11, doi:10.1007/s10723-016-9379-6 **[Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter](http://biorxiv.org/content/early/2016/09/22/075457)** - [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 + [Björn Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nathan Coraor](/people/nate/), Rolf Backofen, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *bioRxiv* (16 September 2016), 075457, doi:10.1101/075457 **[Genotyping of evolving prokaryotic populations](https://doi.org/10.7287/peerj.preprints.2449v1)** Markus Zojer, Lisa N. Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei. *PeerJ Preprints* (14 September 2016), doi:10.7287/peerj.preprints.2449v1 diff --git a/content/galaxy-updates/2016-12/index.md b/content/galaxy-updates/2016-12/index.md index 937d2b2201..8c0f4f586a 100644 --- a/content/galaxy-updates/2016-12/index.md +++ b/content/galaxy-updates/2016-12/index.md @@ -100,13 +100,13 @@ There are [a plenitude of Galaxy related events coming up](/src/events/index.md) December 8 The Community Hub Contribution Convergence (CHCC) Around the world Online - Dannon Baker, Dave Clements + Dannon Baker, Dave Clements December 15 Galaxy Training Materials: Community creation, curation, and use and The new Galaxy Hub: Community creation, curation, and use Online Online - Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements + Björn Grüning, Bérénice Batut, Dannon Baker and Dave Clements December 15-16 @@ -180,7 +180,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on oth Some highlights from last month: -* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) +* [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://f1000research.com/articles/5-2757/v1), [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Galaxy Team](/src/galaxy-team), [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/), *F1000Research* 2016, 5:2757 (doi: 10.12688/f1000research.9821.1) * [How Are You – and How’s Your Microbiome?](https://theanalyticalscientist.com/issues/1116/how-are-you-and-hows-your-microbiome/), Pratik Jagtap, *The Analytical Scientist*, November 2016 * [Computational workflow for the fine-grained analysis of metagenomic samples](https://doi.org/10.1186/s12864-016-3063-x), Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles, *BMC Genomics*, Vol. 17, No. S8. (25 October 2016), doi:10.1186/s12864-016-3063-x * [Big Data Smart Socket (BDSS): A System that Abstracts Data Transfer Habits from End Users](https://doi.org/10.1093/bioinformatics/btw679), Nick A. Watts, Frank A. Feltus, *Bioinformatics* (26 October 2016), btw679, doi:10.1093/bioinformatics/btw679 diff --git a/content/galaxy-updates/2017-06/index.md b/content/galaxy-updates/2017-06/index.md index d878e89aba..3c7d3df353 100644 --- a/content/galaxy-updates/2017-06/index.md +++ b/content/galaxy-updates/2017-06/index.md @@ -31,7 +31,7 @@ If you missed the May 31 regular registration deadline then don't worry because **The Galaxy Project: from the Planck epoch to Montpellier** -[Dr. Anton Nekrutenko](/people/anton/) and [Dr. James Taylor](/src/people/james-taylor/) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. +[Dr. Anton Nekrutenko](/people/anton/) and [Dr. James Taylor](/people/james-taylor/) will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017. If you are reading this, you probably already know who they are. If not, see their [bios here](https://gcc2017.sciencesconf.org/). @@ -211,7 +211,7 @@ Some highlights from the papers added last month: *Nucleic Acids Research* (02 May 2017), doi:10.1093/nar/gkx315 * [Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers](https://doi.org/10.1371/journal.pcbi.1005425) - [Björn A. Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 + [Björn A. Grüning](/people/bjoern-gruening/), [Helena Rasche](/people/helena-rasche/), Boris Rebolledo-Jaramillo, [Carl Eberhard](/people/carl-eberhard/), Torsten Houwaart, [John Chilton](/people/john-chilton/), [Nate Coraor](/people/nate/), Rolf Backofen, [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/). *PLOS Computational Biology*, Vol. 13, No. 5. (25 May 2017), e1005425, doi:10.1371/journal.pcbi.1005425 * [MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization](https://doi.org/10.1093/bioinformatics/btx320) Katherine M. McCoy, Margaret L. Antonio, Tim van Opijnen. *Bioinformatics* (11 May 2017), doi:10.1093/bioinformatics/btx320 diff --git a/content/galaxy-updates/2017-09/index.md b/content/galaxy-updates/2017-09/index.md index b309296e61..2b0b488af5 100644 --- a/content/galaxy-updates/2017-09/index.md +++ b/content/galaxy-updates/2017-09/index.md @@ -17,7 +17,7 @@ Welcome to the September 2017 *[Galactic News](/src/galaxy-updates/index.md)*, a Some highlights from the recently added pubs: * [2017 Galaxy community update](https://doi.org/10.7490/f1000research.1114388.1) - [Dan Blankenberg](/people/dan/), [Jeremy Goecks](/src/people/jeremy-goecks/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 + [Dan Blankenberg](/people/dan/), [Jeremy Goecks](/people/jeremy-goecks/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114388.1 * [Approaches for small RNA-seq in Galaxy](https://doi.org/10.7490/f1000research.1114423.1) Mallory Freeberg, [James Taylor](/people/james-taylor/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114423.1 @@ -26,7 +26,7 @@ Some highlights from the recently added pubs: Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis. *GigaScience*, Vol. 6, No. 8. (August 2017), pp. 1-7, doi:10.1093/gigascience/gix048 * [Building an open, collaborative, online infrastructure for bioinformatics training](https://doi.org/10.7490/f1000research.1114447.1) - Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/people/dave-clements/), [Björn Grüning](/src/people/bjoern-gruening/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 + Bérénice Batut, [Galaxy Training Network](https://training.galaxyproject.org/), [Dave Clements](/people/dave-clements/), [Björn Grüning](/people/bjoern-gruening/). *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114447.1 * [Galaxy-compatible Tool for Rapid Aptamer Clustering and HT-SELEX Data Analysis](https://doi.org/10.22377/ajp.v11i02.1265) Nikita A. Skrylnik, *Asian Journal of Pharmaceutics (AJP)*, Vol. 11, No. 02. (2017), doi:10.22377/ajp.v11i02.1265 @@ -56,7 +56,7 @@ Some highlights from the recently added pubs: Chao Zhang, Jochem Bijlard, Christine Staiger, et al. *F1000Research*, Vol. 6 (16 August 2017), 1488, doi:10.12688/f1000research.12168.1 * [The backbone of research reproducibility-sustainable and flexible tool deployment](https://doi.org/10.7490/f1000research.1114482.1) - [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/src/people/john-chilton/), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 + [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Dale Ryan, Yasset Perez-Riverol. *F1000Research* In Bioinformatics Open Source Conference 2017, Vol. 6 (2017), doi:10.7490/f1000research.1114482.1 * [ToolDog-generating tool descriptors from the ELIXIR tool registry](https://doi.org/10.7490/f1000research.1114473.1) Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison, Hervé Ménager. *F1000Research* In 2017 Galaxy Community Conference, Vol. 6 (2017), doi:10.7490/f1000research.1114473.1 diff --git a/content/galaxy-updates/2018-02/index.md b/content/galaxy-updates/2018-02/index.md index 693d10e3ea..d4be9e5741 100644 --- a/content/galaxy-updates/2018-02/index.md +++ b/content/galaxy-updates/2018-02/index.md @@ -88,7 +88,7 @@ morning session will include presentations on genomic and metagenomic data analy [Galaxy Administrators Course](https://github.com/galaxyproject/dagobah-training)
-A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/people/bjoern-gruening/) and [Enis Afgan](/src/people/enis-afgan/) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. +A very successful and inspiring Galaxy admin workshop was held in Oslo in January, Thanks to 33 highly motivated participants and Nicola Soranzo, Marius Van Den Beek, Abdulrahman Azab, [Björn Grüning](/people/bjoern-gruening/) and [Enis Afgan](/people/enis-afgan/) as instructors! Thanks also to [ELIXIR](https://www.elixir-europe.org/), [de.NBI](https://www.denbi.de/), and [ELIXIR Norway](https://www.elixir-europe.org/about-us/who-we-are/nodes/norway) for sponsoring this event. Plenty of materials for Galaxy administration are now [up to date and available online](https://github.com/galaxyproject/dagobah-training). The workshop included a sneak [preview of what's coming in the 18.01 release](https://galaxyproject.github.io/dagobah-training/2018-oslo/whatsnew/18.01.html#1) from [Nate Coraor](/people/nate/). diff --git a/content/galaxy-updates/2018-08/index.md b/content/galaxy-updates/2018-08/index.md index 7027a76390..8b9727bc7d 100644 --- a/content/galaxy-updates/2018-08/index.md +++ b/content/galaxy-updates/2018-08/index.md @@ -300,19 +300,19 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t This included a new paper to reference [whenever using, extending, or referencing Galaxy](/src/citing-galaxy/index.md#primary-publication): -* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 +* [**The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update**](https://doi.org/10.1093/nar/gky379), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Vahid Jalili](/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/people/jeremy-goecks/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379 A new paper to reference [when discussing Galaxy in the context of reproducibility](/src/citing-galaxy/index.md#reproducibility): -* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/src/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 +* [**Practical Computational Reproducibility in the Life Sciences**](https://doi.org/10.1016/j.cels.2018.03.014), [Björn Grüning](/people/bjoern-gruening/), [John Chilton](/people/john-chilton/), Johannes Köster, Ryan Dale, Nicola Soranzo, [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Jeremy Goecks](/people/jeremy-goecks/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 631-635, doi:10.1016/j.cels.2018.03.014 And a new paper to reference [when discussing Galaxy training](/src/citing-galaxy/index.md#training): -* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 +* [**Community-Driven Data Analysis Training for Biology**](https://doi.org/10.1016/j.cels.2018.05.012), [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/people/bjoern-gruening/). *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1 And a new paper to cite [when discussing Galaxy in a cloud context](/src/citing-galaxy/index.md#cloud): -* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/src/people/james-taylor/), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 +* [**CloudLaunch: Discover and deploy cloud applications**](https://doi.org/10.1016/j.future.2018.04.037), [Enis Afgan](/people/enis-afgan/), Andrew Lonie, [James Taylor](/people/james-taylor/), Nuwan Goonasekera. *Future Generation Computer Systems*, 2018, doi:10.1016/j.future.2018.04.037 Other highlighted papers include: diff --git a/content/news/201502-galaxy-admins/index.md b/content/news/201502-galaxy-admins/index.md index 921fb4715d..ec4679d6ed 100644 --- a/content/news/201502-galaxy-admins/index.md +++ b/content/news/201502-galaxy-admins/index.md @@ -6,10 +6,10 @@ date: "2015-01-28" The first [GalaxyAdmins](/src/community/galaxy-admins/index.md) [meetup of 2015](/src/community/galaxy-admins/meetups/2015-02-19/index.md) will happen online [on Thursday, 19 February](http://bit.ly/1yZJSkN). [GalaxyAdmins](/src/community/galaxy-admins/index.md) is a special interest group for Galaxy community members who are responsible for Galaxy installations. -A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/), and [Hans-Rudolf Hotz](/src/people/hansrudolf-hotz/) will lead a short discussion on *GalaxyAdmins direction*. +A summary of both the user and admin/developer [2014 Galaxy Community Questionnaires](/src/news/2014-questionnaire/index.md) will be presented by [Dave Clements](/people/dave-clements/), a *Galaxy Project Update* will be offered by a [Galaxy Team member](/src/galaxy-team/), and [Hans-Rudolf Hotz](/people/hansrudolf-hotz/) will lead a short discussion on *GalaxyAdmins direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. We are looking forward to starting this group again, -[Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/src/people/dave-clements/) +[Hans-Rudolf Hotz](/people/hansrudolf-hotz/) and [Dave Clements](/people/dave-clements/) diff --git a/content/news/2018-12-galaxy-admins/index.md b/content/news/2018-12-galaxy-admins/index.md index b4b182ef3a..340c4f310e 100644 --- a/content/news/2018-12-galaxy-admins/index.md +++ b/content/news/2018-12-galaxy-admins/index.md @@ -13,14 +13,14 @@ Got some ideas? **[Nominate them](https://docs.google.com/forms/d/e/1FAIpQLSfv25 We hope to see you in February, -[Helena Rasche](/people/helena-rasche/) and [Dave Clements](/src/people/dave-clements/) +[Helena Rasche](/people/helena-rasche/) and [Dave Clements](/people/dave-clements/)
Q: Why did the bimonthly meetups go away for *two years?*

-A: In early 2017, [Hans-Rudolf](/people/hansrudolf-hotz/) stepped down after several years of leading the group. [Dave C](/people/dave-clements/) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/src/people/helena-rasche/) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.* +A: In early 2017, [Hans-Rudolf](/people/hansrudolf-hotz/) stepped down after several years of leading the group. [Dave C](/people/dave-clements/) *promised* Hans-Rudolf that he would keep these going. But then, Dave saw something shiny, and then, a while later, he heard [Helena](/people/helena-rasche/) calling, as if from a great distance, saying "I want those GalaxyAdmins meetups again." And so *they are back*, with Helena leading us fearlessly into the future.*

diff --git a/content/news/2019-01-galaxy-update/index.md b/content/news/2019-01-galaxy-update/index.md index 05539a2f14..8b217199ae 100644 --- a/content/news/2019-01-galaxy-update/index.md +++ b/content/news/2019-01-galaxy-update/index.md @@ -212,11 +212,11 @@ These and [other Galaxy related events](/src/events/index.md) are coming up in t *[Galactic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BGalactic)* and *[Stellar](https://www.zotero.org/groups/1732893/galaxy/tags/%2BStellar)* publications from December: -* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/src/people/bjoern-gruening/), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; +* **[Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud](https://doi.org/10.1101/488643)**, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, [Enis Afgan](/people/enis-afgan/), Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf J.M. Weber, [Bjoern Gruening](/people/bjoern-gruening/), Reza Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann, *bioRxiv* 488643; doi: 10.1101/488643 * **[PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud](https://doi.org/10.1093/gigascience/giy149)**, Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, [Pablo Moreno](/src/blog/2018-08-cotm-pablo-moreno/index.md), Steffen Neumann, Jon Ander Novella, Claire O'Donovan, Jake T M Pearce, Alina Peluso, Marco Enrico Piras, Luca Pireddu, Michelle A C Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R Viant, Ralf J M Weber, Gianluigi Zanetti, Christoph Steinbeck, *GigaScience*, giy149, doi: 10.1093/gigascience/giy149 -* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/people/vahid-jalili/), [Enis Afgan](/people/enis-afgan/), [James Taylor](/src/people/james-taylor/), [Jeremy Goecks](/src/people/jeremy-goecks/), *bioRxiv* 506238, doi: 10.1101/506238 +* **[Cloud Bursting Galaxy: Federated Identity and Access Management](https://doi.org/10.1101/506238)**, [Vahid Jalili](/people/vahid-jalili/), [Enis Afgan](/people/enis-afgan/), [James Taylor](/people/james-taylor/), [Jeremy Goecks](/people/jeremy-goecks/), *bioRxiv* 506238, doi: 10.1101/506238 * **[SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data](https://doi.org/10.1093/bioinformatics/bty947 )**, Jamie Soul, Tim E Hardingham, Ray P Boot-Handford, Jean-Marc Schwartz, *Bioinformatics*, bty947, doi: 10.1093/bioinformatics/bty947 diff --git a/content/news/2019-10-hacktoberfest/index.md b/content/news/2019-10-hacktoberfest/index.md index f37864466c..f21956e944 100644 --- a/content/news/2019-10-hacktoberfest/index.md +++ b/content/news/2019-10-hacktoberfest/index.md @@ -15,4 +15,4 @@ Not sure what to contribute? Here are a few suggestions to get you started: * Get your hands dirty with some DevOps topics, check out Galaxy’s incubator project: [CloudVE](https://github.com//cloudve) See you online,
-[Alex Ostrovsky](/people/alex-ostrovsky/) and [Enis Afgan](/src/people/enis-afgan/) +[Alex Ostrovsky](/people/alex-ostrovsky/) and [Enis Afgan](/people/enis-afgan/) diff --git a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md index f3e4cd113d..d0aeef452a 100644 --- a/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md +++ b/content/news/areferencemodelfordeployingapplicationsinvirtualizedenvironments/index.md @@ -4,4 +4,4 @@ date: "2011-09-01" ---
Concurrency and Computation: Practice & Experience
-A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/src/people/dannon-baker/) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. +A new paper, "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full)," by [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/) *et al.* has been published in *[Concurrency and Computation: Practice and Experience](http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291532-0634)*. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization. diff --git a/content/news/bio-blend-v0.5.3/index.md b/content/news/bio-blend-v0.5.3/index.md index fad79795c6..47a004ac89 100644 --- a/content/news/bio-blend-v0.5.3/index.md +++ b/content/news/bio-blend-v0.5.3/index.md @@ -34,4 +34,4 @@ This is mostly an incremental bug fix release with the following summary of chan Enjoy and please let us know what you think, -[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/src/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/src/people/helena-rasche/) +[Enis](/people/enis-afgan/) & [John](/people/john-chilton/) & [Nicola Soranzo](/people/nicola-soranzo/) & Simone Leo & [Helena Rasche](/people/helena-rasche/) diff --git a/content/news/cloudman-release201401/index.md b/content/news/cloudman-release201401/index.md index a560d10057..521718bea2 100644 --- a/content/news/cloudman-release201401/index.md +++ b/content/news/cloudman-release201401/index.md @@ -32,4 +32,4 @@ For more details on the new features, see the the [CHANGELOG](https://bitbucket. Enjoy and please let us know what you think, -[Enis Afgan](/people/enis-afgan/) and [Dannon Baker](/src/people/dannon-baker/) +[Enis Afgan](/people/enis-afgan/) and [Dannon Baker](/people/dannon-baker/) diff --git a/content/news/conda-dependency-codefest-report/index.md b/content/news/conda-dependency-codefest-report/index.md index e8e89217fe..3c34b30abe 100644 --- a/content/news/conda-dependency-codefest-report/index.md +++ b/content/news/conda-dependency-codefest-report/index.md @@ -38,4 +38,4 @@ Infrastructure: Thanks to everyone who participated! -[Rémi Marenco](/people/remi-marenco/). [Nitesh Turaga](/people/nitesh-turaga/), and [Björn Grüning](/src/people/bjoern-gruening/) +[Rémi Marenco](/people/remi-marenco/). [Nitesh Turaga](/people/nitesh-turaga/), and [Björn Grüning](/people/bjoern-gruening/) diff --git a/content/news/galaxy-current-protocols/index.md b/content/news/galaxy-current-protocols/index.md index e0b14da1eb..1ebd129dc6 100644 --- a/content/news/galaxy-current-protocols/index.md +++ b/content/news/galaxy-current-protocols/index.md @@ -7,10 +7,10 @@ date: "2012-06-18" Two new Galaxy-related papers are now available in [Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html): **["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html)** - [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/).
+ [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 10.5.

**["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html)** - [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/src/people/james-taylor/).
+ [Enis Afgan](/people/enis-afgan/), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/people/james-taylor/).
*[Current Protocols in Bioinformatics](http://cda.currentprotocols.com/WileyCDA/CurPro3Category/L1-1000.html)*. 2012 June: Unit 11.9. Both papers feature hands-on, step by step protocols, accompanied by numerous and detailed figures at each step. diff --git a/content/news/galaxy-tour-de-france2012/index.md b/content/news/galaxy-tour-de-france2012/index.md index 0e5b1cfd03..ae494501b1 100644 --- a/content/news/galaxy-tour-de-france2012/index.md +++ b/content/news/galaxy-tour-de-france2012/index.md @@ -4,7 +4,7 @@ date: "2012-04-25" ---
Galaxy Tour de France 2012
-We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/src/people/james-taylor/). +We are pleased to announce the **[Galaxy Tour de France 2012](/src/events/galaxy-tour-de-france2012/index.md)**, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in [Perpignan, Lyon and Paris](/src/events/galaxy-tour-de-france2012/index.md#itinerary). Each day will feature a *[Galaxy for Biologists](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the morning, and a *[Galaxy for Developers](/src/events/galaxy-tour-de-france2012/index.md)* workshop in the afternoon. All workshops will be taught by [Galaxy Team](/galaxy-team/) members [Nate Coroar](/people/nate/), [Anton Nekrutenko](/people/anton/) and [James Taylor](/people/james-taylor/). Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. diff --git a/content/news/liste-de-diffusion-galaxy-france/index.md b/content/news/liste-de-diffusion-galaxy-france/index.md index a556ac3829..de1ef5c9af 100644 --- a/content/news/liste-de-diffusion-galaxy-france/index.md +++ b/content/news/liste-de-diffusion-galaxy-france/index.md @@ -28,6 +28,6 @@ Pour vous aider dans votre utilisation de Galaxy, voici une liste de liens utile A très bientôt sur la liste Galaxy France, -Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/people/dave-clements/) & [Jennifer Jackson](/src/people/jennifer-jackson/). +Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, [Dave Clements](/people/dave-clements/) & [Jennifer Jackson](/people/jennifer-jackson/). Alban Lermine diff --git a/content/news/s-g2014-report/index.md b/content/news/s-g2014-report/index.md index 8dc3da5db4..8bd0011831 100644 --- a/content/news/s-g2014-report/index.md +++ b/content/news/s-g2014-report/index.md @@ -15,4 +15,4 @@ We would like to thank for the financial support we got from [SystemsX.ch](http: Running the event at two different places caused some logistical problems - some participants even learned about European geography. But the event was again a great success and we got a lot of great feedback. We are looking forward to the next Swiss German Galaxy Tour. -[Björn](/people/bjoern-gruening/) and [Hans-Rudolf](/src/people/hansrudolf-hotz/) +[Björn](/people/bjoern-gruening/) and [Hans-Rudolf](/people/hansrudolf-hotz/) diff --git a/content/people/dave-bouvier/index.md b/content/people/dave-bouvier/index.md index 1a56ebbe39..4650fa5598 100644 --- a/content/people/dave-bouvier/index.md +++ b/content/people/dave-bouvier/index.md @@ -1,4 +1,4 @@ -
![](/src/people/dave-bouvier/davebouvierflag200.jpeg)
+
![](/people/dave-bouvier/davebouvierflag200.jpeg)
# Dave Bouvier diff --git a/content/people/dave-clements/index.md b/content/people/dave-clements/index.md index 5da14aa0e5..4b2bdcb25e 100644 --- a/content/people/dave-clements/index.md +++ b/content/people/dave-clements/index.md @@ -38,10 +38,10 @@ My pre-bioinformatics career included ## Publications -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). -* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/src/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/src/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/src/people/bjoern-gruening/). -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/) -* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/) +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Vahid Jalili](/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/people/jeremy-goecks/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). +* [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/people/bjoern-gruening/). +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/) +* [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/) * [The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data](http://database.oxfordjournals.org/content/2011/bar051.full), in *[Database](http://database.oxfordjournals.org/)*, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main * [Organization of the pronephric kidney revealed by large-scale gene expression mapping](http://genomebiology.com/2008/9/5/R84); in *[Genome Biology](http://genomebiology.com/2008/9/5/)*, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli * [A high-resolution anatomical ontology of the developing murine genitourinary tract](https://doi.org/10.1016/j.modgep.2007.03.002); in *[Gene Expression Patterns](http://www.elsevier.com/locate/modgep)*, 7(6), pp. 680-699 (June 2007). Melissa H. Little, Jane Brennan, Kylie Georgas, Jamie A. Davies, Duncan R. Davidson, Richard A. Baldock, Annemiek Beverdam, John F. Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Cullen-McEwen, Jean Fleming, Thierry Gilbert, Doris Herzlinger, Derek Houghton, Matt H. Kaufman, Elena Kleymenova, Peter A. Koopman, Alfor G. Lewis, Andrew P. McMahon, Cathy L. Mendelsohn, Eleanor K. Mitchell, Bree A. Rumballe, Derina E. Sweeney, M. Todd Valerius, Gen Yamada, Yiya Yang and Jing Yu @@ -317,7 +317,7 @@ Are coming, the next time I need to do a biosketch. March 7 - Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam + Galaxy Workshop
with Carl Eberhard, Dannon Baker, Raj Ayyampalayam University of Georgia, Athens, Georgia, United States Slides
diff --git a/content/people/radhika-khetani/index.md b/content/people/radhika-khetani/index.md index 1a34e6c310..47da6101e8 100644 --- a/content/people/radhika-khetani/index.md +++ b/content/people/radhika-khetani/index.md @@ -1,4 +1,4 @@ -
![](/src/people/radhika-khetani/pic.jpg)
+
![](/people/radhika-khetani/pic.jpg)
# Radhika Khetani diff --git a/content/people/tori-r/index.md b/content/people/tori-r/index.md index 9b16d4f942..7623770b27 100644 --- a/content/people/tori-r/index.md +++ b/content/people/tori-r/index.md @@ -9,7 +9,7 @@ less boring and not take so long. - + @@ -19,7 +19,7 @@ less boring and not take so long.
Me presenting my mentorship
- + diff --git a/content/use/galaxy-test/index.md b/content/use/galaxy-test/index.md index b11dc6c663..cfc796fc29 100644 --- a/content/use/galaxy-test/index.md +++ b/content/use/galaxy-test/index.md @@ -16,7 +16,7 @@ user_support: quotas: - "Storage and computational quotas. See [Test](/src/test/index.md) for details" citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "[Project tagged publications](https://www.zotero.org/groups/1732893/galaxy/tags/%2BProject) in [Galaxy Publication library](/src/publication-library/index.md)." - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: diff --git a/content/use/imaging/index.md b/content/use/imaging/index.md index d6ff22aac0..9f5276b8d6 100644 --- a/content/use/imaging/index.md +++ b/content/use/imaging/index.md @@ -26,6 +26,6 @@ citations: pub_libraries: - "Imaging EU" sponsors: - - "[Greg von Kuster](/people/greg_vonkuster/), [Björn Grüning](/src/people/bjoern-gruening/) and Thomas Wollmann" + - "[Greg von Kuster](/people/greg_vonkuster/), [Björn Grüning](/people/bjoern-gruening/) and Thomas Wollmann" - "The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/freiburg/) but also collectively by groups and individuals from across Europe" --- diff --git a/content/use/usegalaxy-eu/index.md b/content/use/usegalaxy-eu/index.md index 876ab31176..6831d90460 100644 --- a/content/use/usegalaxy-eu/index.md +++ b/content/use/usegalaxy-eu/index.md @@ -18,7 +18,7 @@ user_support: quotas: - "Storage and computational quotas." citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/src/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/src/people/nitesh-turaga/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/src/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.eu" diff --git a/content/use/usegalaxy-org/index.md b/content/use/usegalaxy-org/index.md index 1511230ad4..8a7f724ed0 100644 --- a/content/use/usegalaxy-org/index.md +++ b/content/use/usegalaxy-org/index.md @@ -11,7 +11,7 @@ summary: "The [Galaxy Project](/galaxy-project/) free public server; biomedical comments: - "Strong on genomics; good central repository for shared Galaxy objects. See [Main](/main/) for more." citations: - - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/), [Vahid Jalili](/src/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/src/people/jeremy-goecks/), [James Taylor](/src/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" + - "**[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379)**, [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Vahid Jalili](/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/people/jeremy-goecks/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.org" From 6db6944ffb9214eab4a733f3e7212fa36a5f1948 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 17:35:15 -0400 Subject: [PATCH 10/24] Fix Greg links --- content/citing-galaxy/index.md | 4 ++-- content/community/galaxy-admins/meetups/2013-01-16/index.md | 4 ++-- content/community/galaxy-admins/meetups/index.md | 2 +- content/events/archive/wayback/index.md | 2 +- content/events/gcc2012/abstracts/index.md | 2 +- content/events/gcc2012/program/index.md | 4 ++-- content/events/gcc2012/training-day/index.md | 2 +- content/events/gcc2013/abstracts/talks/index.md | 2 +- content/events/gcc2013/bof/tool-developers/index.md | 2 +- content/events/gcc2013/program/index.md | 4 ++-- content/events/gcc2013/training-day/index.md | 4 ++-- content/events/gcc2014/abstracts/talks/index.md | 2 +- content/events/gcc2014/program/index.md | 4 ++-- content/events/gcc2014/training-day/index.md | 4 ++-- content/events/ismb2012/index.md | 2 +- content/galaxy-team/index.md | 2 +- content/galaxy-updates/2014-03/index.md | 2 +- content/galaxy-updates/2016-09/index.md | 2 +- content/people/dave-clements/index.md | 2 +- content/use/galaxy-test/index.md | 2 +- content/use/imaging/index.md | 2 +- content/use/usegalaxy-eu/index.md | 2 +- 22 files changed, 29 insertions(+), 29 deletions(-) diff --git a/content/citing-galaxy/index.md b/content/citing-galaxy/index.md index 2e367b054c..c0347805db 100644 --- a/content/citing-galaxy/index.md +++ b/content/citing-galaxy/index.md @@ -63,7 +63,7 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## DataSource Tools -* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg_vonkuster/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. +* [Daniel Blankenberg](/people/dan/), [Nate Coraor](/people/nate/), [Gregory Von Kuster](/people/greg-vonkuster/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and The [Galaxy Team](/src/galaxy-team/). **[Integrating diverse databases into an unified analysis framework: a Galaxy approach](https://academic.oup.com/database/article/doi/10.1093/database/bar011/463445)**. *Database (Oxford)*. 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011. ## External Display Applications @@ -80,7 +80,7 @@ Cite these papers if you want to cite a particular aspect of Galaxy. ## ToolShed -* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg_vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 +* [Daniel Blankenberg](/people/dan/), [Gregory Von Kuster](/people/greg-vonkuster/), [Emil Bouvier](/people/dave-bouvier/), [Dannon Baker](/people/dannon-baker/), [Enis Afgan](/people/enis-afgan/), [Nicholas Stoler](http://nstoler.com/), the [Galaxy Team](/src/galaxy-team/), [James Taylor](/people/james-taylor/) and [Anton Nekrutenko](/people/anton/). **[Dissemination of scientific software with Galaxy ToolShed](http://genomebiology.biomedcentral.com/articles/10.1186/gb4161)**. *Genome Biology* (2014) 15:403 doi:10.1186/gb4161 ## Training & Education diff --git a/content/community/galaxy-admins/meetups/2013-01-16/index.md b/content/community/galaxy-admins/meetups/2013-01-16/index.md index 931e845d6d..e4ad0f7022 100644 --- a/content/community/galaxy-admins/meetups/2013-01-16/index.md +++ b/content/community/galaxy-admins/meetups/2013-01-16/index.md @@ -6,7 +6,7 @@ The January 2013 [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) was held Wednesday, January 16, 2013 at 10am US central time. [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." -[Greg Von Kuster](/people/greg_vonkuster/) also gave a Galaxy Project update. +[Greg Von Kuster](/people/greg-vonkuster/) also gave a Galaxy Project update.
My poster (click to enlarge)
@@ -23,7 +23,7 @@ The January 2013 [GalaxyAdmins Meetup](/src/community/galaxy-admins/meetups/2013 - + diff --git a/content/community/galaxy-admins/meetups/index.md b/content/community/galaxy-admins/meetups/index.md index c8c0370f68..7ac567ae44 100644 --- a/content/community/galaxy-admins/meetups/index.md +++ b/content/community/galaxy-admins/meetups/index.md @@ -66,7 +66,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * [2013-03-20 Web Meetup](/src/community/galaxy-admins/meetups/2013-03-20/index.md) * [Hailiang Leon Mei](mailto:hailiang DOT mei AT nbic DOT nl) discuss NBIC's recent experiences deploying the [NBIC Galaxy](http://galaxy.nbic.nl/) at [SURFsara's HPC cloud](https://www.surfsara.nl/). [Dan Blankenberg](/people/dan/) discusses the new release policy and upcoming *Data Manager* features. * [2013-01-16 Web Meetup](/src/community/galaxy-admins/meetups/2013-01-16/index.md) - * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/people/greg_vonkuster/) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/) + * [John Chilton](https://www.msi.umn.edu/users/chilton) of the [Minnesota Supercomputing Institute](https://www.msi.umn.edu/) covered "Deploying Production Galaxy Environments on [OpenStack](http://www.openstack.org/) with [CloudBioLinux](http://cloudbiolinux.org/) and CloudMan." [Greg von Kuster](/people/greg-vonkuster/) also gave an update on recent developments in the [Galaxy Tool Shed](/src/toolshed/) **2012** diff --git a/content/events/archive/wayback/index.md b/content/events/archive/wayback/index.md index 8a11f7e0c7..5bbeb43664 100644 --- a/content/events/archive/wayback/index.md +++ b/content/events/archive/wayback/index.md @@ -4627,7 +4627,7 @@ Listing of Galaxy events from 2016 and before. See the main [Galactic Events](/s - + diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index 88b59d89fc..cc7ed64339 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -452,7 +452,7 @@ GenomeSpace is a software environment that provides a connection layer between b
-**[Greg von Kuster](/people/greg_vonkuster/)1** +**[Greg von Kuster](/people/greg-vonkuster/)1** 1 [Penn State University](http://psu.edu/) diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index 7f8429b718..fcde6c8454 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -55,7 +55,7 @@ See the [Training Day page](/src/events/gcc2012/training-day/index.md) for compl - + @@ -130,7 +130,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from | 11:55 |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Liefeld.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Liefeld.pptx), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=cc90a8540a7f4ec) (starts @ 54:10), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=afa05c3a39584a7)*
*[GenomeSpace](/src/events/gcc2012/abstracts/index.md#genomespace)*
Ted Liefeld, Broad Institute
| | **12:15-1:10** | **Lunch** | | **1:10-2:50** | **Session 7**
Moderator: Ross Lazarus, [BakerIDI](http://www.bakeridi.edu.au/) | -| **1:10** |
*[PDF](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.pdf), [PPT](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.ppt),[Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad)*
*[Tool Shed and Changes to Galaxy Distributions](/src/events/gcc2012/abstracts#tool_shed_and_hanges_to_galaxy_distributions)*
[Greg von Kuster](/people/greg_vonkuster/), Penn State University
| +| **1:10** |
*[PDF](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.pdf), [PPT](https://deport/galaxyproject.org/hub/attachments/documents/presentations/gcc2012/vonKuster.ppt),[Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad)*
*[Tool Shed and Changes to Galaxy Distributions](/src/events/gcc2012/abstracts#tool_shed_and_hanges_to_galaxy_distributions)*
[Greg von Kuster](/people/greg-vonkuster/), Penn State University
| | **1:30** | **Lightning Talks** | | |
*[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Helseth.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Helseth.pptx), [Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad) (starts @ 24:40)*
*Customizing Galaxy for a Hospital Environment*
Larry Helseth, NorthShore University HealthSystem
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Coraor.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad) (starts @ 30:30)*
*ObjectStore*
Nate Coraor, Penn State University
| diff --git a/content/events/gcc2012/training-day/index.md b/content/events/gcc2012/training-day/index.md index ac8b11a16a..984413bb6a 100644 --- a/content/events/gcc2012/training-day/index.md +++ b/content/events/gcc2012/training-day/index.md @@ -49,7 +49,7 @@ Register for the Training Day at the same time you [Register](/src/events/gcc201 - + diff --git a/content/events/gcc2013/abstracts/talks/index.md b/content/events/gcc2013/abstracts/talks/index.md index 98b239da5a..aa5ea04d49 100644 --- a/content/events/gcc2013/abstracts/talks/index.md +++ b/content/events/gcc2013/abstracts/talks/index.md @@ -430,7 +430,7 @@ We will present an overview of the requirements to move Galaxy into the Clinical
Greg Von Kuster
-**[Greg von Kuster](/people/greg_vonkuster/)**, [Daniel Blankenberg](/people/dan/) +**[Greg von Kuster](/people/greg-vonkuster/)**, [Daniel Blankenberg](/people/dan/) Penn State / Galaxy Team *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2013/VonKusterToolShed.pdf), [Vimeo](https://vimeo.com/74347850)* diff --git a/content/events/gcc2013/bof/tool-developers/index.md b/content/events/gcc2013/bof/tool-developers/index.md index f88a06ca86..903bef9289 100644 --- a/content/events/gcc2013/bof/tool-developers/index.md +++ b/content/events/gcc2013/bof/tool-developers/index.md @@ -33,7 +33,7 @@ If you are interested, please add your name below and/or send an email to the [I * [Björn Grüning](mailto:bjoern.gruening AT pharmazie DOT uni-freiburg DOT de) * [JJ Johnson](mailto:jj AT umn DOT edu) * Peter Cock -* [Greg Von Kuster](/people/greg_vonkuster/) +* [Greg Von Kuster](/people/greg-vonkuster/) * [Dave Bouvier](/people/dave-bouvier/) * [Dan Blankenberg](/people/dan/) * [Christian Andreetta](http://www.computing.uni.no/staff?nickname=christiana) diff --git a/content/events/gcc2013/program/index.md b/content/events/gcc2013/program/index.md index e162fc245c..67a814a35f 100644 --- a/content/events/gcc2013/program/index.md +++ b/content/events/gcc2013/program/index.md @@ -58,7 +58,7 @@ Workshops will be hands-on and participants will be strongly encouraged to bring - + @@ -367,7 +367,7 @@ The second and final day of the conference will feature [accepted talks](/src/e - + diff --git a/content/events/gcc2013/training-day/index.md b/content/events/gcc2013/training-day/index.md index 47caccc1a2..829181c057 100644 --- a/content/events/gcc2013/training-day/index.md +++ b/content/events/gcc2013/training-day/index.md @@ -64,7 +64,7 @@ You [register](/src/events/gcc2013/register/index.md) for the Training Day (and - + @@ -405,7 +405,7 @@ See each individual workshop's list of prerequisite for specifics.
Presenter John Chilton, Minnesota Supercomputing Institute
Greg Von Kuster, Penn State University 		John Chilton, Minnesota Supercomputing Institute
Greg Von Kuster, Penn State University
Links Galaxy Next Generation Sequencing Functionality from Sample Tracking to SNP Calling
ABRF 2011 		San Antonio, Texas, United States Greg von Kuster Greg von Kuster
February 2-5
2:00 WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
 WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
 WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
 WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
2:00 WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
 WS7: Galaxy Tool Shed
Greg von Kuster & Nate Coraor
 WS8: Variant and SNP Analysis with Galaxy
Erik Garrison
 WS1: Integrating Tools & Data Sources
Dan Blankenberg & Ross Lazarus
15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
13:30
Slides, Vimeo
Enhancing the Galaxy Tool Shed
Greg Von Kuster, Penn State University
Slides, Vimeo
Enhancing the Galaxy Tool Shed
Greg Von Kuster, Penn State University
13:50
15:00 Advanced Tool and Data Source Configuration
Ross Lazarus, Dan Blankenberg
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Galaxy Tool Shed
Greg Von Kuster, Dave Bouvier
Variant and SNP Analysis with Galaxy
Erik Garrison, Anton Nekrutenko
RNA-Seq Analysis with Galaxy
Jeroen F.J. Laros, Wibowo Arindrarto, Leon Mei
ChIP-Seq Analysis with Galaxy
Alban Lermine, Valentina Boeva
- + diff --git a/content/events/gcc2014/abstracts/talks/index.md b/content/events/gcc2014/abstracts/talks/index.md index 83f0a9b465..5b19ea5f78 100644 --- a/content/events/gcc2014/abstracts/talks/index.md +++ b/content/events/gcc2014/abstracts/talks/index.md @@ -167,7 +167,7 @@ An overview of where the Galaxy Project is and where it is going.
Greg Von Kuster
-**[Greg von Kuster](/people/greg_vonkuster/)1** and the [Galaxy Team](/src/galaxy-team/) +**[Greg von Kuster](/people/greg-vonkuster/)1** and the [Galaxy Team](/src/galaxy-team/) 1 [Penn State University](http://psu.edu/), State College, Pennsylvania, United States
diff --git a/content/events/gcc2014/program/index.md b/content/events/gcc2014/program/index.md index 0d97a785d9..d71135baab 100644 --- a/content/events/gcc2014/program/index.md +++ b/content/events/gcc2014/program/index.md @@ -54,7 +54,7 @@ Topics were nominated and then voted on by the Galaxy Community. There are 15 s - + @@ -229,7 +229,7 @@ Moderator: [Ravi Madduri](http://www.mcs.anl.gov/person/ravi-madduri), [Argonne - + diff --git a/content/events/gcc2014/training-day/index.md b/content/events/gcc2014/training-day/index.md index 8e7cec9ee9..181ed98110 100644 --- a/content/events/gcc2014/training-day/index.md +++ b/content/events/gcc2014/training-day/index.md @@ -50,7 +50,7 @@ Meeting participants select which Training Day topics to attend when they [regis - + @@ -329,7 +329,7 @@ See each individual workshop's list of prerequisite for specifics.
Instructors Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University 		Greg Von Kuster, Penn State University
Dave Bouvier, Penn State University
Content 12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
4:00 The Galaxy Tool Shed: A Framework for Building Galaxy Tools
Greg von Kuster, Penn State University
The Galaxy Tool Shed: A Framework for Building Galaxy Tools
Greg von Kuster, Penn State University
4:20 12:30 Galaxy on a Cluster - User and Project Management
Nikolay Vazov & Katerina Michalickova
 Galaxy Automation: Using the API
Dannon Baker & Carl Eberhard
 Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
Tool Development from bright idea to toolshed - Designing a Galaxy Tool
Greg Von Kuster, Björn Grüning & Peter Cock
RNA-Seq Analysis with Galaxy and the Tuxedo Suite
Saskia Hiltemann, Youri Hoogstrate & Hailiang (Leon) Mei
3D Genome Analysis with Galaxy
Jonas Paulsen, Tonje Lien Gulbrandsen, Morten Johansen & Karen Reddy
- + diff --git a/content/events/ismb2012/index.md b/content/events/ismb2012/index.md index 69858800e1..3df1916b6d 100644 --- a/content/events/ismb2012/index.md +++ b/content/events/ismb2012/index.md @@ -77,7 +77,7 @@ Galaxy had a significant presence at [ISMB](http://www.iscb.org/ismb2012) and [B - + diff --git a/content/galaxy-team/index.md b/content/galaxy-team/index.md index 358ba483b8..274e6b4a46 100644 --- a/content/galaxy-team/index.md +++ b/content/galaxy-team/index.md @@ -242,7 +242,7 @@ Luke Sargent
![Greg von Kuster](/src/images/people/greg.png) -[Greg von Kuster](/people/greg_vonkuster/) +[Greg von Kuster](/people/greg-vonkuster/) [Penn State](http://www.bx.psu.edu)
diff --git a/content/galaxy-updates/2014-03/index.md b/content/galaxy-updates/2014-03/index.md index 22d5a8717b..91ad25aba3 100644 --- a/content/galaxy-updates/2014-03/index.md +++ b/content/galaxy-updates/2014-03/index.md @@ -9,7 +9,7 @@ Welcome to the March 2014 *[Galaxy Update](/src/galaxy-updates/index.md)*, a mon *54 papers* were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in Febrary. Some papers that may be particularly interesting to the Galaxy community: -* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg_vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/people/james-taylor/) and [Nekrutenko](/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 +* [Dissemination of scientific software with Galaxy ToolShed](https://doi.org/10.1186/gb4161), by [Blankenberg](/people/dan/), [Von Kuster](/people/greg-vonkuster/), [Bouvier](/people/dave-bouvier/), [Baker](/people/dannon-baker/), [Afgan](/people/enis-afgan/), Stoler, the [Galaxy Team](/src/galaxy-team/), [Taylor](/people/james-taylor/) and [Nekrutenko](/people/anton/), *Genome Biology,* Vol. 15, No. 2. (20 February 2014), 403, doi:10.1186/gb4161 * [Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis](https://doi.org/10.1371/journal.pone.0087301), by Khushi, *et al.,* *PLoS ONE*, Vol. 9, No. 2. (12 February 2014), e87301, doi:10.1371/journal.pone.0087301 diff --git a/content/galaxy-updates/2016-09/index.md b/content/galaxy-updates/2016-09/index.md index 8b587e2540..3e457ef19a 100644 --- a/content/galaxy-updates/2016-09/index.md +++ b/content/galaxy-updates/2016-09/index.md @@ -559,7 +559,7 @@ Other Galaxy packages that haven't had a release in the past four months can be # Other News -* From [Greg Von Kuster](/people/greg_vonkuster/): +* From [Greg Von Kuster](/people/greg-vonkuster/): [Galaxy tools for Constructive Solid Geometry (Galaxy CSG flavor)](https://github.com/gregvonkuster/galaxy-csg/blob/master/README.md) * [How to Build Bioinformatic Pipelines Using Galaxy](http://www.the-scientist.com/?articles.view/articleNo/46670/title/How-to-Build-Bioinformatic-Pipelines-Using-Galaxy), and article by Jeffrey M. Perkel in *The Scientist*. diff --git a/content/people/dave-clements/index.md b/content/people/dave-clements/index.md index 4b2bdcb25e..10ffcc34cf 100644 --- a/content/people/dave-clements/index.md +++ b/content/people/dave-clements/index.md @@ -40,7 +40,7 @@ My pre-bioinformatics career included * [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update](https://doi.org/10.1093/nar/gky379) [Enis Afgan](/people/enis-afgan/), *Nucleic Acids Research*, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. [Dannon Baker](/people/dannon-baker/), [Bérénice Batut](http://bebatut.fr/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Vahid Jalili](/people/vahid-jalili/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Jeremy Goecks](/people/jeremy-goecks/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Daniel Blankenberg](/people/dan/). * [Community-Driven Data Analysis Training for Biology](https://doi.org/10.1016/j.cels.2018.05.012), *Cell Systems*, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. [Bérénice Batut](http://bebatut.fr/), Saskia Hiltemann, Andrea Bagnacani, [Dannon Baker](/people/dannon-baker/), Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, [Hans-Rudolf Hotz](/people/hansrudolf-hotz/), Torsten Houwaart, Pratik Jagtap, [Delphine Lariviere](/people/delphine-lariviere/), Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, [James Taylor](/people/james-taylor/), Rolf Backofen, [Anton Nekrutenko](/people/anton/), [Björn Grüning](/people/bjoern-gruening/). -* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/) +* [The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full). *Nucleic Acids Research* (2016) doi: 10.1093/nar/gkw343. [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg-vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/) * [Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html), in *Current Protocols in Bioinformatics*. 2012 June: Unit 10.5. [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Dave Clements](/people/dave-clements/), [Daniel Blankenberg](/people/dan/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), [Galaxy Team](/src/galaxy-team/) * [The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data](http://database.oxfordjournals.org/content/2011/bar051.full), in *[Database](http://database.oxfordjournals.org/)*, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main * [Organization of the pronephric kidney revealed by large-scale gene expression mapping](http://genomebiology.com/2008/9/5/R84); in *[Genome Biology](http://genomebiology.com/2008/9/5/)*, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli diff --git a/content/use/galaxy-test/index.md b/content/use/galaxy-test/index.md index cfc796fc29..c99b0b4cd1 100644 --- a/content/use/galaxy-test/index.md +++ b/content/use/galaxy-test/index.md @@ -16,7 +16,7 @@ user_support: quotas: - "Storage and computational quotas. See [Test](/src/test/index.md) for details" citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg-vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "[Project tagged publications](https://www.zotero.org/groups/1732893/galaxy/tags/%2BProject) in [Galaxy Publication library](/src/publication-library/index.md)." - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: diff --git a/content/use/imaging/index.md b/content/use/imaging/index.md index 9f5276b8d6..eb6ef57679 100644 --- a/content/use/imaging/index.md +++ b/content/use/imaging/index.md @@ -26,6 +26,6 @@ citations: pub_libraries: - "Imaging EU" sponsors: - - "[Greg von Kuster](/people/greg_vonkuster/), [Björn Grüning](/people/bjoern-gruening/) and Thomas Wollmann" + - "[Greg von Kuster](/people/greg-vonkuster/), [Björn Grüning](/people/bjoern-gruening/) and Thomas Wollmann" - "The [Freiburg Galaxy Team](https://usegalaxy-eu.github.io/freiburg/) but also collectively by groups and individuals from across Europe" --- diff --git a/content/use/usegalaxy-eu/index.md b/content/use/usegalaxy-eu/index.md index 6831d90460..7d33ddf92a 100644 --- a/content/use/usegalaxy-eu/index.md +++ b/content/use/usegalaxy-eu/index.md @@ -18,7 +18,7 @@ user_support: quotas: - "Storage and computational quotas." citations: - - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg_vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" + - "[The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update](http://nar.oxfordjournals.org/content/44/W1/W3.full), [Enis Afgan](/people/enis-afgan/), [Dannon Baker](/people/dannon-baker/), [Marius van den Beek](http://www.ibps.upmc.fr/en/ibps/directory/1921-Marius-Van+Den+Beek), [Daniel Blankenberg](/people/dan/), [Dave Bouvier](/people/dave-bouvier/), [Martin Čech](/people/marten/), [John Chilton](/people/john-chilton/), [Dave Clements](/people/dave-clements/), [Nate Coraor](/people/nate/), [Carl Eberhard](/people/carl-eberhard/), [Björn Grüning](/people/bjoern-gruening/), [Aysam Guerler](/people/guerler/), [Jennifer Hillman-Jackson](/people/jennifer-jackson/), [Greg Von Kuster](/people/greg-vonkuster/), [Helena Rasche](https://github.com/hexylena), [Nicola Soranzo](http://biowiki.crs4.it/biowiki/NicolaSoranzo), [Nitesh Turaga](/people/nitesh-turaga/), [James Taylor](/people/james-taylor/), [Anton Nekrutenko](/people/anton/), and [Jeremy Goecks](/people/jeremy-goecks/). *Nucleic Acids Research* (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343" - "See [Citing Galaxy](/src/citing-galaxy/index.md)" pub_libraries: - "UseGalaxy.eu" From f97442147a47407cee9e116e0a3b7332830872d6 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 25 Sep 2021 21:46:40 -0400 Subject: [PATCH 11/24] content-wide src/.../index.md replacement --- content/admin/capacity-planning/index.md | 8 ++--- .../performance/cluster/legacy/index.md | 2 +- .../admin/config/tool-dependencies/index.md | 2 +- content/admin/data-integration/index.md | 6 ++-- content/admin/data-preparation/index.md | 6 ++-- content/admin/datatypes/index.md | 2 +- content/admin/disk-quotas/index.md | 2 +- content/admin/faq/index.md | 12 +++---- content/admin/get-galaxy/index.md | 2 +- content/admin/index.md | 8 ++--- content/admin/internals/data-sources/index.md | 2 +- content/admin/linkbox.md | 8 ++--- content/admin/maintenance/index.md | 4 +-- content/admin/reference-data-repo/index.md | 4 +-- .../index.md | 8 ++--- content/admin/tool-panel/index.md | 2 +- .../add-tool-from-toolshed-tutorial/index.md | 8 ++--- .../admin/tools/add-tool-tutorial/index.md | 4 +-- content/admin/tools/data-managers/index.md | 2 +- content/admin/tools/linkbox.md | 6 ++-- .../training/galaxy-admin-tutorial/index.md | 2 +- .../data-libraries/library-templates/index.md | 2 +- .../uploading-library-files/index.md | 2 +- 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content/support/tool-issues/index.md | 4 +-- .../support/troubleshoot-an-error/index.md | 2 +- content/team-set-up/index.md | 8 ++--- content/test/index.md | 14 ++++---- content/tools/index.md | 6 ++-- .../advanced-repository-features/index.md | 2 +- content/toolshed/advanced-topics/index.md | 2 +- .../toolshed/contributions/2014-12/index.md | 2 +- .../toolshed/contributions/2015-04/index.md | 2 +- .../toolshed/contributions/2015-05/index.md | 2 +- .../toolshed/contributions/2015-07/index.md | 2 +- .../toolshed/contributions/2015-08/index.md | 2 +- .../toolshed/contributions/2015-09/index.md | 2 +- .../toolshed/contributions/2015-11/index.md | 2 +- .../toolshed/contributions/2015-12/index.md | 2 +- .../toolshed/contributions/2016-01/index.md | 2 +- .../toolshed/contributions/2016-02/index.md | 2 +- .../toolshed/contributions/2016-03/index.md | 2 +- .../toolshed/contributions/2016-05/index.md | 2 +- .../toolshed/contributions/2016-06/index.md | 2 +- 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content/workshop-demo/index.md | 2 +- 412 files changed, 1343 insertions(+), 1343 deletions(-) diff --git a/content/admin/capacity-planning/index.md b/content/admin/capacity-planning/index.md index fcf44f0220..156568cbc7 100644 --- a/content/admin/capacity-planning/index.md +++ b/content/admin/capacity-planning/index.md @@ -15,11 +15,11 @@ Note that Galaxy itself, and many of the basic tools, can run on an average or e ## Can we use the Cloud? -Absolutely. In fact, if your needs tend to be characterized by long periods of no use (days / weeks / months) interspersed by short periods of intense use, then you should consider the [Cloud](/src/cloud/index.md). Setting up a compute cluster / server farm (if you need something that big) can take months, as you may be delayed repeatedly by details like air conditioning upgrades, electrical capacity, and finding a sys admin. +Absolutely. In fact, if your needs tend to be characterized by long periods of no use (days / weeks / months) interspersed by short periods of intense use, then you should consider the [Cloud](/cloud/). Setting up a compute cluster / server farm (if you need something that big) can take months, as you may be delayed repeatedly by details like air conditioning upgrades, electrical capacity, and finding a sys admin. -See the [Cloud page](/src/cloud/index.md) for information on getting started with the cloud. +See the [Cloud page](/cloud/) for information on getting started with the cloud. ## See Also -* [Cloud](/src/cloud/index.md) - Galaxy on the cloud options -* [Public Galaxy Servers](/src/use/index.md) - a list of known, publicly accessible, Galaxy servers. +* [Cloud](/cloud/) - Galaxy on the cloud options +* [Public Galaxy Servers](/use/) - a list of known, publicly accessible, Galaxy servers. diff --git a/content/admin/config/performance/cluster/legacy/index.md b/content/admin/config/performance/cluster/legacy/index.md index 73c6b05476..d4a76c8bbb 100644 --- a/content/admin/config/performance/cluster/legacy/index.md +++ b/content/admin/config/performance/cluster/legacy/index.md @@ -445,4 +445,4 @@ If your sudo config contains `Defaults requiretty`, this option must be disab -Some maintenance and support of this code will be provided via the usual [Support](/src/support/index.md) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team. +Some maintenance and support of this code will be provided via the usual [Support](/support/) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team. diff --git a/content/admin/config/tool-dependencies/index.md b/content/admin/config/tool-dependencies/index.md index 613ef79f8e..e9142153c1 100644 --- a/content/admin/config/tool-dependencies/index.md +++ b/content/admin/config/tool-dependencies/index.md @@ -1,6 +1,6 @@ ## Tool Dependencies -Galaxy provides a method for managing the dependencies of Galaxy tools installed from the [Tool Shed](/src/toolshed/index.md). In this case, it is simply necessary to set the `tool_dependency_dir` option of `config/galaxy.ini` to a path writable by the Galaxy server. +Galaxy provides a method for managing the dependencies of Galaxy tools installed from the [Tool Shed](/toolshed/). In this case, it is simply necessary to set the `tool_dependency_dir` option of `config/galaxy.ini` to a path writable by the Galaxy server. However, some tools which have not been migrated to the Tool Shed still require manual installation of dependent binaries. In addition, administrators may choose to utilize existing versions of dependencies already installed on the system, rather than rely on versions installed from the Tool Shed. The documentation below covers these cases. diff --git a/content/admin/data-integration/index.md b/content/admin/data-integration/index.md index 812cd03abc..dd8851acc5 100644 --- a/content/admin/data-integration/index.md +++ b/content/admin/data-integration/index.md @@ -4,7 +4,7 @@ Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see: **[Data Managers Overview](/src/admin/tools/data-managers/index.md)** and our **[Data Managers Tutorial](https://github.com/galaxyproject/dagobah-training/blob/2017-montpellier/sessions/05-reference-genomes/ex1-reference-genomes.md)**. -Built-in data files are critical for many Galaxy tools. This page will describe how to get data into your local instance of Galaxy in a general way. For instructions specific for organizing and indexing data for use with tools, see **[Data Preparation](/src/admin/data-preparation/index.md)**. Additional instructions are available for reviewing or retrieving the exact data hosted on the public [Main](/src/main/index.md) instance or for performing more complex data prep used by specific tool groups. +Built-in data files are critical for many Galaxy tools. This page will describe how to get data into your local instance of Galaxy in a general way. For instructions specific for organizing and indexing data for use with tools, see **[Data Preparation](/src/admin/data-preparation/index.md)**. Additional instructions are available for reviewing or retrieving the exact data hosted on the public [Main](/main/) instance or for performing more complex data prep used by specific tool groups. - Review or retrieve [https://usegalaxy.org](https://usegalaxy.org) reference genomes, indexes, and loc files. All methods are described at http://datacache.galaxyproject.org/, with more rsync server help at **[Usegalaxy.org Rsync](/src/admin/use-galaxy-rsync/index.md)** - "Fetch Alignment" tools data prep: **[Reference MAFs](/src/admin/reference-mafs/index.md)** @@ -21,7 +21,7 @@ First you need to determine what type of data you need. Usually these are `.fast There are several ways to get the data. If you don't already have the right file on your system, you will need to get it from a site such as [UCSC](http://hgdownload.soe.ucsc.edu/downloads.html). -Or, if you would like to obtain the data as available on the public Galaxy [Main](/src/main/index.md) instance, these can retrieved from the rsync server. Read more here: **[Rsync](/src/admin/use-galaxy-rsync/index.md)** +Or, if you would like to obtain the data as available on the public Galaxy [Main](/main/) instance, these can retrieved from the rsync server. Read more here: **[Rsync](/src/admin/use-galaxy-rsync/index.md)** ### Set up the loc file @@ -79,7 +79,7 @@ Also see the **[Rsync](/src/admin/use-galaxy-rsync/index.md)** wiki if you want Final and most important item needed is to include any new reference genomes in the builds.txt file. This is the list of reference genomes appear in the Genome or Database/Build search box when you upload a file or change a file's metadata (Where to find these? See the Rsync link directly above for screenshots). -To modify the builds.txt file, add a line to `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` for your genome. The format of this line can vary, but should contain enough information to uniquely identify the genome, the source, any external build nomenclature, and the **dbkey** selected for use within your [Galaxy](/src/admin/get-galaxy/index.md) instance. See the public [Main](/src/main/index.md) server for examples: [https://usegalaxy.org](https://usegalaxy.org) +To modify the builds.txt file, add a line to `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` for your genome. The format of this line can vary, but should contain enough information to uniquely identify the genome, the source, any external build nomenclature, and the **dbkey** selected for use within your [Galaxy](/src/admin/get-galaxy/index.md) instance. See the public [Main](/main/) server for examples: [https://usegalaxy.org](https://usegalaxy.org) ### Restart the server diff --git a/content/admin/data-preparation/index.md b/content/admin/data-preparation/index.md index 033932a798..3344223d49 100644 --- a/content/admin/data-preparation/index.md +++ b/content/admin/data-preparation/index.md @@ -2,7 +2,7 @@ **Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see [Data Managers Overview](/src/admin/tools/data-managers/index.md)** and our **[Data Managers Tutorial](https://github.com/galaxyproject/dagobah-training/blob/2017-montpellier/sessions/05-reference-genomes/ex1-reference-genomes.md)**. -**NOTE: Be aware that that as of early 2014, builds are incorporated into the Galaxy schema in tables. [Data Managers](/src/admin/tools/data-managers/index.md) are recommended to index new genomes (these are found in the [ToolShed](/src/toolshed/index.md). *This wiki is considered legacy and provided as a reference.*** +**NOTE: Be aware that that as of early 2014, builds are incorporated into the Galaxy schema in tables. [Data Managers](/src/admin/tools/data-managers/index.md) are recommended to index new genomes (these are found in the [ToolShed](/toolshed/). *This wiki is considered legacy and provided as a reference.*** # Builds list changes @@ -10,7 +10,7 @@ If you still choose to do this manually, follow the instructions at [Data Integr # Data and indexes hosted at http://usegalaxy.org -Using the Galaxy team's version of reference genomes and indexes can often be a good strategy for those working with both a local and the public **[Main](/src/main/index.md)** instance. All options are described here http://datacache.galaxyproject.org/. More details about the rsync server and the contents is at **[Usegalaxy.org Rsync](/src/admin/use-galaxy-rsync/index.md)**. +Using the Galaxy team's version of reference genomes and indexes can often be a good strategy for those working with both a local and the public **[Main](/main/)** instance. All options are described here http://datacache.galaxyproject.org/. More details about the rsync server and the contents is at **[Usegalaxy.org Rsync](/src/admin/use-galaxy-rsync/index.md)**. ## What's in this wiki ? @@ -380,7 +380,7 @@ Megablast in Galaxy was updated to use [NCBI BLAST+](http://blast.ncbi.nlm.nih.g Get the indexes: download directly at NCBI from [ftp://ftp.ncbi.nlm.nih.gov/blast/db/](ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Create your own, Usage: `formatdb -i .fa -p F -n "" -v 2000` -The Galaxy [Main](/src/main/index.md) public instance uses htgs, wgs, and nt from NCBI. +The Galaxy [Main](/main/) public instance uses htgs, wgs, and nt from NCBI. Put the data files in an organized hierarchy such as: ` /galaxy-dist/tool-data/blast/
//.* ` diff --git a/content/admin/datatypes/index.md b/content/admin/datatypes/index.md index 3703422de8..a3f2129b4f 100644 --- a/content/admin/datatypes/index.md +++ b/content/admin/datatypes/index.md @@ -1,6 +1,6 @@ -Hub page for [administering](/src/admin/index.md) Galaxy data types. +Hub page for [administering](/admin/) Galaxy data types. * [Admin/ReferenceMAFs](/src/admin/reference-mafs/index.md) * [Adding Completely new Datatypes](/src/admin/datatypes/adding-complete-datatypes/index.md) diff --git a/content/admin/disk-quotas/index.md b/content/admin/disk-quotas/index.md index 927be82edd..1f89980165 100644 --- a/content/admin/disk-quotas/index.md +++ b/content/admin/disk-quotas/index.md @@ -46,7 +46,7 @@ galaxy: `allow_user_dataset_purge` is not explicitly required for quotas but strongly encouraged, since without it users will have to wait for cleanup scripts to expire and purge their data to lower their disk usage. -Once enabled, you can create quotas in the [administration interface](/src/admin/index.md) by clicking the link for "Manage quotas" in the left panel. Quotas can have one of three "operations": +Once enabled, you can create quotas in the [administration interface](/admin/) by clicking the link for "Manage quotas" in the left panel. Quotas can have one of three "operations": * `=` : The quota is exactly the amount specified * `+` : The amount specified will be added to the amounts of the user's other associated quota definitions diff --git a/content/admin/faq/index.md b/content/admin/faq/index.md index 6b6f2ade12..8afcdafd01 100644 --- a/content/admin/faq/index.md +++ b/content/admin/faq/index.md @@ -5,7 +5,7 @@ title: Frequently Asked Questions for Galaxy Administration -See [Learn/FAQ](/src/learn/faq/index.md) for questions about using any Galaxy instance, and [Main/FAQ](/src/main/faq/index.md) for questions specifically about using Galaxy's free public server [Main](/src/main/index.md). +See [Learn/FAQ](/src/learn/faq/index.md) for questions about using any Galaxy instance, and [Main/FAQ](/src/main/faq/index.md) for questions specifically about using Galaxy's free public server [Main](/main/). @@ -21,15 +21,15 @@ See [Copyrights and Licenses](/src/admin/license/index.md). ## Using Galaxy -The Galaxy Community has created Galaxy instances in many different forms and for many different applications. The [Galaxy Platform Directory](/src/use/index.md) lists the options we know about, including: +The Galaxy Community has created Galaxy instances in many different forms and for many different applications. The [Galaxy Platform Directory](/use/) lists the options we know about, including: * Free public Galaxy servers, * cloud services that support Galaxy instances, and * virtual machines and containers that can be easily deployed for your own server. -Which is **right** for you? Explore the directory, especially the section on [Which Platform / Platform type to use](/src/use/index.md#which-platform-platform-type-to-choose/). +Which is **right** for you? Explore the directory, especially the section on [Which Platform / Platform type to use](/use/#which-platform-platform-type-to-choose/). -Tools and workflows contributed by [community members](/src/community/index.md) worldwide) are served through the **[Main ToolShed](/src/toolshed/index.md)** and genome data/indexes through an **[rsync service](/src/admin/data-integration/index.md)**. +Tools and workflows contributed by [community members](/community/) worldwide) are served through the **[Main ToolShed](/toolshed/)** and genome data/indexes through an **[rsync service](/src/admin/data-integration/index.md)**. ---- @@ -127,5 +127,5 @@ The following alignment tools available in Galaxy enable this: ## Any other question -
Galaxy Search
-[Galaxy Search](/src/search/index.md) searches all online Galaxy resources. This includes this hub, the [Mailing Lists](/src/mailing-lists/index.md), [Main](/src/main/index.md), the [Tool Shed](/src/toolshed/index.md), and the [Galaxy source code](https://github.com/galaxyproject/galaxy). +
Galaxy Search
+[Galaxy Search](/search/) searches all online Galaxy resources. This includes this hub, the [Mailing Lists](/src/mailing-lists/index.md), [Main](/main/), the [Tool Shed](/toolshed/), and the [Galaxy source code](https://github.com/galaxyproject/galaxy). diff --git a/content/admin/get-galaxy/index.md b/content/admin/get-galaxy/index.md index 3fd4ed6d4f..45edfe85f9 100644 --- a/content/admin/get-galaxy/index.md +++ b/content/admin/get-galaxy/index.md @@ -68,7 +68,7 @@ http: 0.0.0.0 ## Become an Admin -To control Galaxy through the UI (installing tools, managing users, creating groups, etc.), user must become an [administrator](/src/admin/index.md). Only registered users can become admins. To give a user admin privileges add the user's Galaxy login email to the configuration file `config/galaxy.yml`. If you don't have the file set it up using the instructions [above](#configure). The entry looks like this: +To control Galaxy through the UI (installing tools, managing users, creating groups, etc.), user must become an [administrator](/admin/). Only registered users can become admins. To give a user admin privileges add the user's Galaxy login email to the configuration file `config/galaxy.yml`. If you don't have the file set it up using the instructions [above](#configure). The entry looks like this: ``` # this should be a comma-separated list of valid Galaxy users diff --git a/content/admin/index.md b/content/admin/index.md index fdacd2c971..b140e89452 100644 --- a/content/admin/index.md +++ b/content/admin/index.md @@ -18,12 +18,12 @@ When an admin user logs into Galaxy, they will see an "Admin" menu item in the t ## Deploying * [Install own Galaxy](/src/admin/get-galaxy/index.md) -* [Run on the Cloud Infrastructure](/src/cloudman/index.md) +* [Run on the Cloud Infrastructure](/cloudman/) * [Maintaining an Instance](/src/admin/maintenance/index.md) ## Configuration -* [Authentication and Authorization](/src/authnz/index.md) +* [Authentication and Authorization](/authnz/) * [Production Configuration](/src/admin/config/index.md) * [Installing Tools](/src/admin/tools/add-tool-from-toolshed-tutorial/index.md) * [Tool Panel](/src/admin/tool-panel/index.md) @@ -50,7 +50,7 @@ When an admin user logs into Galaxy, they will see an "Admin" menu item in the t ## Development Resources -* [Developer's hub](/src/develop/index.md) +* [Developer's hub](/develop/) ## Data Resources @@ -69,4 +69,4 @@ When an admin user logs into Galaxy, they will see an "Admin" menu item in the t * [Galaxy-Admins discussion group](/src/community/galaxy-admins/index.md) * [Switching to Github from Bitbucket](/src/admin/switching-to-github-from-bitbucket/index.md) -[Search all Galaxy resources](/src/search/index.md) +[Search all Galaxy resources](/search/) diff --git a/content/admin/internals/data-sources/index.md b/content/admin/internals/data-sources/index.md index 972d365a26..037bd5e9a9 100644 --- a/content/admin/internals/data-sources/index.md +++ b/content/admin/internals/data-sources/index.md @@ -15,7 +15,7 @@ Small example of both communication protocols: ## Adding a new DataSource -DataSources are configured as a special type of [tool](/src/tools/index.md). +DataSources are configured as a special type of [tool](/tools/). Checklist for DataSource tools: diff --git a/content/admin/linkbox.md b/content/admin/linkbox.md index a9b472f7d7..c3921ca64f 100644 --- a/content/admin/linkbox.md +++ b/content/admin/linkbox.md @@ -1,18 +1,18 @@
-**[Admin](/src/admin/index.md)** +**[Admin](/admin/)** --- [Get Galaxy](/src/admin/get-galaxy/index.md) [Config](/src/admin/config/index.md) -[Tool Shed](/src/toolshed/index.md) +[Tool Shed](/toolshed/) [Data Libs](/src/admin/data-libraries/index.md) [Datatypes](/src/admin/datatypes/index.md) -[Develop](/src/develop/index.md) +[Develop](/develop/) [Quotas](/src/admin/disk-quotas/index.md) [FAQ](/src/admin/faq/index.md) [Tutorials](/src/admin/training/index.md) -[CloudMan](/src/cloudman/index.md) +[CloudMan](/cloudman/)
diff --git a/content/admin/maintenance/index.md b/content/admin/maintenance/index.md index d43859f9da..2aa49fb4e9 100644 --- a/content/admin/maintenance/index.md +++ b/content/admin/maintenance/index.md @@ -4,13 +4,13 @@ Maintaining a Galaxy instance is important to do, something that cannot be under ## Security Notices -If you maintain a [public instance of Galaxy](/src/use/index.md) it is recommended to sign up for the public servers [mailing list](https://lists.galaxyproject.org/lists/galaxy-public-servers.lists.galaxyproject.org/) to receive security fixes with priority. Also consider adding your instance to the [Galaxy Platform Directory](/src/use/index.md) so more people can discover it. +If you maintain a [public instance of Galaxy](/use/) it is recommended to sign up for the public servers [mailing list](https://lists.galaxyproject.org/lists/galaxy-public-servers.lists.galaxyproject.org/) to receive security fixes with priority. Also consider adding your instance to the [Galaxy Platform Directory](/use/) so more people can discover it. ## General Update Procedures Many admins update to each new release, though update frequency largely depends on your local instance's needs (e.g. new Galaxy features your users will want) and how much disruption your user base will tolerate (in terms of downtime + UI changes, etc) -1. Read [release notes](/src/docs/index.md#releases) and look for possible breakage, security fixes, new features, +1. Read [release notes](/docs/#releases) and look for possible breakage, security fixes, new features, 1. Update code to the chosen release branch (release_17.01 here). * New Galaxy repository: `$ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git` * Update of existing repository: `$ git checkout release_17.01 && git pull --ff-only origin release_17.01` diff --git a/content/admin/reference-data-repo/index.md b/content/admin/reference-data-repo/index.md index 2292f41394..19e62cc5cf 100644 --- a/content/admin/reference-data-repo/index.md +++ b/content/admin/reference-data-repo/index.md @@ -1,6 +1,6 @@ # usegalaxy.org Reference Data -[usegalaxy.org](http://usegalaxy.org) ([Main](/src/main/index.md) is home to over 4 TB of reference data. This is +[usegalaxy.org](http://usegalaxy.org) ([Main](/main/) is home to over 4 TB of reference data. This is comprised mainly of genome sequence builds and associated prebuilt indexes for the tools installed on usegalaxy.org, as well as the Galaxy-specific configuration files that make the data known to those tools. Because preparing this data for your own **[local](/src/admin/get-galaxy/index.md)** Galaxy server or an external application can be a laborious @@ -300,7 +300,7 @@ $ rsync -avzP rsync://datacache.galaxyproject.org/indexes/microbes/63 . ### Organization and DBKEY Genomes are organized in directories by reference genome **dbkey**. If you are not sure of the **dbkey**, it can be -found in the [Main](/src/main/index.md) user interface. This value is what is populated into the *"database"* attribute +found in the [Main](/main/) user interface. This value is what is populated into the *"database"* attribute for a dataset. Or, it is the last value in parenthesis *(dbkey)* at the end of the full reference genome build name in two specific places in the [usegalaxy.org](https://usegalaxy.org/) interface: diff --git a/content/admin/ten-simple-steps-galaxy-as-a-service/index.md b/content/admin/ten-simple-steps-galaxy-as-a-service/index.md index b1835b7a87..7c4b2b4464 100644 --- a/content/admin/ten-simple-steps-galaxy-as-a-service/index.md +++ b/content/admin/ten-simple-steps-galaxy-as-a-service/index.md @@ -19,7 +19,7 @@ Björn Grüning (gruening@informatik.uni-freiburg.de)⁵⋅⁶ -Galaxy is an open source, web-based platform for data intensive biomedical research (https://galaxyproject.org). Its popularity has been steadily increasing world wide well beyond the Bioinformatics field. More and more [public](/src/use/index.md) and private Galaxy servers are being set up. Providing 10 basic rules, this document tells you what is important when you set up a Galaxy server from scratch, what are the pitfalls you might run into, how to interact with the potential users of the service you are going to offer, how to make efficient use of your resources, and how to make sure, the Galaxy instance you have set up is really used in the end. Although, the Galaxy platform is evolving very fast, these rules will continue to be applicable, because they are very general, and less of a technical nature. +Galaxy is an open source, web-based platform for data intensive biomedical research (https://galaxyproject.org). Its popularity has been steadily increasing world wide well beyond the Bioinformatics field. More and more [public](/use/) and private Galaxy servers are being set up. Providing 10 basic rules, this document tells you what is important when you set up a Galaxy server from scratch, what are the pitfalls you might run into, how to interact with the potential users of the service you are going to offer, how to make efficient use of your resources, and how to make sure, the Galaxy instance you have set up is really used in the end. Although, the Galaxy platform is evolving very fast, these rules will continue to be applicable, because they are very general, and less of a technical nature. This article has been based on a presentation given at the Training Day at the Galaxy Community Conferences in Norwich, UK and Bloomington, IN in July 2015 and June 2016, respectively. ## Rule 1: There is no such thing as 'Free Lunch' @@ -29,11 +29,11 @@ Although, the initial setup up of a Galaxy instance is simple, running, maintain ## Rule 2: Check: what are you actually asked for -Before you start any work, talk to the person(s) who asked you to set up a Galaxy server. Why Galaxy and what is the expectation? Even more important (in case they are not the same) talk to the people who will use your service. What do they want to use Galaxy for? Are they aware of the many [public Galaxy servers](/src/use/index.md) in addition the instance offered by the [Galaxy team](/src/main/index.md)? Or, are other tools and resources better suited for the expected tasks? -Once, you agreed on using Galaxy, you need to define which tools the new Galaxy server should offer. The [Galaxy Tool Shed](/src/toolshed/index.md) provide access to thousands of freely available tools and dependencies packages. Getting tools from the Tool Shed also helps to manage external tool dependencies. Of course you can develop your own tools. Often this might be the very reason why setting up a new, local Galaxy server. But keep in mind, there is no need for inventing the wheel again. Most likely, you can improve an existing tool instead. If you develop your own tools, please consider sharing them with the community and make them available through the Galaxy Tool Shed. +Before you start any work, talk to the person(s) who asked you to set up a Galaxy server. Why Galaxy and what is the expectation? Even more important (in case they are not the same) talk to the people who will use your service. What do they want to use Galaxy for? Are they aware of the many [public Galaxy servers](/use/) in addition the instance offered by the [Galaxy team](/main/)? Or, are other tools and resources better suited for the expected tasks? +Once, you agreed on using Galaxy, you need to define which tools the new Galaxy server should offer. The [Galaxy Tool Shed](/toolshed/) provide access to thousands of freely available tools and dependencies packages. Getting tools from the Tool Shed also helps to manage external tool dependencies. Of course you can develop your own tools. Often this might be the very reason why setting up a new, local Galaxy server. But keep in mind, there is no need for inventing the wheel again. Most likely, you can improve an existing tool instead. If you develop your own tools, please consider sharing them with the community and make them available through the Galaxy Tool Shed. There are also other decisions you need to make early, which you hopefully can agree on during these discussions with the potential users and sponsors, as they will have effects on how to set-up the server: -* Will this be a [public server](/src/use/index.md), or just an internal service for your lab or institute? +* Will this be a [public server](/use/), or just an internal service for your lab or institute? * Do you rely on local (i.e. Galaxy managed) or on [external authentication](/src/admin/config/external-user-auth/)? * Will there be sensible data on the server? * Will the data be stored in one place or [distributed](/src/admin/objectstore/)? diff --git a/content/admin/tool-panel/index.md b/content/admin/tool-panel/index.md index 82b595ca51..b2fbaf58d7 100644 --- a/content/admin/tool-panel/index.md +++ b/content/admin/tool-panel/index.md @@ -21,7 +21,7 @@ In the past, the file named by your **tool_config_file** configuration setting i ### Tool Shed tools -With the introduction of the Galaxy [Tool Shed](/src/toolshed/index.md) the **tool_config_file** setting allows for a comma-separated list of files (e.g., `tool_config_file = tool_conf.xml,shed_tool_conf.xml`,etc.). The additional shed-related tool panel configuration files (**shed_tool_conf.xml**, etc.) are automatically changed when you install or uninstall a Tool Shed repository (that contains tools) to your Galaxy. +With the introduction of the Galaxy [Tool Shed](/toolshed/) the **tool_config_file** setting allows for a comma-separated list of files (e.g., `tool_config_file = tool_conf.xml,shed_tool_conf.xml`,etc.). The additional shed-related tool panel configuration files (**shed_tool_conf.xml**, etc.) are automatically changed when you install or uninstall a Tool Shed repository (that contains tools) to your Galaxy. ### Migrated tools diff --git a/content/admin/tools/add-tool-from-toolshed-tutorial/index.md b/content/admin/tools/add-tool-from-toolshed-tutorial/index.md index 61d25ab574..38964ece9b 100644 --- a/content/admin/tools/add-tool-from-toolshed-tutorial/index.md +++ b/content/admin/tools/add-tool-from-toolshed-tutorial/index.md @@ -3,7 +3,7 @@ title: Installing Tools into Galaxy --- ## Ways to get tools into Galaxy -* Install a tool from the [Tool Shed](/src/toolshed/index.md). The process has to be completed by an administrator and can be done through the [Admin Interface](/src/admin/index.md). +* Install a tool from the [Tool Shed](/toolshed/). The process has to be completed by an administrator and can be done through the [Admin Interface](/admin/). * If the tool you need does not exist in the Tool Shed you can add it to your Galaxy instance manually. Please see the [Add Tool Tutorial](/src/admin/tools/add-tool-tutorial/index.md). * Automated installation - The process of installing tools from Tool Shed can be performed in an automated way using a set of scripts. This is particularly useful if you are trying to install a large number of tools. The required scripts are available as an [Ansible](https://www.ansible.com/home) playbook from [here](https://github.com/afgane/galaxy-tools-playbook). Please see that page for complete instructions. @@ -39,7 +39,7 @@ To install tools from a Tool Shed you need to have [Mercurial](https://www.mercu ## Open the Tool Shed -Go to Galaxy [Admin Interface](/src/admin/index.md) and click `Install new tools`. +Go to Galaxy [Admin Interface](/admin/) and click `Install new tools`. You will see the following in the middle panel: @@ -83,8 +83,8 @@ The tool will show up in the tool panel of the section you selected, and the use ![Tool Installation](/src/admin/tools/add-tool-from-toolshed-tutorial/tool_installation.png) -You can monitor the installation progress of the tool if you click on `Monitor installing tool shed repositories` in the [Admin Interface](/src/admin/index.md). +You can monitor the installation progress of the tool if you click on `Monitor installing tool shed repositories` in the [Admin Interface](/admin/). -You can also check the states of all installed tools if you click `Manage installed tool shed repositories` in the [Admin Interface](/src/admin/index.md). +You can also check the states of all installed tools if you click `Manage installed tool shed repositories` in the [Admin Interface](/admin/). ![Repository Status](/src/admin/tools/add-tool-from-toolshed-tutorial/repo_status.png) diff --git a/content/admin/tools/add-tool-tutorial/index.md b/content/admin/tools/add-tool-tutorial/index.md index 82e5baf703..5c9d3713cc 100644 --- a/content/admin/tools/add-tool-tutorial/index.md +++ b/content/admin/tools/add-tool-tutorial/index.md @@ -1,7 +1,7 @@ --- title: Adding custom tools to Galaxy --- -A vast number of well-implemented tools are available for Galaxy through the [Galaxy Tool Shed](/src/toolshed/index.md). Users with admin privileges can freely install any tools from the Tool Shed to their Galaxy instance via the [admin interface](/src/admin/index.md). A short tutorial describing how to install tools from the Tool Shed is available [here](/src/admin/tools/add-tool-from-toolshed-tutorial/index.md). +A vast number of well-implemented tools are available for Galaxy through the [Galaxy Tool Shed](/toolshed/). Users with admin privileges can freely install any tools from the Tool Shed to their Galaxy instance via the [admin interface](/admin/). A short tutorial describing how to install tools from the Tool Shed is available [here](/src/admin/tools/add-tool-from-toolshed-tutorial/index.md). The list of available tools in the Tool Shed can be found [here](http://toolshed.g2.bx.psu.edu). If a tool is not currently in the Tool Shed, it can be wrapped and added to Galaxy and later shared in the Tool Shed with the rest of the world. The steps outlined below will guide users through the creation of a custom tool in Galaxy. There are also helpful instructions in this [tutorial for Creating a Histogram Tool](/src/admin/tools/adding-tools/index.md). @@ -100,6 +100,6 @@ Note the correspondence between elements of the tool definition file (Step 3) an ### 6. (optional) Upload the tool to Galaxy's Tool Shed. -To share the tool with the Galaxy community, upload it to the [Galaxy Tool Shed](/src/toolshed/index.md). Users can now install the tool into their Galaxies seamlessly via the [Admin interface](/src/admin/index.md). If the tool is well-written and tested it can even make it to the [Main Galaxy instance](/src/main/index.md) or other [Public Galaxy Servers](/src/use/index.md)! +To share the tool with the Galaxy community, upload it to the [Galaxy Tool Shed](/toolshed/). Users can now install the tool into their Galaxies seamlessly via the [Admin interface](/admin/). If the tool is well-written and tested it can even make it to the [Main Galaxy instance](/main/) or other [Public Galaxy Servers](/use/)! To get started sharing and publishing your tool, check out the [How to publish a tool in the Tool Shed](/src/toolshed/publish-tool/index.md) tutorial. diff --git a/content/admin/tools/data-managers/index.md b/content/admin/tools/data-managers/index.md index e575b6f626..24e69bbcd6 100644 --- a/content/admin/tools/data-managers/index.md +++ b/content/admin/tools/data-managers/index.md @@ -10,7 +10,7 @@ For a video overview on Data Managers, see this [presentation from GCC2013](http # Tutorial -The most up-to-date methods, including how to use Data Manager repositories in the [ToolShed](/src/toolshed/index.md): [GCC2014 TrainingDay](/src/events/gcc2014/training-day/index.md#tool-development-from-bright-idea-to-toolshed-data-managers) +The most up-to-date methods, including how to use Data Manager repositories in the [ToolShed](/toolshed/): [GCC2014 TrainingDay](/src/events/gcc2014/training-day/index.md#tool-development-from-bright-idea-to-toolshed-data-managers) # What Kind of Data is Supported diff --git a/content/admin/tools/linkbox.md b/content/admin/tools/linkbox.md index 278dc7aab0..2168487fee 100644 --- a/content/admin/tools/linkbox.md +++ b/content/admin/tools/linkbox.md @@ -1,15 +1,15 @@
-# [Galaxy Tools](/src/tools/index.md) +# [Galaxy Tools](/tools/) ---- [Install from ToolShed](/src/admin/tools/add-tool-from-toolshed-tutorial/index.md) [Create Custom Tool](/src/admin/tools/add-tool-tutorial/index.md) [Complete Tool Syntax](/src/admin/tools/tool-config-syntax/index.md) ---- -**[Galaxy ToolShed](/src/toolshed/index.md)** +**[Galaxy ToolShed](/toolshed/)** [Publishing Tools](/src/toolshed/publish-tool/index.md) -[Utilities Commission](/src/iuc/index.md) +[Utilities Commission](/iuc/) [Hosting Tool Shed](/src/toolshed/hosting-a-local-toolshed/index.md)
diff --git a/content/admin/training/galaxy-admin-tutorial/index.md b/content/admin/training/galaxy-admin-tutorial/index.md index 7002beb4c5..dcc62017cb 100644 --- a/content/admin/training/galaxy-admin-tutorial/index.md +++ b/content/admin/training/galaxy-admin-tutorial/index.md @@ -10,5 +10,5 @@ See the [Galaxy Tutorial page](http://gmod.org/wiki/Galaxy%20Tutorial) at the [G * [You can make local genomes, alignments, and other data available to Galaxy](/src/admin/data-integration/index.md) * [You can customize what external applications are available for displaying datasets](/src/admin/tools/external-display-applications-tutorial/index.md) * [You can customize the datatypes for a Galaxy instance](/src/admin/datatypes/adding-datatypes/index.md) -* [You can instantiate Galaxy on the cloud using CloudMan](/src/cloudman/index.md) +* [You can instantiate Galaxy on the cloud using CloudMan](/cloudman/) * [You can find even more at the Galaxy Hub](/src/index.md) diff --git a/content/archive/data-libraries/library-templates/index.md b/content/archive/data-libraries/library-templates/index.md index 56a601de02..aba511b3f1 100644 --- a/content/archive/data-libraries/library-templates/index.md +++ b/content/archive/data-libraries/library-templates/index.md @@ -6,7 +6,7 @@ Data library templates provide a way to associate information (metadata) with th is based on a Galaxy form, which must be defined before the template can be associated with a data library or any of it's contents. There are several types of Galaxy forms, and forms on which data library templates are based must be of type "Library information template". -This document assumes that you are in the Admin perspective which is available only to [admin users](/src/admin/index.md) +This document assumes that you are in the Admin perspective which is available only to [admin users](/admin/) and is accessed by clicking on the "Admin" link in the top Galaxy menu bar. However, users that are not admin users can also be granted permission to add and edit data library templates, although they will be doing so from the Data Libraries perspective which is accessible by clicking on the "Data Libraries" option in the "Shared Data" pop-up menu in the top Galaxy menu bar. For information about setting data diff --git a/content/archive/data-libraries/uploading-library-files/index.md b/content/archive/data-libraries/uploading-library-files/index.md index a8fc8b8048..7a440861e6 100644 --- a/content/archive/data-libraries/uploading-library-files/index.md +++ b/content/archive/data-libraries/uploading-library-files/index.md @@ -4,7 +4,7 @@ ### Options for Uploading Files from the Admin Perspective -There are currently four options available to a Galaxy [admin](/src/admin/index.md) user for uploading files to a data library. +There are currently four options available to a Galaxy [admin](/admin/) user for uploading files to a data library. Some of these same options are available to all regular users that have been granted permission to add items to a Data Library or folder, but this section describes the features from the Galaxy admin perspective which is accessed by clicking on the "Admin" link in the top Galaxy menu bar. diff --git a/content/archive/dev-news-briefs/2011-08-30/index.md b/content/archive/dev-news-briefs/2011-08-30/index.md index 5a209d4bca..a19c07ce5f 100644 --- a/content/archive/dev-news-briefs/2011-08-30/index.md +++ b/content/archive/dev-news-briefs/2011-08-30/index.md @@ -36,17 +36,17 @@ And there is now an updated [Galaxy](http://galaxyproject.org) article on Wikipe #### Revised and New Content * *Learn*: A hub page for resources on learning how to use Galaxy. - * [Learn](/src/learn/index.md) + * [Learn](/learn/) * *News Page and RSS Feed*: News items of interest to the Galaxy community - * [News](/src/news/index.md) + * [News](/news/) * *Events*: Comprehensive listing of upcoming (and past) Galaxy Events - * [Events](/src/events/index.md) + * [Events](/events/) * *Get Involved and Outreach*: How to get involved with Galaxy and how to spread the word. * [GetInvolved](/src/get-involved/index.md) - * [Outreach](/src/outreach/index.md) + * [Outreach](/outreach/) * *Public Galaxy Servers*: A list of publicly available Galaxy servers. If you have one, please add it to the list. - [PublicGalaxyServers](/src/use/index.md) + [PublicGalaxyServers](/use/) ### Tool Shed @@ -77,7 +77,7 @@ And there is now an updated [Galaxy](http://galaxyproject.org) article on Wikipe * *AWS Genomics Event* * [http://aws.amazon.com/genomicsevent](http://aws.amazon.com/genomicsevent) * September 22, Seattle, Washington, United States - * *Developing distributed analysis pipelines with shared community resources using [CloudBioLinux](http://www.cloudbiolinux.org) and [CloudMan](/src/cloudman/index.md),* Brad Chapman + * *Developing distributed analysis pipelines with shared community resources using [CloudBioLinux](http://www.cloudbiolinux.org) and [CloudMan](/cloudman/),* Brad Chapman ## Updated & Improved @@ -165,7 +165,7 @@ And there is now an updated [Galaxy](http://galaxyproject.org) article on Wikipe * While no *hard* quotas are currently implemented at the public Galaxy [Main](http://usegalaxy.org) instance, we do ask that users stay within certain usage limits: [Main Quotas](http://galaxyproject.org/wiki/Main#Quotas) * If you find that you require additional resources, please consider the alternative Galaxy options explained at: - [BigPicture/Choices](/src/use/index.md) + [BigPicture/Choices](/use/) ### Bug Fixes diff --git a/content/archive/dev-news-briefs/2011-10-25/index.md b/content/archive/dev-news-briefs/2011-10-25/index.md index 4351a8fc42..43540c47ff 100644 --- a/content/archive/dev-news-briefs/2011-10-25/index.md +++ b/content/archive/dev-news-briefs/2011-10-25/index.md @@ -15,7 +15,7 @@ date: 2011-10-25 ## News
pointing-finger
-* Keep current on all things Galaxy at our [News](/src/news/index.md) and [Events](/src/events/index.md) wikis. +* Keep current on all things Galaxy at our [News](/news/) and [Events](/events/) wikis. * Galaxy is still [hiring](/src/galaxy-is-hiring/index.md)! ## What's New @@ -24,11 +24,11 @@ date: 2011-10-25 * Data and Job Quotas announced earlier today by email, Galaxy wiki, Twitter, and News Items/RSS feed. * [Email](http://lists.bx.psu.edu/pipermail/galaxy-user/2011-October/003467.html) message from the team to galaxy-user and galaxy-dev [mailing lists](/src/mailing-lists/index.md). - * [Main](/src/main/index.md) wiki with limits, FAQ, and related links. + * [Main](/main/) wiki with limits, FAQ, and related links. * [Managing Datasets](/src/learn/managing-datasets/index.md) wiki contains detailed help to organize, clone, copy, save, and delete unneeded data. * [Disk Quotas](/src/admin/disk-quotas/index.md) wiki has administrative information on how Galaxy's disk space accounting works, how to keep it up to date, and how to enable and manage quotas * Twitter [#galaxyproject](http://twitter.com/#galaxyproject). - * [Galaxy News](/src/news/index.md) Items and RSS feed. + * [Galaxy News](/news/) Items and RSS feed. ---- @@ -128,7 +128,7 @@ date: 2011-10-25 ### Bug Fixes -
bugs
+
bugs
* Tasked jobs will now inherit the parent job's user information correctly. * Remove unspecified build validators from Cuffdiff wrapperfixes [https://bitbucket.org/galaxy/galaxy-central/issue/631](https://bitbucket.org/galaxy/galaxy-central/issue/631). diff --git a/content/archive/dev-news-briefs/2011-11-18/index.md b/content/archive/dev-news-briefs/2011-11-18/index.md index 1b13245fd7..10f2d5db77 100644 --- a/content/archive/dev-news-briefs/2011-11-18/index.md +++ b/content/archive/dev-news-briefs/2011-11-18/index.md @@ -15,7 +15,7 @@ date: 2011-11-18 ## News & Events
pointing-finger
-* Keep current on all things Galaxy at our [News](/src/news/index.md) and [Events](/src/events/index.md) wikis. +* Keep current on all things Galaxy at our [News](/news/) and [Events](/events/) wikis. * Galaxy is still [hiring](/src/galaxy-is-hiring/index.md)! ### GCC 2012 is Scheduled! @@ -37,8 +37,8 @@ Please reserve July 25-27 on your calendars! * A one day [Galaxy Developer Workshop](http://evomics.org/workshops/galaxy-developer-workshop/) is being held in [Galaxy Developer Workshop](http://evomics.org/workshops/galaxy-developer-workshop/) in [Český Krumlov, Czech Republic](http://www.ckrumlov.info/php/) * Registration deadline is December 15, but you are encouraged to register early, so we can gauge demand. * This workshop is immediately following the [Workshop on Genomics](http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-krumlov/2012), which also features Galaxy content, and is still accepting applications. -* Galaxy will have presentations at [PAG 2012 (January, San Diego)](/src/events/pag2012/index.md) on using Galaxy, both on [Main](/src/main/index.md) and in the [Cloud](/src/cloudman/index.md) -* There are also [events](/src/events/index.md) at the [University of Manchester](http://www.nowgen.org.uk/facilities/events/event.php?id=30) and [DDBJ](http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ) in January. +* Galaxy will have presentations at [PAG 2012 (January, San Diego)](/src/events/pag2012/index.md) on using Galaxy, both on [Main](/main/) and in the [Cloud](/cloudman/) +* There are also [events](/events/) at the [University of Manchester](http://www.nowgen.org.uk/facilities/events/event.php?id=30) and [DDBJ](http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ) in January. ---- ## What's New @@ -81,19 +81,19 @@ There are two Tool Sheds supported by the core Galaxy team: * **[FastQC:](http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/)** * Wrapper updated to handle changes in HTML output from the most recent FastQC release 0.10.0 from [Babraham Bioinformatics](http://www.bioinformatics.bbsrc.ac.uk/) * If you see a broken FastQC html report in the UI, then an older version is being used. **[Upgrading FastQC to version 0.10.0](http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) is required** - * Galaxy [Main](/src/main/index.md) is running version 0.10.0 + * Galaxy [Main](/main/) is running version 0.10.0 * **[Picard:](http://picard.sourceforge.net/)** * Wrapper updated to handle changes to command line parameters for `CollectInsertSizeMetrics.jar` in version 1.56 * If you see an error message about an unrecognized parameter `"DEVIATIONS"` (related to Insertion size metrics), then an older version is being used. **[Upgrading Picard to version 1.56](http://sourceforge.net/projects/picard/files/) is required** * Update Picard tools to use `tool-data/shared/jars/picard/*` instead of `tool-data/shared/jars/*` - * Galaxy [Main](/src/main/index.md) is running version 1.56 + * Galaxy [Main](/main/) is running version 1.56 * **[TopHat:](http://tophat.cbcb.umd.edu/)** * Wrapper updated to support versions 1.3.* * If you see an error message about "tophat: option --max-insertion-length not recognized", then an older version is being used. **[Upgrading TopHat to at least version 1.3.1 (with 1.3.3 preferred)](http://tophat.cbcb.umd.edu/) is required** - * Galaxy [Main](/src/main/index.md) is running version 1.3.3 + * Galaxy [Main](/main/) is running version 1.3.3 * **[Cufflinks:](http://cufflinks.cbcb.umd.edu/)** * Improved documentation for gene annotation dataset parameters - * Galaxy [Main](/src/main/index.md) is running version 1.0.3 + * Galaxy [Main](/main/) is running version 1.0.3 * Upgraded tool **Convert Formats -> SFF converter** to use *[sff_extract](http://bioinf.comav.upv.es/sff_extract/download.html)* version 0.2.10 * **[SAMTools:](http://samtools.sourceforge.net/)** * Handle SAMTools stderr messages causing an error state when using [FreeBayes](http://github.com/ekg/freebayes) @@ -149,7 +149,7 @@ There are two Tool Sheds supported by the core Galaxy team: ### Bug Fixes -
bugs
+
bugs
* Grid fixes: (a) make operation buttons work after refresh and (b) show message each time * Force absolute path when creating temporary directory used when importing histories. Fixes [https://bitbucket.org/galaxy/galaxy-central/issue/667](https://bitbucket.org/galaxy/galaxy-central/issue/667) diff --git a/content/archive/dev-news-briefs/2012-01-20/index.md b/content/archive/dev-news-briefs/2012-01-20/index.md index 224f58ad1f..147462d2bd 100644 --- a/content/archive/dev-news-briefs/2012-01-20/index.md +++ b/content/archive/dev-news-briefs/2012-01-20/index.md @@ -28,13 +28,13 @@ Galaxy now has a layer between the front end and disk files, and this layer is t * **[TopHat:](http://tophat.cbcb.umd.edu/)** * Wrapper accepts versions 1.3.1-1.4.0, with at least 1.3.3 recommended. 1.4.0 is preferred. - * Galaxy [Main](/src/main/index.md) is now running version 1.4.0. + * Galaxy [Main](/main/) is now running version 1.4.0. * **[Cufflinks, CuffCompare, CuffDiff:](http://cufflinks.cbcb.umd.edu/)** * Wrapper accepts versions 1.1.0-1.3.0. 1.3.0 is preferred. - * Galaxy [Main](/src/main/index.md) is now running version 1.3.0 for all Cuff* tools. + * Galaxy [Main](/main/) is now running version 1.3.0 for all Cuff* tools. * **[SAMTools mpileup:](http://samtools.sourceforge.net/mpileup.shtml)** * Wrapper for use in local instances. - * Not available on Galaxy [Main](/src/main/index.md) at this time. + * Not available on Galaxy [Main](/main/) at this time. * **[GenomeSpace](http://www.genomespace.org/)** import from file browser tool updated to use their newer API. * **[EBI ENA SRA](http://www.ebi.ac.uk/ena/)** tool contributed by Iain Cleland. * **[Picard](http://sourceforge.net/projects/picard/) Interval List to [BED6](http://genome.ucsc.edu/FAQ/FAQformat.html#format1)** converter added. @@ -88,14 +88,14 @@ Galaxy now has a layer between the front end and disk files, and this layer is t * Do not allow public user names to be changed within the tool shed if the user has created a tool shed repository. * Don't allow repository names to be changed if the repository has been cloned at least 1 time. * More new tool shed features documented in the following new Galaxy wiki sections: - * [Including proprietary data types that subclass from Galaxy data types in the distribution](/src/toolshed/index.md#including-proprietary-data-types-that-subclass-from-galaxy-data-types-in-the-distribution) - * [Including proprietary data types that use class modules contained in your repository](/src/toolshed/index.md#including-proprietary-data-types-that-use-class-modules-contained-in-your-repository) - * [Including datatype converters and display applications](/src/toolshed/index.md#including-datatype-converters-and-display-applications) - * [Automatic installation of Galaxy tool shed repository data types into a local Galaxy instance](/src/toolshed/index.md#automatic-installation-of-galaxy-tool-shed-repository-data-types-into-a-local-galaxy-instance) - * [Getting updates for tool shed repositories installed in a local Galaxy instance](/src/toolshed/index.md#getting-updates-for-tool-shed-repositories-installed-in-a-local_galaxy_instance) - * [Migrating tools from the Galaxy distribution to the Galaxy main tool shed](/src/toolshed/index.md#migrating-tools-from-the-galaxy-distribution-to-the-galaxy-main-tool-shed) - * [Configuring your Galaxy server to automatically install tools eliminated from the Galaxy distribution](/src/toolshed/index.md#configuring-your-galaxy-server-to-automatically-install-tools-eliminated-from-the-galaxy-distribution) - * [Use case: automatically install the Emboss tools and datatypes into a local Galaxy instance](/src/toolshed/index.md#use-case-automatically-install-the-emboss-tools-and-datatypes-into-a-local-galaxy-instance) + * [Including proprietary data types that subclass from Galaxy data types in the distribution](/toolshed/#including-proprietary-data-types-that-subclass-from-galaxy-data-types-in-the-distribution) + * [Including proprietary data types that use class modules contained in your repository](/toolshed/#including-proprietary-data-types-that-use-class-modules-contained-in-your-repository) + * [Including datatype converters and display applications](/toolshed/#including-datatype-converters-and-display-applications) + * [Automatic installation of Galaxy tool shed repository data types into a local Galaxy instance](/toolshed/#automatic-installation-of-galaxy-tool-shed-repository-data-types-into-a-local-galaxy-instance) + * [Getting updates for tool shed repositories installed in a local Galaxy instance](/toolshed/#getting-updates-for-tool-shed-repositories-installed-in-a-local_galaxy_instance) + * [Migrating tools from the Galaxy distribution to the Galaxy main tool shed](/toolshed/#migrating-tools-from-the-galaxy-distribution-to-the-galaxy-main-tool-shed) + * [Configuring your Galaxy server to automatically install tools eliminated from the Galaxy distribution](/toolshed/#configuring-your-galaxy-server-to-automatically-install-tools-eliminated-from-the-galaxy-distribution) + * [Use case: automatically install the Emboss tools and datatypes into a local Galaxy instance](/toolshed/#use-case-automatically-install-the-emboss-tools-and-datatypes-into-a-local-galaxy-instance) ## Tool Shed Contributions @@ -112,7 +112,7 @@ Galaxy now has a layer between the front end and disk files, and this layer is t ## Bug Fixes -
bugs
+
bugs
* Support display of extra files/composite types in published items. Fixes [https://bitbucket.org/galaxy/galaxy-central/issue/628](https://bitbucket.org/galaxy/galaxy-central/issue/628) * Standardize code and error messages on 'public name' rather than 'username' * When exporting a history archive, use user dataset names rather than Galaxy dataset names. Fixes [https://bitbucket.org/galaxy/galaxy-central/issue/680](https://bitbucket.org/galaxy/galaxy-central/issue/680) diff --git a/content/archive/dev-news-briefs/2012-01-27/index.md b/content/archive/dev-news-briefs/2012-01-27/index.md index 3170cc26ca..fdb020982d 100644 --- a/content/archive/dev-news-briefs/2012-01-27/index.md +++ b/content/archive/dev-news-briefs/2012-01-27/index.md @@ -42,7 +42,7 @@ date: 2012-01-27 * **flagstat** (existing) requires versions 0.1.16-0.1.18. * **[Mpileup](http://samtools.sourceforge.net/mpileup.shtml)** (new) requires versions 0.1.16-0.1.18. * **[Pileup](http://samtools.sourceforge.net/pileup.shtml)** (existing) requires versions 0.1.12-0.1.16, with 0.1.16 *strongly* preferred and tool dependency directory configuration (if upgrading other SAMtools to 0.1.18). - * Galaxy **[Main](/src/main/index.md)** is running SAMtools version 0.1.18 for all with the exception of Pileup version 0.1.16. + * Galaxy **[Main](/main/)** is running SAMtools version 0.1.18 for all with the exception of Pileup version 0.1.16. * Updated **[TopHat](http://tophat.cbcb.umd.edu/)** tests for version 1.4.0. * Updated **[Cufflinks, CuffCompare, CuffDiff](http://cufflinks.cbcb.umd.edu/)** tests for version 1.3.0. * Better error reporting in **[Cufflinks](http://cufflinks.cbcb.umd.edu/)**. @@ -73,7 +73,7 @@ date: 2012-01-27 ## Tool Shed -* **[Tool Shed](/src/toolshed/index.md)** fixes: +* **[Tool Shed](/toolshed/)** fixes: * Fix for handling a tool data table entry when uploading to a tool shed repository. * Reset all metadata on all changeset revisions of a tool shed repsoitory whenever a new change set is introduced. This will result in a more standardized set of valid changeset revisions that can be installed. * Fix for generating workflow metadata and viewing workflows in tool shed repositories. @@ -82,7 +82,7 @@ date: 2012-01-27 ## Bug Fixes -
bugs
+
bugs
* Python 2.5 support was broken in the last stable release, this has been fixed * A broken unit test under 2.5 will not be fixed until the next release, however - this can safely be ignored. * A fix to not use math.isnan because it is not compatible with python 2.5 has been made. @@ -103,4 +103,4 @@ The **[GalaxyTeam](http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam/)* Join us at **Twitter [@galaxyproject](http://twitter.com/#galaxyproject)** ---- -Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-01-27 +Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/docs/) on 2012-01-27 diff --git a/content/archive/dev-news-briefs/2012-03-12/index.md b/content/archive/dev-news-briefs/2012-03-12/index.md index f70a3712f7..325e7beeee 100644 --- a/content/archive/dev-news-briefs/2012-03-12/index.md +++ b/content/archive/dev-news-briefs/2012-03-12/index.md @@ -128,10 +128,10 @@ Trackster visualization of [ENCODE](http://genome.ucsc.edu/ENCODE/) and Composit # CloudMan -**[CloudMan](/src/cloudman/index.md)** -* A larger tools volume (10GB vs old 2GB) is now the default for any new [CloudMan](/src/cloudman/index.md) cluster making it easier to customize your Galaxy Cloud instances -* A [preliminary support for OpenNebula cloud type](http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py) exists within [CloudMan](/src/cloudman/index.md) (thanks to Mattias de Hollander) -* Please continue to use AMI **ami-da58aab3** for Galaxy Cloud clusters, as listed on [usegalaxy.org/cloud](/src/cloudman/index.md). There is another AMI dated from Feb 26, 2012 that was not created by the Galaxy Team and is not supported by us. +**[CloudMan](/cloudman/)** +* A larger tools volume (10GB vs old 2GB) is now the default for any new [CloudMan](/cloudman/) cluster making it easier to customize your Galaxy Cloud instances +* A [preliminary support for OpenNebula cloud type](http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py) exists within [CloudMan](/cloudman/) (thanks to Mattias de Hollander) +* Please continue to use AMI **ami-da58aab3** for Galaxy Cloud clusters, as listed on [usegalaxy.org/cloud](/cloudman/). There is another AMI dated from Feb 26, 2012 that was not created by the Galaxy Team and is not supported by us. # Source @@ -156,14 +156,14 @@ Trackster visualization of [ENCODE](http://genome.ucsc.edu/ENCODE/) and Composit # Bug Fixes -
bugs
+
bugs
* Fix for 'Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION): Multiple Content-Disposition headers received.' error occuring when downloading certain datasets using Chrome browser * Correction to *History Size* calculation to accurately filter out 'purged' datasets in the summary size * Various bug fixes for Object Store, with a particular focus on the Distributed Object Store # Announcements -**[News](/src/news/index.md)** +**[News](/news/)** **March 2012** ***[Galaxy Update](/src/galaxy-updates/2012-03/index.md)*** @@ -202,4 +202,4 @@ The **[GalaxyTeam](http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam/)* Join us at **Twitter [@galaxyproject](http://twitter.com/#galaxyproject)** or just read our tweets **[Galaxy on Twitter](/src/galaxy-on-twitter/index.md)** ---- -
Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/src/docs/index.md) on 2012-03-12 + Jennifer Jackson, [Galaxy Team](/galaxy-team/). Posted to [DevNewsBriefs](/docs/) on 2012-03-12 diff --git a/content/archive/dev-news-briefs/2012-05-11/index.md b/content/archive/dev-news-briefs/2012-05-11/index.md index 4ddaf98a95..dbff54f543 100644 --- a/content/archive/dev-news-briefs/2012-05-11/index.md +++ b/content/archive/dev-news-briefs/2012-05-11/index.md @@ -88,7 +88,7 @@ Tools using the process described at '[Admin/Tools/MultipleOutputFiles](/src/adm * *Genome Analysis Toolkit (beta) tool group includes*: Depth of Coverage on BAM files; Print Reads from BAM files; Realigner Target; Creator for use in local realignment; Indel Realigner - perform local realignment; Count Covariates on BAM files; Table Recalibration on BAM files; Analyze Covariates - draw plots; Unified Genotyper SNP and indel caller; Variant Annotator; Variant Filtration on VCF files; Select Variants from VCF files; Variant Recalibrator; Apply Variant Recalibration; Validate Variants; Eval Variants; Combine Variants. * Additional tool documentation developing over next few months. For now, refer to [GATK tool author help](http://www.broadinstitute.org/gsa/wiki). -gatk-workflow +gatk-workflow * **NGS: Variant Detection** * Added **[FreeBayes](http://github.com/ekg/freebayes)** latest version (a46483351fd0196637614121868fb5c386612b55) * Requires **[SAM Tools](http://samtools.sourceforge.net/), version 0.1.16-0.1.18** *strongly recommended* @@ -117,7 +117,7 @@ Tools using the process described at '[Admin/Tools/MultipleOutputFiles](/src/adm
# Tool Shed -[Tool Shed](/src/toolshed/index.md) +[Tool Shed](/toolshed/) * **Features** * The tool shed's upload process will automatically eliminate undesired directories (.svn, .git, .hg, .cvs) and file (hgrc, .jhg_archival.txt, .DS_Store) from the archive before committing the contents to the repository. This provides for a more pristine environment for those that install the repository locally. * You can now browse your invalid tools in the tool shed, and clicking on an invalid tools will display information about why it is invalid. The definition of a valid tool in the tool shed has always been restricted to the tool properly loading in a Galaxy instance and that no required dependent files are missing. If a tool is not valid, it will not be returned in a search and it cannot be automatically installed (unless it belongs to a repository containing other valid tools). Only valid tools should be shared in the tool shed or its value will diminish over time. Tool developers should browse their invalid tools and make corrections to them if necessary. @@ -180,7 +180,7 @@ Tools using the process described at '[Admin/Tools/MultipleOutputFiles](/src/adm
# Bug Fixes -
bugs
+
bugs
* `fasta_to_len` conversion now uses only the first word in the description line from input [FASTA](/src/learn/datatypes/index.md#fasta) datasets to create the *identifier name* for sequences. This is standards compliant and used by default for automatic conversion. * Add necessary space after threads option in [Cuffmerge](http://cufflinks.cbcb.umd.edu/). * The dataset cleanup scripts will no longer error out if database_connection is not explicitly set in the Galaxy config file. Addresses mailing list questions: @@ -204,7 +204,7 @@ Tools using the process described at '[Admin/Tools/MultipleOutputFiles](/src/adm
# Announcements -[News](/src/news/index.md), *[May 2012 Galaxy Update](/src/galaxy-updates/2012-05/index.md)* +[News](/news/), *[May 2012 Galaxy Update](/src/galaxy-updates/2012-05/index.md)* ## GCC2012 Update diff --git a/content/archive/dev-news-briefs/2012-07-20/index.md b/content/archive/dev-news-briefs/2012-07-20/index.md index 8e3346273a..62bcd6c482 100644 --- a/content/archive/dev-news-briefs/2012-07-20/index.md +++ b/content/archive/dev-news-briefs/2012-07-20/index.md @@ -23,10 +23,10 @@ The [2012 Galaxy Community Conference (GCC2012)](/src/events/gcc2012/index.md) i
# FreeBayes Migration -The tool **Human Genome Variation -> [Freebayes](http://bioinformatics.bc.edu/marthlab/FreeBayes)** has moved from the Galaxy distribution to the Galaxy Main **[Tool Shed](/src/toolshed/index.md)**. +The tool **Human Genome Variation -> [Freebayes](http://bioinformatics.bc.edu/marthlab/FreeBayes)** has moved from the Galaxy distribution to the Galaxy Main **[Tool Shed](/toolshed/)**. ```FreeBayes``` - is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on [BAM](/src/datatypes/index.md#bam) alignment files, which are produced by most contemporary short-read aligners. + is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on [BAM](/datatypes/#bam) alignment files, which are produced by most contemporary short-read aligners.
# EMBOSS Update @@ -88,7 +88,7 @@ Several changes made in in determining errors from tool exit codes and output.
# Tool Shed -[Tool Shed](/src/toolshed/index.md) +[Tool Shed](/toolshed/) * *Enhancements* * The tool shed's category grid is now displayed when searching and browsing tool sheds from a local Galaxy instance. * This category grid's search feature searches valid repository names and descriptions when browsing a tool shed from Galaxy. @@ -97,13 +97,13 @@ Several changes made in in determining errors from tool exit codes and output.
# Bug Fixes -
bugs
+
bugs
* Support Unvalidated values when exporting histories
# Announcements -[News](/src/news/index.md), *[July 2012 Galaxy Update](/src/galaxy-updates/2012-07/index.md)* +[News](/news/), *[July 2012 Galaxy Update](/src/galaxy-updates/2012-07/index.md)* ## Collaboration The new RGalaxy package in Bioconductor. [Read more …](/src/news/r-galaxy-wrap-r-functions-as-tools/index.md) diff --git a/content/archive/dev-news-briefs/2012-09-07/index.md b/content/archive/dev-news-briefs/2012-09-07/index.md index fee5169845..d2c9291427 100644 --- a/content/archive/dev-news-briefs/2012-09-07/index.md +++ b/content/archive/dev-news-briefs/2012-09-07/index.md @@ -19,14 +19,14 @@ date: 2012-09-07
# BLAST+ Migration -The tool set **[NCBI BLAST+](http://blast.ncbi.nlm.nih.gov/)** has moved from the Galaxy distribution to the Galaxy Main **[Tool Shed](/src/toolshed/index.md)**. +The tool set **[NCBI BLAST+](http://blast.ncbi.nlm.nih.gov/)** has moved from the Galaxy distribution to the Galaxy Main **[Tool Shed](/toolshed/)**. -Migration scripts will run upon Galaxy's first launch (after updating to this release) that will automatically handle installing **BLAST** (and **blastxml**) from the **[Tool Shed](/src/toolshed/index.md)**. +Migration scripts will run upon Galaxy's first launch (after updating to this release) that will automatically handle installing **BLAST** (and **blastxml**) from the **[Tool Shed](/toolshed/)**.
# Reference Genome rsync Server -If you would like to obtain the same *reference genome builds and indexes* as available on the public **Galaxy [Main](/src/main/index.md)** instance, these can retrieved from the rsync server at: +If you would like to obtain the same *reference genome builds and indexes* as available on the public **Galaxy [Main](/main/)** instance, these can retrieved from the rsync server at: ``` datacache.g2.bx.psu.edu ``` @@ -57,7 +57,7 @@ As reported in the *[July 20th, 2012 News Brief](/src/archive/dev-news-briefs/20 * One benefit is that **BAM** results can be used as input to **[Cufflinks](http://cufflinks.cbcb.umd.edu/)** without an [intermediate sorting step](http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2). * *NOTE:* If you are using an older version of *Bowtie* or uploading your own results, sorting is still required before running *Cufflinks*, whether in [SAM](/src/learn/datatypes/index.md#sam) or [BAM](/src/learn/datatypes/index.md#bam) format. * *New* - * **[Galaxy RNA-seq Analysis Exercise](http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise)** on [Main](/src/main/index.md) + * **[Galaxy RNA-seq Analysis Exercise](http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise)** on [Main](/main/) * Walks through sample protocol step-by-step using paired-end data, initial read QC through **[CuffDiff](http://cufflinks.cbcb.umd.edu/)** analysis * Includes **[iGenomes](http://tophat.cbcb.umd.edu/igenomes.html)** sourced **[reference annotation GTF](http://tophat.cbcb.umd.edu/igenomes.html)**, an answer key, and bonus resources @@ -69,7 +69,7 @@ As reported in the *[July 20th, 2012 News Brief](/src/archive/dev-news-briefs/20 * *New* * Addition of **interactive phylogenetic tree visualization**. -interactive-phylo-tree +interactive-phylo-tree
# Galaxy Track Browser (GTB) @@ -114,7 +114,7 @@ $ sh run.sh --daemon/sh run.sh --stop-daemon
# Tool Shed -[Tool Shed](/src/toolshed/index.md) +[Tool Shed](/toolshed/) * *Fixes* * Several miscellaneous fixes for using a **[SQLite](http://www.sqlite.org/)** database with a local tool shed. * It is no longer possible to change the name of a repository in the tool shed at during the time when the repository is first being cloned. @@ -143,23 +143,23 @@ Now the above entry still works, but the following entry is also ok (notice the * The implementation for importing proprietary datatype class modules included in a tool shed repository now supports class module files whose name conflicts with a **[Python](http://www.python.org/)** standard library module name. For example, if a proprietary datatype class module is named `xml.py`, it will now be correctly imported even though the name conflicts with the Python standard library's xml module. * The repository tip is now displayed in a column that is separate from the repository's installable changeset revisions in the tool shed. -repository-grid.png +repository-grid.png * Additional information has been added to the "Tool metadata" page, which is displayed when you choose the "View tool metadata" option from a tool's pop-up menu. This menu is available in 2 locations: when viewing the repository in a tool shed, and when viewing a repository (which includes tools) that has been installed into a local Galaxy instance. The additional information added to the Tool metadata page includes: * information about tool dependencies if they have been defined in the repository * requirements defined in the tool config `` tag set * The tool's version lineage information, an example of which is shown here for a sample tool named **Filter** -view-tool-metadata-page.png +view-tool-metadata-page.png * In addition to browsing repositories that you own, you can now also browse repositories for which you have been granted "write" permission. Here is a snapshot of the new Galaxy tool shed menu. -toolshed-menu.png +toolshed-menu.png
# Bug Fixes -
bugs
+
bugs
* *General* * Fix permissions problems on `stdout/stderr/errorcode` files when running jobs as the [real system user](/src/archive/dev-news-briefs/2012-01-27/index.md#run-cluster-jobs-as-the-real-user). * Galaxy will no longer try to modify permissions of [linked library uploads](/src/admin/Data Libraries/Uploading Library Files/index.md). @@ -187,7 +187,7 @@ Now the above entry still works, but the following entry is also ok (notice the
# Announcements -[News](/src/news/index.md), *[August](/src/galaxy-updates/2012-09/index.md)* and *[September](/src/galaxy-updates/2012-09/index.md)* *2012 Galaxy Updates* +[News](/news/), *[August](/src/galaxy-updates/2012-09/index.md)* and *[September](/src/galaxy-updates/2012-09/index.md)* *2012 Galaxy Updates*
September 2012 Galaxy Update
@@ -223,7 +223,7 @@ The Galaxy is expanding! Please help it grow. * [Bioinformatics & Integrative Genomics Specialist - Manager Bioinformatics Consulting Core](http://www.nature.com/naturejobs/science/jobs/275747-Bioinformatics-Integrative-Genomics-Specialist-Manager-Bioinformatics-Consulting-Core) @ Leuven, Belgium * [Internship @ EMBL Heidelberg building an emBASE-Galaxy Bridge](http://www.sfbi.fr/content/development-embase-galaxy-bridge) -Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/src/news/index.md) and include it the next [Galaxy Update](/src/galaxy-updates/index.md) and [News Brief](/src/docs/index.md). +Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/news/) and include it the next [Galaxy Update](/src/galaxy-updates/index.md) and [News Brief](/docs/).

---- diff --git a/content/archive/dev-news-briefs/2012-09-20/index.md b/content/archive/dev-news-briefs/2012-09-20/index.md index 78322b73ce..388954f2bc 100644 --- a/content/archive/dev-news-briefs/2012-09-20/index.md +++ b/content/archive/dev-news-briefs/2012-09-20/index.md @@ -63,13 +63,13 @@ Full instructions for getting started with a **Galaxy CloudMan Instance**, inclu
***Access here*** -cloudlaunch-main +cloudlaunch-main
**Then, *login with your credentials* and go!** -cloudlaunch-home +cloudlaunch-home
# Galaxy Tool Factory @@ -84,7 +84,7 @@ Imagine you have a simple sh or R script you need to run quickly in Galaxy - wit * Select the **Tool Factory** tool. Cut and paste the R (or perl/python/sh) script into the typical Galaxy **Tool Factory** form, select the small sample input file and click execute to run it! The help text on the form includes working examples showing how to pass input/output file paths in each available scripting language. -toolfactory +toolfactory * Check the output. If the script didn't work right, use the redo button on the output to recreate the form and edit the script. @@ -128,16 +128,16 @@ For example, let's take a look at a Galaxy instance into which 2 revisions of a **Here is our Galaxy tool panel** - notice the single link to the installed *Filter* tool. -tool-panel +tool-panel **Clicking the *Filter* link in the tool panel displays the Filter tool's page**, where you can select the version you want. -filter-tool-page +filter-tool-page
# Tool Shed -[Tool Shed](/src/toolshed/index.md) +[Tool Shed](/toolshed/) * *Tool shed features for Galaxy tools* * The primary intent of the tool shed is for sharing Galaxy tools, workflows and other useful Galaxy utilities. Galaxy tools are generally developed within a local Galaxy environment, proven to be functionally correct within that environment, and then uploaded to a tool shed for sharing. With a couple of exceptions, tool features are defined within the Galaxy framework, and have nothing to do with the tool shed. [Read more…](/src/toolshed/tool-features/index.md) * *Pushing changes to a tool shed repository using hg from the command line* @@ -167,7 +167,7 @@ For example, let's take a look at a Galaxy instance into which 2 revisions of a
# Bug Fixes -
bugs
+
bugs
* *General* * Fix bug in [__init__.py](http://bitbucket.org/galaxy/galaxy-central/changeset/3f12146d6d81e08f662ada2011a6973e4230512d) with respect to stdout, stderr, and exit code handling. * Fix [create_all_fasta_loc.py](https://bitbucket.org/galaxy/galaxy-central/changeset/8153e8d25009d71a523e0f2df24ed12922825d8f#chg-scripts/loc_files/create_all_fasta_loc.py) to work when `inspect_dir` is not set. @@ -179,7 +179,7 @@ For example, let's take a look at a Galaxy instance into which 2 revisions of a
# Announcements -[News](/src/news/index.md), *[September 2012 Galaxy Update](/src/galaxy-updates/2012-09/index.md)* +[News](/news/), *[September 2012 Galaxy Update](/src/galaxy-updates/2012-09/index.md)*
---- diff --git a/content/archive/dev-news-briefs/2012-10-05/index.md b/content/archive/dev-news-briefs/2012-10-05/index.md index 011d4fb6a5..cb7853b5dd 100644 --- a/content/archive/dev-news-briefs/2012-10-05/index.md +++ b/content/archive/dev-news-briefs/2012-10-05/index.md @@ -69,7 +69,7 @@ If called with the `--help` option, it will output usage information. The datas
# Tool Shed -The **[Tool Shed](/src/toolshed/index.md)** wiki has been re-written with a new, cleaner presentation. *[Check it out!](/src/toolshed/index.md)* +The **[Tool Shed](/toolshed/)** wiki has been re-written with a new, cleaner presentation. *[Check it out!](/toolshed/)* ### New tool shed features @@ -203,7 +203,7 @@ Tool changes that enable clearer experimental tracking and ease reproducibility
# Announcements -[News](/src/news/index.md), *[October 2012 Galaxy Update](/src/galaxy-updates/2012-10/index.md)* +[News](/news/), *[October 2012 Galaxy Update](/src/galaxy-updates/2012-10/index.md)* **[Highlights](/src/news/2012-10-galaxy-update/index.md):** diff --git a/content/archive/dev-news-briefs/2012-10-23/index.md b/content/archive/dev-news-briefs/2012-10-23/index.md index 36c688e9ae..453601b7bd 100644 --- a/content/archive/dev-news-briefs/2012-10-23/index.md +++ b/content/archive/dev-news-briefs/2012-10-23/index.md @@ -29,7 +29,7 @@ date: 2012-10-23 Administrators are always encouraged to install the latest release not only to incorporate new features, but to take advantage of the current set of security and bug fixes inherent in any project with a fast paced development cycle. This is even more strongly advised for those running public instances. The Galaxy team takes security very seriously and strives to quickly and clearly communicate when a security issue is identified. We have an amazing community that is instrumental in the discovery and resolution of problems when they are uncovered - and we want to thank them for their contributions and support. Galaxy is truly a team effort and transparency and information flow is our priority. -We also intend to learn from recent actions in these areas that fell short of a best effort. The security corrections and priority of the changes to the `Compute` tool in the prior distribution lacked the details and urgency notice it deserved. The move from *Bitbucket* to *[Trello](/src/issues/index.md)* for community collaboration in issue reporting also lacked the information and timely documentation that would have made the transition processes smoother. Both are covered in more detail in this News Brief. Our goals are to provide a remedy for the immediate issues and to create a successful communications and collaborations model for the future. We value your feedback - please let us know how we are doing as the new tools are put into practice. +We also intend to learn from recent actions in these areas that fell short of a best effort. The security corrections and priority of the changes to the `Compute` tool in the prior distribution lacked the details and urgency notice it deserved. The move from *Bitbucket* to *[Trello](/issues/)* for community collaboration in issue reporting also lacked the information and timely documentation that would have made the transition processes smoother. Both are covered in more detail in this News Brief. Our goals are to provide a remedy for the immediate issues and to create a successful communications and collaborations model for the future. We value your feedback - please let us know how we are doing as the new tools are put into practice. 1. **[Compute Tool Security Fix](/src/archive/dev-news-briefs/2012-10-23/index.md#compute-tool-security-fix)** 2. **[New Trello Issue Board](/src/archive/dev-news-briefs/2012-10-23/index.md#new-trello-issue-board)** @@ -49,7 +49,7 @@ https://bitbucket.org/galaxy/galaxy-dist/changeset/685a17af92dfd6a2e3d7e3c9a3a4b
# New Trello Issue Board -The Galaxy project now has a [new issue tracking system](/src/issues/index.md). The public facing ***[Trello](http://trello.com)*** board is accessible from **http://galaxyproject.org/trello''' to perform simple web issue reporting. The direct link into the ''Trello'' board is '''https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45'''. Please note that the same guidelines about creating issues used previously at ''Bitbucket'' apply here as well - report software issues and change requests, but get support and ask questions on the mailing list: galaxy-dev@bx.psu.edu. +The Galaxy project now has a [new issue tracking system](/issues/). The public facing ***[Trello](http://trello.com)*** board is accessible from **http://galaxyproject.org/trello''' to perform simple web issue reporting. The direct link into the ''Trello'' board is '''https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45'''. Please note that the same guidelines about creating issues used previously at ''Bitbucket'' apply here as well - report software issues and change requests, but get support and ask questions on the mailing list: galaxy-dev@bx.psu.edu. To add new cards, the community can quickly fill out the form at http://galaxyproject.org/trello and submit (use markdown for formatting, if desired), but comment on and vote for issues directly on the *[Trello](https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45)* issue board itself. @@ -62,7 +62,7 @@ The Galaxy wiki and other related resources have now been updated to point to th
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### Tool Shed Enhancements inside of Galaxy @@ -123,7 +123,7 @@ shed_tool_conf.xml # Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### Tool Shed Enhancements inside of Galaxy @@ -162,7 +162,7 @@ All Galaxy instance maintainers are *strongly encouraged* to run the latest rele
# Announcements -[News](/src/news/index.md), ***[November 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-11)*** +[News](/news/), ***[November 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-11)*** ### Highlights diff --git a/content/archive/dev-news-briefs/2012-12-03/index.md b/content/archive/dev-news-briefs/2012-12-03/index.md index 5fbdfd6ce1..ad7b2982b4 100644 --- a/content/archive/dev-news-briefs/2012-12-03/index.md +++ b/content/archive/dev-news-briefs/2012-12-03/index.md @@ -45,7 +45,7 @@ Harris, R.S. (2007) *[Improved pairwise alignment of genomic DNA](http://www.bx. **[CloudMan](http://usegalaxy.org/cloud)** -[CloudMan](/src/cloudman/index.md) offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration. +[CloudMan](/cloudman/) offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration. This update brings a large number of updates and new features, the most prominent ones being: * Support for Eucalyptus cloud middleware; thanks to Alex Richter. Also, CloudMan can now run on the HPcloud in basic mode (note that there is no public image available on the HPcloud at the moment and one would thus need to be built by you). @@ -65,7 +65,7 @@ This update comes as a result of 175 code changesets; for a complete list of cha
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### Improvements in the display of repository dependencies and contents in the tool shed @@ -177,7 +177,7 @@ All Galaxy instance maintainers are *strongly encouraged* to run the latest rele
# Announcements -[News](/src/news/index.md), ***[December 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-12)*** +[News](/news/), ***[December 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-12)***
2013 Galaxy Community Conference (GCC2013)
diff --git a/content/archive/dev-news-briefs/2012-12-20/index.md b/content/archive/dev-news-briefs/2012-12-20/index.md index 93d9c8fab3..4e7d7b8fa4 100644 --- a/content/archive/dev-news-briefs/2012-12-20/index.md +++ b/content/archive/dev-news-briefs/2012-12-20/index.md @@ -42,7 +42,7 @@ When a tool shed repository is installed into your local Galaxy instance, metada
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### Galaxy Enhancement related to installed tool shed repositories @@ -159,7 +159,7 @@ Although there are no specific known security fixes in this distribution, all Ga
# Announcements -[News](/src/news/index.md), ***[December 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-12)*** +[News](/news/), ***[December 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-12)***
2013 Galaxy Community Conference (GCC2013)

diff --git a/content/archive/dev-news-briefs/2013-01-11/index.md b/content/archive/dev-news-briefs/2013-01-11/index.md index bac8300284..ff640e8ea0 100644 --- a/content/archive/dev-news-briefs/2013-01-11/index.md +++ b/content/archive/dev-news-briefs/2013-01-11/index.md @@ -41,7 +41,7 @@ There are three categories of repository dependencies which will be discussed in
# Other Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### Galaxy fixes and enhancements related to tool shed features @@ -58,7 +58,7 @@ There are three categories of repository dependencies which will be discussed in
# Data -1. Many new reference genome datasets, indexes, and liftOver files have been added to the **public [Main](/src/main/index.md) Galaxy instance** and **rsync** download area ([get the data](http://wiki.galaxyproject.org/Admin/Data%20Integration#Get_the_data)). Among these, the following full reference genomes sourced from **[UCSC](http://genome.ucsc.edu/)** were added: +1. Many new reference genome datasets, indexes, and liftOver files have been added to the **public [Main](/main/) Galaxy instance** and **rsync** download area ([get the data](http://wiki.galaxyproject.org/Admin/Data%20Integration#Get_the_data)). Among these, the following full reference genomes sourced from **[UCSC](http://genome.ucsc.edu/)** were added: * `Budgerigar Sep. 2011 (WUSTL v6.3/melUnd1)` * `Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4)` * `Cow Oct. 2011 (Baylor Btau_4.6.1/bosTau7) (bosTau7)` @@ -73,7 +73,7 @@ There are three categories of repository dependencies which will be discussed in * `Turkey Dec. 2009 (TGC Turkey_2.01/melGal1)` * `X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) (xenTro3)` 2. #2 Additional genomes, indexes, and related datasets will continue to be published over the next several weeks and highlights will appear in subsequent News Briefs. -3. #3 The genome "`Yeast (Saccharomyces cerevisiae): Saccharomyces_cerevisiae_S288C_SGD2010`" has been discovered to be mislabeled, representing the Apr. 2011 release from SGD (not Feb. 2010), which makes it identical to the "`sacCer3`" genome from UCSC. This genome will be redacted on the [Main](/src/main/index.md) server and users should migrate to using the "`sacCer3`" genome build as the alternative. Any chromosome naming issues associated with the `Saccharomyces_cerevisiae_S288C_SGD2010 build` (due to names of format "chr3" instead of the author published "chrIII") will also be resolved by migrating to this new, correct, reference genome build. +3. #3 The genome "`Yeast (Saccharomyces cerevisiae): Saccharomyces_cerevisiae_S288C_SGD2010`" has been discovered to be mislabeled, representing the Apr. 2011 release from SGD (not Feb. 2010), which makes it identical to the "`sacCer3`" genome from UCSC. This genome will be redacted on the [Main](/main/) server and users should migrate to using the "`sacCer3`" genome build as the alternative. Any chromosome naming issues associated with the `Saccharomyces_cerevisiae_S288C_SGD2010 build` (due to names of format "chr3" instead of the author published "chrIII") will also be resolved by migrating to this new, correct, reference genome build.
# Visualization @@ -122,7 +122,7 @@ Although there are no specific known security fixes in this distribution, all Ga
# Announcements -[News](/src/news/index.md), ***[January 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-13)*** +[News](/news/), ***[January 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-13)***
Training Day diff --git a/content/archive/dev-news-briefs/2013-02-08/index.md b/content/archive/dev-news-briefs/2013-02-08/index.md index 8b814b5a81..6f187604b2 100644 --- a/content/archive/dev-news-briefs/2013-02-08/index.md +++ b/content/archive/dev-news-briefs/2013-02-08/index.md @@ -69,7 +69,7 @@ This process will not only allow us to deploy important bug fixes on to the `sta
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### New Tool Shed Features @@ -140,7 +140,7 @@ All repositories dependencies and tool dependencies that are defined for each re
# Data -1. **Megablast** indexes for the divisions `nt`, `htgs`, and `wgs` have been updated on the public [Main](/src/main/index.md) Galaxy server dated `28jan2013`. +1. **Megablast** indexes for the divisions `nt`, `htgs`, and `wgs` have been updated on the public [Main](/main/) Galaxy server dated `28jan2013`. 2. **NGS Data Set-up** wiki updated and simplified. [View here...](http://wiki.galaxyproject.org/Admin/NGS Local Setup) 3. **Rsync** server hosts download of the same `.loc` files used by the Galaxy team (to be used as additional examples, or starter files if you use our rsync reference genome data. [Read more...](http://wiki.galaxyproject.org/Admin/Data%20Integration#Get_the_data) @@ -230,7 +230,7 @@ Although there are no specific known security fixes in this distribution, all Ga
# Announcements -[News](/src/news/index.md), ***[February 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-02)*** +[News](/news/), ***[February 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-02)*** ## GCC2013 diff --git a/content/archive/dev-news-briefs/2013-04-01/index.md b/content/archive/dev-news-briefs/2013-04-01/index.md index c0c51ee5ea..feab5908ad 100644 --- a/content/archive/dev-news-briefs/2013-04-01/index.md +++ b/content/archive/dev-news-briefs/2013-04-01/index.md @@ -166,7 +166,7 @@ An abstracted interface has been created for the data manager to download, gener
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### New Tool Shed Features @@ -295,7 +295,7 @@ Although there are no specific known security fixes in this distribution, all Ga
# Announcements -[News](/src/news/index.md), ***[April 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-04)*** +[News](/news/), ***[April 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-04)*** ## GCC2013 diff --git a/content/archive/dev-news-briefs/2013-06-03/index.md b/content/archive/dev-news-briefs/2013-06-03/index.md index 4a6c7c3e9c..3dcba19003 100644 --- a/content/archive/dev-news-briefs/2013-06-03/index.md +++ b/content/archive/dev-news-briefs/2013-06-03/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2013-06-03 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
@@ -62,7 +62,7 @@ When a tool shed repository is installed into your local Galaxy instance, metada
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ### New Tool Shed Features @@ -288,7 +288,7 @@ Although there are no specific known security fixes in this distribution, all Ga
# Project Updates -**[News](/src/news/index.md)**, ***[June 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-06)*** +**[News](/news/)**, ***[June 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-06)***

diff --git a/content/archive/dev-news-briefs/2013-08-12/index.md b/content/archive/dev-news-briefs/2013-08-12/index.md index d3c220dda5..31973f4e49 100644 --- a/content/archive/dev-news-briefs/2013-08-12/index.md +++ b/content/archive/dev-news-briefs/2013-08-12/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2013-08-12 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2013_08_12](/src/news/2013-08-12-galaxy-distribution/index.md) @@ -131,7 +131,7 @@ When a tool shed repository is installed into your local Galaxy instance, metada
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ## New Tool Shed Features @@ -266,7 +266,7 @@ Details: Only Galaxy instances with `allow_user_impersonation = True` set in the # Project Updates -**[News](/src/news/index.md)**, ***[August 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-08)*** +**[News](/news/)**, ***[August 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-08)*** ## GCC 2013 Wrap-up diff --git a/content/archive/dev-news-briefs/2013-11-04/index.md b/content/archive/dev-news-briefs/2013-11-04/index.md index f4605166d5..f3ac483ad0 100644 --- a/content/archive/dev-news-briefs/2013-11-04/index.md +++ b/content/archive/dev-news-briefs/2013-11-04/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-11-04 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2013_11_04](/src/news/2013-11-04-galaxy-distribution/index.md) @@ -194,7 +194,7 @@ Third, the tools can be completely disabled by removing them from the tool confi
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ## Galaxy Tool Migration Framework Enhancements See above: [New Tool Migrations](/src/archive/dev-news-briefs/2013-11-04/index.md#new-tool-migrations) @@ -345,8 +345,8 @@ Several beneficial enhancements have bee added to the support for [defining tool # Project Updates -1. [News](/src/news/index.md) -1. [Events](/src/events/index.md) +1. [News](/news/) +1. [Events](/events/) 1. [Videos on Vimeo](https://vimeo.com/galaxyproject) 1. *[November 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-11)* 1. *[October 2013 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2013-10)* diff --git a/content/archive/dev-news-briefs/2014-02-10/index.md b/content/archive/dev-news-briefs/2014-02-10/index.md index f56c7c3253..fa523f328b 100644 --- a/content/archive/dev-news-briefs/2014-02-10/index.md +++ b/content/archive/dev-news-briefs/2014-02-10/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-02-10 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2014_02_10](/src/news/2014-02-10-galaxy-distribution/index.md) @@ -201,7 +201,7 @@ Thanks to our Galaxy community contributors!
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ## Tool Migration Framework Also see above: [New Tool Migrations](/src/archive/dev-news-briefs/2014-02-10/index.md#new-tool-migrations) @@ -261,8 +261,8 @@ Also see above: [New Tool Migrations](/src/archive/dev-news-briefs/2014-02-10/in # Project Updates -1. [News](/src/news/index.md) -1. [Events](/src/events/index.md) +1. [News](/news/) +1. [Events](/events/) 1. [Videos on Vimeo](https://vimeo.com/galaxyproject) 1. *[February 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-02)* 1. *[January 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-01)* @@ -278,7 +278,7 @@ The **[Galaxy Team](http://wiki.galaxyproject.org/GalaxyTeam)** is a part of the **[Galaxy](http://usegalaxy.org )** is supported in part by **[NSF](http://www.nsf.gov/)**, **[NHGRI](http://www.genome.gov/)**, the **[Huck Institutes of the Life Sciences](http://www.huck.psu.edu/)**, and **[The Institute for CyberScience at Penn State](http://www.ics.psu.edu/)**, and **[Johns Hopkins University](http://www.jhu.edu/)**. -The *[public Main instance](/src/main/index.md)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. +The *[public Main instance](/main/)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. Follow us on **Twitter [@galaxyproject](http://twitter.com/galaxyproject)** or read our tweets at **[Galaxy on Twitter](/src/galaxy-on-twitter/index.md)** diff --git a/content/archive/dev-news-briefs/2014-04-14/index.md b/content/archive/dev-news-briefs/2014-04-14/index.md index 4f0dfef864..c4aaa44663 100644 --- a/content/archive/dev-news-briefs/2014-04-14/index.md +++ b/content/archive/dev-news-briefs/2014-04-14/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-04-14 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2014_04_14](/src/news/2014-04-14-galaxy-distribution/index.md) @@ -180,7 +180,7 @@ Thanks to our Galaxy community contributors!
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ## Documentation 1. Reorganization of the Tool Shed wiki is underway! See current changes https://wiki.galaxyproject.org[/ToolShed](/src/archive/dev-news-briefs/2014-04-14/ToolShed/index.md) and what is next up https://trello.com/c/Gg0jnll7 @@ -223,8 +223,8 @@ Thanks to our Galaxy community contributors! # Project Updates -1. [News](/src/news/index.md) -1. [Events](/src/events/index.md) +1. [News](/news/) +1. [Events](/events/) 1. [Videos on Vimeo](https://vimeo.com/galaxyproject) 1. *[April 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-04)* 1. *[March 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-03)* @@ -239,7 +239,7 @@ The **[Galaxy Team](http://wiki.galaxyproject.org/GalaxyTeam)** is a part of the **[Galaxy](http://usegalaxy.org )** is supported in part by **[NSF](http://www.nsf.gov/)**, **[NHGRI](http://www.genome.gov/)**, the **[Huck Institutes of the Life Sciences](http://www.huck.psu.edu/)**, and **[The Institute for CyberScience at Penn State](http://www.ics.psu.edu/)**, and **[Johns Hopkins University](http://www.jhu.edu/)**. -The *[public Main instance](/src/main/index.md)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. +The *[public Main instance](/main/)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. Follow us on **Twitter [@galaxyproject](http://twitter.com/galaxyproject)** or read our tweets at **[Galaxy on Twitter](/src/galaxy-on-twitter/index.md)** diff --git a/content/archive/dev-news-briefs/2014-06-02/index.md b/content/archive/dev-news-briefs/2014-06-02/index.md index 25f529c769..25a8ec39f7 100644 --- a/content/archive/dev-news-briefs/2014-06-02/index.md +++ b/content/archive/dev-news-briefs/2014-06-02/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-06-02 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2014_06_02](/src/news/2014-06-02-galaxy-distribution/index.md) @@ -196,7 +196,7 @@ If you haven't claimed your account yet at *[Galaxy Biostar](/src/support/biosta
# Tool Shed -**[Tool Shed](/src/toolshed/index.md)** +**[Tool Shed](/toolshed/)** ## Repositories @@ -226,8 +226,8 @@ If you haven't claimed your account yet at *[Galaxy Biostar](/src/support/biosta # Project Updates -1. [News](/src/news/index.md) -1. [Events](/src/events/index.md) +1. [News](/news/) +1. [Events](/events/) 1. *[May 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-05)* 1. *[June 2014 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2014-06)* @@ -241,7 +241,7 @@ The **[Galaxy Team](http://wiki.galaxyproject.org/GalaxyTeam)** is a part of the **[Galaxy](http://usegalaxy.org )** is supported in part by **[NSF](http://www.nsf.gov/)**, **[NHGRI](http://www.genome.gov/)**, the **[Huck Institutes of the Life Sciences](http://www.huck.psu.edu/)**, and **[The Institute for CyberScience at Penn State](http://www.ics.psu.edu/)**, and **[Johns Hopkins University](http://www.jhu.edu/)**. -The *[public Main instance](/src/main/index.md)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. +The *[public Main instance](/main/)* of **Galaxy** at **[http://usegalaxy.org](http://usegalaxy.org)** utilizes infrastructure generously provided by the **[iPlant Collaborative](http://www.iplantcollaborative.org/)** at the **[Texas Advanced Computing Center](https://www.tacc.utexas.edu/)**, with support from the **[National Science Foundation](http://www.nsf.gov/)**. Follow us on **Twitter [@galaxyproject](http://twitter.com/galaxyproject)** or read our tweets at **[Galaxy on Twitter](/src/galaxy-on-twitter/index.md)** diff --git a/content/archive/dev-news-briefs/2014-08-11/index.md b/content/archive/dev-news-briefs/2014-08-11/index.md index 524446b3bc..0ff7fb4ba1 100644 --- a/content/archive/dev-news-briefs/2014-08-11/index.md +++ b/content/archive/dev-news-briefs/2014-08-11/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-08-11 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2014_08_11](/src/news/2014-08-11-galaxy-distribution/index.md) @@ -159,4 +159,4 @@ Docker integration provides even greater security with [Pulsar](https://github.c # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/admin/) • [Issues](/issues/) • [Big Picture](/src/galaxy-project/index.md) • [Community](/community/) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/cloudman/) • [Tool Shed](/toolshed/) • [Develop](/develop/) • [News Briefs](/docs/) • [Servers](/use/) • [Learn](/learn/) • [Support](/support/) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/news/) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/events/) • [Teach](/teach/) • [Issues](/issues/) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2014-10-06/index.md b/content/archive/dev-news-briefs/2014-10-06/index.md index f0df75dee5..fea19bf6b8 100644 --- a/content/archive/dev-news-briefs/2014-10-06/index.md +++ b/content/archive/dev-news-briefs/2014-10-06/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2014-10-06 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2014_10_06](/src/news/2014-10-06-galaxy-distribution/index.md) @@ -142,4 +142,4 @@ Several enhancements and improvements have been made to facilitate easier viewin # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Issues](/src/issues/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/admin/) • [Issues](/issues/) • [Big Picture](/src/galaxy-project/index.md) • [Community](/community/) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/cloudman/) • [Tool Shed](/toolshed/) • [Develop](/develop/) • [News Briefs](/docs/) • [Servers](/use/) • [Learn](/learn/) • [Support](/support/) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/news/) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/events/) • [Teach](/teach/) • [Issues](/issues/) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2015-01-13-stable-additions/index.md b/content/archive/dev-news-briefs/2015-01-13-stable-additions/index.md index c3055141e1..2f959c4455 100644 --- a/content/archive/dev-news-briefs/2015-01-13-stable-additions/index.md +++ b/content/archive/dev-news-briefs/2015-01-13-stable-additions/index.md @@ -7,7 +7,7 @@ date: 2015-01-13 These represent changes introduced after the initial release. May also be tracked in [Trello](https://trello.com/galaxyproject).
-[back to all News Briefs](/src/docs/index.md) +[back to all News Briefs](/docs/) ## Review prior distribution @@ -41,5 +41,5 @@ These represent changes introduced after the initial release. May also be tracke * Various low-vulnerability-level security fixes. [U6yj2pPr](https://trello.com/c/U6yj2pPr)


-[back to all News Briefs](/src/docs/index.md) +[back to all News Briefs](/docs/)

diff --git a/content/archive/dev-news-briefs/2015-01-13/index.md b/content/archive/dev-news-briefs/2015-01-13/index.md index 577fbe57dd..982cae15e9 100644 --- a/content/archive/dev-news-briefs/2015-01-13/index.md +++ b/content/archive/dev-news-briefs/2015-01-13/index.md @@ -3,7 +3,7 @@ title: Development News Brief date: 2015-01-13 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Distribution Summary 2015_01_13](/src/news/2015-01-13-galaxy-distribution/index.md) @@ -140,7 +140,7 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Fixed an improper redirect during user password reset. [https://trello.com/c/ROONezok](https://trello.com/c/ROONezok) 1. Fixed Workflow import to correctly set the `uuid`. Contributed by Kyle Ellrott. [https://trello.com/c/4UP6Gfo9](https://trello.com/c/4UP6Gfo9) 1. Corrected a few small bugs in docs and pylint. See ticket/changesets for details. Contributed by [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/HVm9vKl2](https://trello.com/c/HVm9vKl2) -1. Corrected a boolean parameter handling issue that occurred during a Workflow’s runtime execution. ’’Incorporating this fix is critical for proper Workflow execution.’’. The problem manifested as certain tool parameters executing »in the reverse state« when used within Workflows (exclusively, and never when tools were executed directly outside of Workflows). A tool »re-run« form will reveal the issue and various failure errors are known to have resulted. If a prior successful Workflow now fails, and your instance as not yet included in this changeset yet, the issue could likely be the root cause of Workflow tool errors. The problem impacted the [Main](/src/main/index.md) public Galaxy instance at [http://usegalaxy.org](http://usegalaxy.org) for a short time window in November. The fix was applied to the public instance and added to the Stable branch under [latest_2014.10.06](/src/archive/dev-news-briefs/2014-10-06/index.md) upon discovery/resolution, at a priority, during this same time frame. Reported by Andrea Pinna. [https://trello.com/c/zdHaxzSn](https://trello.com/c/zdHaxzSn) [https://trello.com/c/sXUwBJgb](https://trello.com/c/sXUwBJgb) +1. Corrected a boolean parameter handling issue that occurred during a Workflow’s runtime execution. ’’Incorporating this fix is critical for proper Workflow execution.’’. The problem manifested as certain tool parameters executing »in the reverse state« when used within Workflows (exclusively, and never when tools were executed directly outside of Workflows). A tool »re-run« form will reveal the issue and various failure errors are known to have resulted. If a prior successful Workflow now fails, and your instance as not yet included in this changeset yet, the issue could likely be the root cause of Workflow tool errors. The problem impacted the [Main](/main/) public Galaxy instance at [http://usegalaxy.org](http://usegalaxy.org) for a short time window in November. The fix was applied to the public instance and added to the Stable branch under [latest_2014.10.06](/src/archive/dev-news-briefs/2014-10-06/index.md) upon discovery/resolution, at a priority, during this same time frame. Reported by Andrea Pinna. [https://trello.com/c/zdHaxzSn](https://trello.com/c/zdHaxzSn) [https://trello.com/c/sXUwBJgb](https://trello.com/c/sXUwBJgb) 1. Fixed changeset 04a072e to now use the correct `MAKO` method in the masthead. [https://trello.com/c/ZSMVriGJ](https://trello.com/c/ZSMVriGJ) 1. Composite Datatype uploads no longer problematic by assuming groups have a UUID field. [https://trello.com/c/GbZwGPmt](https://trello.com/c/GbZwGPmt) 1. Fixed passing nested parameter replacements to the Workflow run API. Discovered by [Nicola Soranzo](/people/nicola-soranzo/). [https://trello.com/c/WtFpviiw](https://trello.com/c/WtFpviiw) @@ -159,13 +159,13 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte 1. Explore the latest [Galaxy Project](http://galaxyproject.org) news from our team that covers recent Events, Publications, New Tools, and much more in our monthly project reports published in our wiki under [Galaxy Updates](http://wiki.galaxyproject.org/GalaxyUpdates). 1. [Tool Shed Contributions](https://wiki.galaxyproject.org/ToolShed/Contributions). This is a brand-new area previously included directly in the *[Galaxy Updates](http://wiki.galaxyproject.org/GalaxyUpdates)* news letters. Watch as this area develops as we work to summarize new repository updates in a concise and organized format. Feedback about how you would like to see this evolve (including general interest) is welcome. We will be posting a comment/feedback post at [Galaxy Biostar](https://biostar.usegalaxy.org/) to provide an opportunity to for our community to discuss. A summary will be added to [Trello](https://wiki.galaxyproject.org/Issues) once feedback is gathered for review and action. (A link to that post will be updated and added right here in this wiki within the next week - is truly a *brand-new* endeavor to break this out as a distinct wiki resource!!). 1. If you are new to Galaxy or wish to connect with our project more in 2015, these key links can help keep you updated about our activities and updates in real time (or at your own pace). Galaxy is a community project we would like to remind all about of the resources and venues available for news and support. Most reading our News Briefs are familiar with [Development](https://wiki.galaxyproject.org/Develop), [Cloud](https://wiki.galaxyproject.org/Cloud), [Local](https://wiki.galaxyproject.org/Admin/GetGalaxy), and other deployment resources such as [Admin](https://wiki.galaxyproject.org/Admin) plus [Tool](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax) and [Tool Repository](https://wiki.galaxyproject.org/ToolShed) documenation, but below is a short list of even more places to visit and get connected: - * [All News Reports](/src/news/index.md) and the [Hub for Distribution Details](/src/docs/index.md) + * [All News Reports](/news/) and the [Hub for Distribution Details](/docs/) * [Twitter](/src/galaxy-on-twitter/index.md) (wiki summary) or follow us directly at [https://twitter.com/galaxyproject](https://twitter.com/galaxyproject) - * [Events](/src/events/index.md), [Learn](/src/learn/index.md), [Galaxy Biostar](https://biostar.usegalaxy.org/), [Support Resources](/src/support/index.md) with FAQ help, [Mailing list](/src/mailing-lists/index.md) subscription and archvies, and [Vimeo tutorials](http://vimeo.com/galaxyproject) - * All know of [Public Galaxy Main](/src/main/index.md), but have you reviewed the [Other Galaxy Public-hosted Servers](/src/use/index.md) lately? - * [Teach](/src/teach/index.md) resources are an exciting, growing, and key area for expansion throughout 2015, check out what is new! + * [Events](/events/), [Learn](/learn/), [Galaxy Biostar](https://biostar.usegalaxy.org/), [Support Resources](/support/) with FAQ help, [Mailing list](/src/mailing-lists/index.md) subscription and archvies, and [Vimeo tutorials](http://vimeo.com/galaxyproject) + * All know of [Public Galaxy Main](/main/), but have you reviewed the [Other Galaxy Public-hosted Servers](/use/) lately? + * [Teach](/teach/) resources are an exciting, growing, and key area for expansion throughout 2015, check out what is new! * Follow current development real-time and create, comment, and vote on active [Trello](https://trello.com/galaxyproject) tickets. As an open source project, we very much welcome community involvement. Not sure how to get involved or how to [create an account](https://trello.com/b/ijIE4lMx/welcome-board)? We have guidance available **[here...](https://wiki.galaxyproject.org/Issues)**, that includes a form to aid with quick ticket submission. - * [Community](/src/community/index.md) resources. Overview about how we value and seek your input. Have your voice heard and get involved! + * [Community](/community/) resources. Overview about how we value and seek your input. Have your voice heard and get involved! * [Galaxy Project](/src/galaxy-project/index.md) home page (hub for all resources, those listed above and more!) * See our wiki's right side bar menu → for more links to areas of interest to you * Our wiki is absolutely open for community contributions and improvements. We have plans in place for documentation updates in the upcoming year, but we greatly value the knowledge and insight shared through this resource by all that have ideas to make it even better. Let's work together to expand this wiki to meet the needs of the upcoming year as our project matures, as new research/development areas come up, and as Galaxy grows and evolves with new features and enhancements! Create a wiki account and contact us at "outreach at galaxyproject dot org" to become a wiki editor. @@ -178,4 +178,4 @@ Galaxy's tool form forces pages to reload entirely in response to many user inte # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/admin/) • [Issues](/issues/) • [Big Picture](/src/galaxy-project/index.md) • [Community](/community/) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/cloudman/) • [Tool Shed](/toolshed/) • [Develop](/develop/) • [News Briefs](/docs/) • [Servers](/use/) • [Learn](/learn/) • [Support](/support/) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/news/) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/events/) • [Teach](/teach/) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/dev-news-briefs/2015-03/index.md b/content/archive/dev-news-briefs/2015-03/index.md index 265577f186..a6ec5bf95c 100644 --- a/content/archive/dev-news-briefs/2015-03/index.md +++ b/content/archive/dev-news-briefs/2015-03/index.md @@ -2,7 +2,7 @@ title: March 2015 Galaxy Release (v 15.03) date: 2015-03-01 --- -[All News Briefs](/src/docs/index.md) +[All News Briefs](/docs/)
[Galaxy March Release Summary](/src/news/2015-03-galaxy-release/index.md)
@@ -66,7 +66,7 @@ Thus, if you would like to upgrade to the 15.03 release and ensure you do not su # Tool Redesign -Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the [Tool Shed](http://usegalaxy.org/toolsehd) and many are ready for use on Galaxy [Main](/src/main/index.md). Older Workflows may contain tools that automatically map to the new tools or Workflows may need minor adjustments. [c6Lkejro](https://trello.com/c/c6Lkejro) +Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the [Tool Shed](http://usegalaxy.org/toolsehd) and many are ready for use on Galaxy [Main](/main/). Older Workflows may contain tools that automatically map to the new tools or Workflows may need minor adjustments. [c6Lkejro](https://trello.com/c/c6Lkejro) Be sure to check out the new [Galaxy NGS 101](/src/learn/galaxy-ngs101/index.md) wiki (in progress). @@ -199,13 +199,13 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy * Two Hackathons are now scheduled to occur *before* and *during* GCC 2015. * [GCC2015 Coding Hackathon](http://gcc2015.tsl.ac.uk/organisers/hackathon) * New! [GCC2015 Data Wrangling Hackathon](http://gcc2015.tsl.ac.uk/organisers/data-hackathon) -* [All Galaxy News](/src/news/index.md) and the [Hub for Release News](/src/docs/index.md) +* [All Galaxy News](/news/) and the [Hub for Release News](/docs/) * [Twitter](/src/galaxy-on-twitter/index.md) (wiki summary) or follow us directly at [https://twitter.com/galaxyproject](https://twitter.com/galaxyproject) -* [Events](/src/events/index.md), [Learn](/src/learn/index.md), [Galaxy Biostar](https://biostar.usegalaxy.org/), [Support Resources](/src/support/index.md) with FAQ help, [Mailing list](/src/mailing-lists/index.md) subscription and archvies, and [Vimeo tutorials](http://vimeo.com/galaxyproject) -* All know of [Public Galaxy Main](/src/main/index.md), but have you reviewed the [Other Galaxy Public-hosted Servers](/src/use/index.md) lately? -* [Teach](/src/teach/index.md) resources are an exciting, growing, and key area for expansion throughout 2015, check out what is new! +* [Events](/events/), [Learn](/learn/), [Galaxy Biostar](https://biostar.usegalaxy.org/), [Support Resources](/support/) with FAQ help, [Mailing list](/src/mailing-lists/index.md) subscription and archvies, and [Vimeo tutorials](http://vimeo.com/galaxyproject) +* All know of [Public Galaxy Main](/main/), but have you reviewed the [Other Galaxy Public-hosted Servers](/use/) lately? +* [Teach](/teach/) resources are an exciting, growing, and key area for expansion throughout 2015, check out what is new! * Follow current development real-time and create, comment, and vote on active [Trello](https://trello.com/galaxyproject) tickets. As an open source project, we very much welcome community involvement. Not sure how to get involved or how to [create an account](https://trello.com/b/ijIE4lMx/welcome-board)? We have guidance available **[here...](https://wiki.galaxyproject.org/Issues)**, that includes a form to aid with quick ticket submission. -* [Community](/src/community/index.md) resources. Overview about how we value and seek your input. Have your voice heard and get involved! +* [Community](/community/) resources. Overview about how we value and seek your input. Have your voice heard and get involved! * [Galaxy Project](/src/galaxy-project/index.md) home page (hub for all resources, those listed above and more!) * See our wiki's right side bar menu → for more links to areas of interest to you * Our wiki is absolutely open for community contributions and improvements. @@ -225,4 +225,4 @@ Galaxy development has moved to [Github](https://github.com/galaxyproject/galaxy # About Galaxy
UseGalaxy.org
-**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/src/admin/index.md) • [Issues](/src/issues/index.md) • [Big Picture](/src/galaxy-project/index.md) • [Community](/src/community/index.md) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/src/cloudman/index.md) • [Tool Shed](/src/toolshed/index.md) • [Develop](/src/develop/index.md) • [News Briefs](/src/docs/index.md) • [Servers](/src/use/index.md) • [Learn](/src/learn/index.md) • [Support](/src/support/index.md) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/src/news/index.md) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/src/events/index.md) • [Teach](/src/teach/index.md) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) +**[About Galaxy](/src/support/about-galaxy/index.md)** • [Galaxy Project](/src/galaxy-project/index.md) • [Admin](/admin/) • [Issues](/issues/) • [Big Picture](/src/galaxy-project/index.md) • [Community](/community/) • [Get Galaxy](/src/admin/get-galaxy/index.md) • [CloudMan](/cloudman/) • [Tool Shed](/toolshed/) • [Develop](/develop/) • [News Briefs](/docs/) • [Servers](/use/) • [Learn](/learn/) • [Support](/support/) • [Galaxy Biostar](http://biostar.usegalaxy.org) • [News](/news/) • [Twitter](/src/galaxy-on-twitter/index.md) • [Events](/events/) • [Teach](/teach/) • [Cite](/src/citing-galaxy/index.md) • [Galaxy Team](/galaxy-team/) diff --git a/content/archive/library-sample-tracking/index.md b/content/archive/library-sample-tracking/index.md index 0dce35cda8..5bac322545 100644 --- a/content/archive/library-sample-tracking/index.md +++ b/content/archive/library-sample-tracking/index.md @@ -9,7 +9,7 @@ This tutorial provides information about using Galaxy's [Data libraries](/src/ad ## Data Libraries -An "Admin" link will appear in the Galaxy top menu bar when you login to Galaxy as an [admin user](/src/admin/index.md), and clicking the link will display the Admin perspective which includes a menu of features in the left panel. +An "Admin" link will appear in the Galaxy top menu bar when you login to Galaxy as an [admin user](/admin/), and clicking the link will display the Admin perspective which includes a menu of features in the left panel. ![](/src/archive/library-sample-tracking/admin.png) @@ -157,4 +157,4 @@ We've only scratched the surface of what can be done with Galaxy. Here are some * [You can make local genomes, alignments, and other data available to Galaxy](/src/admin/data-integration/index.md) * [You can customize what external applications are available for displaying datasets](/src/admin/tools/External Display Applications Tutorial/index.md) * [You can customize the datatypes for a Galaxy instance](/src/admin/datatypes/Adding Datatypes/index.md) -* [You can instantiate Galaxy on the Amazon cloud](/src/cloudman/index.md) +* [You can instantiate Galaxy on the Amazon cloud](/cloudman/) diff --git a/content/archive/next-gen/index.md b/content/archive/next-gen/index.md index 0ebb7cc06d..c2f283dbd5 100644 --- a/content/archive/next-gen/index.md +++ b/content/archive/next-gen/index.md @@ -51,7 +51,7 @@ $ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini ``` -7. Setup an administration user with the instructions on the standard [Galaxy Admin Interface](/src/admin/index.md). Create a "sequencing" role with this admin user; see the [Galaxy security documentation for more details](/src/learn/Security Features/index.md). Assign that role to any users who will be doing the sequencing work and should have full access to the sample management tools. Regular users -- customers submitting samples -- have access to a limited subset of capabilities. +7. Setup an administration user with the instructions on the standard [Galaxy Admin Interface](/admin/). Create a "sequencing" role with this admin user; see the [Galaxy security documentation for more details](/src/learn/Security Features/index.md). Assign that role to any users who will be doing the sequencing work and should have full access to the sample management tools. Regular users -- customers submitting samples -- have access to a limited subset of capabilities. 8. For integrating Galaxy analysis scripts with the front-end, generate an API key for your user with "sequencing" permissions. First ensure that the API in enabled in your Galaxy universe_wsgi.ini configuration: diff --git a/content/authnz/config/index.md b/content/authnz/config/index.md index d80637df5a..342f7d9de2 100644 --- a/content/authnz/config/index.md +++ b/content/authnz/config/index.md @@ -8,7 +8,7 @@ for user-specific docs, please refer to the [Use page](/src/authnz/use/index.md) # Galaxy Authentication Configuration Options -Galaxy offers [various methods for user authentication](/src/authnz/index.md#user-authentication-and-authorization) +Galaxy offers [various methods for user authentication](/authnz/#user-authentication-and-authorization) (aka login). All the methods share some common concepts, which are explained on this page. The method-specific configurations are explained at the following pages: diff --git a/content/authnz/use/index.md b/content/authnz/use/index.md index 5599dfe6e9..7aac175977 100644 --- a/content/authnz/use/index.md +++ b/content/authnz/use/index.md @@ -13,7 +13,7 @@ or persist their histories on their own cloud-based storage---a feature that is available to anonymous users. -For users convenience, Galaxy offers [various methods](/src/authnz/index.md#user-authentication-and-authorization) +For users convenience, Galaxy offers [various methods](/authnz/#user-authentication-and-authorization) to create a Galaxy user account. (Note that some of these methods can be disabled on the Galaxy instance you're using as per that instance's configuration.) Depending on the method you choose, you may be creating a Galaxy user account explicitly diff --git a/content/blog/2017-10-5000-pubs/index.md b/content/blog/2017-10-5000-pubs/index.md index 81dc3ff1f7..2f6992e26a 100644 --- a/content/blog/2017-10-5000-pubs/index.md +++ b/content/blog/2017-10-5000-pubs/index.md @@ -383,7 +383,7 @@ The most obvious "trend" is that **there are a lot of pubs using Galaxy in their Not all *[Methods](https://www.zotero.org/groups/1732893/galaxy/tags/%2BMethods)* paper say which Galaxy instance(s) they used. But starting in 2013, papers that do mention this are also tagged with *[UseMain](https://www.zotero.org/groups/1732893/galaxy/tags/%2BUseMain)*, *[UsePublic](https://www.zotero.org/groups/1732893/galaxy/tags/%2BUsePublic)*, *[UseLocal](https://www.zotero.org/groups/1732893/galaxy/tags/%2BUseLocal)*, and/or *[UseCloud](https://www.zotero.org/groups/1732893/galaxy/tags/%2BUseCloud)* tags (see [Tags](#tags) below for an explanation of all tags). -**The relative number of *UseMain* and *UsePublic* pubs highlights the increasing availability of publicly accessible Galaxy servers.** In 2013-2014, there are 2 1/2 times as many *UseMain* pubs as *UsePublic* pubs. In 2015 they were about the same, and in 2016-2017, there are nearly twice as many *UsePublic* pubs as there are *UseMain* pubs. This rise reflects the increase in available [public servers](/src/use/index.md) from 21 servers at the start of 2012 to over 90 servers, and 6 services today. +**The relative number of *UseMain* and *UsePublic* pubs highlights the increasing availability of publicly accessible Galaxy servers.** In 2013-2014, there are 2 1/2 times as many *UseMain* pubs as *UsePublic* pubs. In 2015 they were about the same, and in 2016-2017, there are nearly twice as many *UsePublic* pubs as there are *UseMain* pubs. This rise reflects the increase in available [public servers](/use/) from 21 servers at the start of 2012 to over 90 servers, and 6 services today. ## Reproducibility Rising @@ -467,12 +467,12 @@ Topic tags indicate how the publication relates to Galaxy. Here's the current s | [+Workbench](https://www.zotero.org/groups/galaxy/items/tag/+Workbench/) | Publication mentions Galaxy as a platform. | 2011 | | [+Tools](https://www.zotero.org/groups/galaxy/items/tag/+Tools/) | Tools that run in, have been ported to, or interact with Galaxy | 2012 | | [+Cloud](https://www.zotero.org/groups/galaxy/items/tag/+Cloud/) | Publications referencing / extending / discussing Galaxy in a cloud context. | 2013 | -| [+RefPublic](https://www.zotero.org/groups/galaxy/items/tag/+RefPublic/) | References a [publicly accessible Galaxy instance](/src/use/index.md) or a [Galaxy service](/src/use/index.md). This is distinct from the *+UsePublic* tag. | 2013 | +| [+RefPublic](https://www.zotero.org/groups/galaxy/items/tag/+RefPublic/) | References a [publicly accessible Galaxy instance](/use/) or a [Galaxy service](/use/). This is distinct from the *+UsePublic* tag. | 2013 | | [+Unknown](https://www.zotero.org/groups/galaxy/items/tag/+Unknown/) | Publications that we know refer to Galaxy, but we aren't sure how because they are behind a paywall we don't have access to. These are revisited periodically. | 2013 | | [+UseCloud](https://www.zotero.org/groups/galaxy/items/tag/+UseCloud/) | Uses a custom built cloud based instance of Galaxy in its methods. | 2013 | | [+UseLocal](https://www.zotero.org/groups/galaxy/items/tag/+UseLocal/) | Uses a local installation of Galaxy in its methods. | 2013 | -| [+UseMain](https://www.zotero.org/groups/galaxy/items/tag/+UseMain/) | Uses the project's public server, [usegalaxy.org](https://usegalaxy.org/) (a.k.a. [Main](/src/main/index.md), in its methods. | 2013 | -| [+UsePublic](https://www.zotero.org/groups/galaxy/items/tag/+UsePublic/) | Uses a [publicly accessible Galaxy instance](/src/use/index.md) or a [Galaxy service](/src/use/index.md) in its methods. | 2013 | +| [+UseMain](https://www.zotero.org/groups/galaxy/items/tag/+UseMain/) | Uses the project's public server, [usegalaxy.org](https://usegalaxy.org/) (a.k.a. [Main](/main/), in its methods. | 2013 | +| [+UsePublic](https://www.zotero.org/groups/galaxy/items/tag/+UsePublic/) | Uses a [publicly accessible Galaxy instance](/use/) or a [Galaxy service](/use/) in its methods. | 2013 | | [+Visualization](https://www.zotero.org/groups/galaxy/items/tag/+Visualization/) | Publications referencing Galaxy in a visualization and/or visual analytics context. | 2013 | ## Galaxy Featured Tags @@ -486,7 +486,7 @@ With the move to Zotero we added two new sets of tags. The first set is used to ## Public server and services tags -The second set of new tags show which [public Galaxy server](/src/use/index.md) or [service](/src/use/index.md) is used or discussed in publications. These are tagged with the server's name, preceded by a ">". For example, the [>RepeatExplorer](https://www.zotero.org/groups/1732893/galaxy/tags/%3ERepeatExplorer) tag lists all papers that use or reference the [RepeatExplorer](/src/use/repeatexplorer/index.md) public server. +The second set of new tags show which [public Galaxy server](/use/) or [service](/use/) is used or discussed in publications. These are tagged with the server's name, preceded by a ">". For example, the [>RepeatExplorer](https://www.zotero.org/groups/1732893/galaxy/tags/%3ERepeatExplorer) tag lists all papers that use or reference the [RepeatExplorer](/src/use/repeatexplorer/index.md) public server. ## Publisher Tags diff --git a/content/blog/2017-10-a-blog-is-born/index.md b/content/blog/2017-10-a-blog-is-born/index.md index ad09400e10..dab18b2720 100644 --- a/content/blog/2017-10-a-blog-is-born/index.md +++ b/content/blog/2017-10-a-blog-is-born/index.md @@ -6,9 +6,9 @@ image: /src/images/galaxy-logos/galactic-blog-400.png authors: "Dave Clements" --- -Today we launch the new *[Galactic Blog](/src/blog/index.md)*. +Today we launch the new *[Galactic Blog](/blog/)*. -The *Galactic Blog* is a place for longer-form posts that are relevant to Galaxy. (See [Galaxy News](/src/news/index.md) for shorter-form items.) +The *Galactic Blog* is a place for longer-form posts that are relevant to Galaxy. (See [Galaxy News](/news/) for shorter-form items.) **Our very first post is about the [ELIXIR Galaxy Community](/src/blog/2017-10-05-elixir-galaxy-community/index.md) and was written by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/people/bjoern-gruening/).** @@ -18,6 +18,6 @@ The *Galactic Blog* replaces the former *Community Log* and includes all content The Galaxy community needs to know what you are doing. If you done something that others would benefit from then please think about creating a *Galactic Blog* post describing your experiences. -Blog posts can either be directly created to the Hub, or can be posted on your favorite blogging platform and linked to from the [Blog home page](/src/blog/index.md). See [the CONTRIBUTING page](https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md#blog-metadata) for how. +Blog posts can either be directly created to the Hub, or can be posted on your favorite blogging platform and linked to from the [Blog home page](/blog/). See [the CONTRIBUTING page](https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md#blog-metadata) for how. Questions? [Ask us](mailto:outreach@galaxyproject.org). diff --git a/content/blog/2017-10-public-galaxy-dashboard/index.md b/content/blog/2017-10-public-galaxy-dashboard/index.md index dde41be1dc..ca069e3340 100644 --- a/content/blog/2017-10-public-galaxy-dashboard/index.md +++ b/content/blog/2017-10-public-galaxy-dashboard/index.md @@ -10,7 +10,7 @@ authors: "Helena Rasche" ## History For the past month a few Galaxy Developers have been working on monitoring the -[public Galaxy instances](/src/use/index.md) across the universe. We have been making hourly +[public Galaxy instances](/use/) across the universe. We have been making hourly requests to instances which have listed themselves in one of the public Galaxy server lists to request non-sensitive information about their configuration. diff --git a/content/blog/2019-07-galaxy-resources/index.md b/content/blog/2019-07-galaxy-resources/index.md index 9bb3720b71..09c1df1c0e 100644 --- a/content/blog/2019-07-galaxy-resources/index.md +++ b/content/blog/2019-07-galaxy-resources/index.md @@ -68,11 +68,11 @@ The Galaxy community uses Gitter for online chat. [Galaxy's Gitter channel](htt ## Galaxy Events -Looking for workshops, presentations, training, and meetings about Galaxy? The [Galaxy Event Horizon](/src/events/index.md) lists every upcoming Galaxy-related event that the the community is aware of. Events happen around the world, in person and on-line, and almost every week of the year. Take a look. +Looking for workshops, presentations, training, and meetings about Galaxy? The [Galaxy Event Horizon](/events/) lists every upcoming Galaxy-related event that the the community is aware of. Events happen around the world, in person and on-line, and almost every week of the year. Take a look. ## Galaxy Community Conference (GCC) -The largest event in the Galactic Year is the [Galaxy Community Conference, or GCC](/src/gcc/index.md). GCCs include training, talks, posters, birds-of-a-feather gatherings, and a CollaborationFest. GCCs are a week-long event bringing together the full breadth and depth of the Galaxy community to share best practices and challenges, experiences and outlooks. GCCs alternate between North America in even years, and *not North America* in odd years. +The largest event in the Galactic Year is the [Galaxy Community Conference, or GCC](/gcc/). GCCs include training, talks, posters, birds-of-a-feather gatherings, and a CollaborationFest. GCCs are a week-long event bringing together the full breadth and depth of the Galaxy community to share best practices and challenges, experiences and outlooks. GCCs alternate between North America in even years, and *not North America* in odd years. ## Regional & Domain Communities @@ -125,25 +125,25 @@ Really. If you are deploying your own Galaxy service then take a good look at u ## A Galaxy platform to use, *right now* -The [Galaxy Platform Directory](/src/use/index.md) lists over 150 platforms where you can use Galaxy, most of them *right now*, and most of them for *free*. This includes public servers, available on the web, right now; academic cloud services; commercial cloud services; and containers and virtual machines you can use right now. +The [Galaxy Platform Directory](/use/) lists over 150 platforms where you can use Galaxy, most of them *right now*, and most of them for *free*. This includes public servers, available on the web, right now; academic cloud services; commercial cloud services; and containers and virtual machines you can use right now. A couple of platform types are worth special mention: ### UseGalaxy.* -[UseGalaxy servers](/src/usegalaxy/index.md) implement a common core set of tools and reference genomes, and are open to anyone to use. They also contain tools and genomes that are local to each server. Each is backed by significant computational resources and they are excellent places to get started with Galaxy, and to share and publish your results. *And they are free to use, by anyone.* +[UseGalaxy servers](/usegalaxy/) implement a common core set of tools and reference genomes, and are open to anyone to use. They also contain tools and genomes that are local to each server. Each is backed by significant computational resources and they are excellent places to get started with Galaxy, and to share and publish your results. *And they are free to use, by anyone.* ### Academic Cloud Services -[Several academic cloud services](/src/use/index.md) have ready to run Galaxy instances. Many of these are restricted to users within a particular geographic domain, for example, a country, province, or consortium of countries. These are often free to eligible researchers. +[Several academic cloud services](/use/) have ready to run Galaxy instances. Many of these are restricted to users within a particular geographic domain, for example, a country, province, or consortium of countries. These are often free to eligible researchers. Also see [CloudLaunch](#cloudlaunch) ## PanGalactic search -[PanGalactic Search Box](/src/search/index.md) +[PanGalactic Search Box](/search/) -Searching for anything Galaxy related using web search engines is a frustrating process. You are likely to end up with results about football, cars, chocolate, phones, or, the nemesis of all Galaxy web searches: *astronomy.* Don't give up! Use the *[PanGalactic Search](/src/search/index.md)* box at the top of this and every Galaxy Community Hub page. PGS uses Google Custom search to search only the ~40 or so (yes 40) web sites that are relevant to the *one true Galaxy.* +Searching for anything Galaxy related using web search engines is a frustrating process. You are likely to end up with results about football, cars, chocolate, phones, or, the nemesis of all Galaxy web searches: *astronomy.* Don't give up! Use the *[PanGalactic Search](/search/)* box at the top of this and every Galaxy Community Hub page. PGS uses Google Custom search to search only the ~40 or so (yes 40) web sites that are relevant to the *one true Galaxy.* ## Publications @@ -175,7 +175,7 @@ The Galaxy Community is [active on Twitter](/src/galaxy-on-twitter/index.md), an ## What's Going on - In depth: Galactic Blog -[Galactic Blog](/src/blog/index.md) +[Galactic Blog](/blog/) -The *[Galactic Blog](/src/blog/index.md)* brings together longer form posts about Galaxy, from all over the web. Want to know more about [cloud bursting](/src/blog/2019-05-gcr/index.md), [CVMFS](/src/blog/2019-02-cvmfs/index.md), or [Galaxy R Markdown Tools](https://github.com/statonlab/galaxy-r-markdown-tools)? You can find posts on these and many other topics in the [Galactic Blog](/src/blog/index.md) +The *[Galactic Blog](/blog/)* brings together longer form posts about Galaxy, from all over the web. Want to know more about [cloud bursting](/src/blog/2019-05-gcr/index.md), [CVMFS](/src/blog/2019-02-cvmfs/index.md), or [Galaxy R Markdown Tools](https://github.com/statonlab/galaxy-r-markdown-tools)? You can find posts on these and many other topics in the [Galactic Blog](/blog/) diff --git a/content/blog/2019-07-looking-for-galaxy/index.md b/content/blog/2019-07-looking-for-galaxy/index.md index 7aaf893a72..b68705adc5 100644 --- a/content/blog/2019-07-looking-for-galaxy/index.md +++ b/content/blog/2019-07-looking-for-galaxy/index.md @@ -15,7 +15,7 @@ There are *many* lessons here: 1. Don't name your project with a widely used word. 1. Don't use a general search tool when searching for information about a so named project. -Fortunately there is a solution to lesson #5: The **[Pan-Galactic Search](/src/search/index.md)** is a custom Google search engine that searches only websites related to *our* Galaxy. It is available at the top of every page on the Galaxy Community Hub. +Fortunately there is a solution to lesson #5: The **[Pan-Galactic Search](/search/)** is a custom Google search engine that searches only websites related to *our* Galaxy. It is available at the top of every page on the Galaxy Community Hub. Here, as an example, are the top hits when you search for "Galaxy search": diff --git a/content/blog/2020-08-10k-pubs/index.md b/content/blog/2020-08-10k-pubs/index.md index ff698a0b2c..00ae0c0ea7 100644 --- a/content/blog/2020-08-10k-pubs/index.md +++ b/content/blog/2020-08-10k-pubs/index.md @@ -489,7 +489,7 @@ Not all *[Methods](https://www.zotero.org/groups/1732893/galaxy/tags/%2BMethods) * in 2016-2017, there were nearly twice as many *UsePublic* pubs, * and in 2019-2020 there are nearly 3 times as many *UsePublic* as there are *UseMain* pubs. -This rise reflects the increase in available [public platforms](/src/use/index.md) from 21 servers at the start of 2012 to over 150 platforms today. +This rise reflects the increase in available [public platforms](/use/) from 21 servers at the start of 2012 to over 150 platforms today. ## UseLocal ... dropping? @@ -666,12 +666,12 @@ Topic tags indicate how the publication relates to Galaxy. Here's the current s | [+Workbench](https://www.zotero.org/groups/galaxy/items/tag/+Workbench/) | Publication mentions Galaxy as a platform. | 2011 | | [+Tools](https://www.zotero.org/groups/galaxy/items/tag/+Tools/) | Tools that run in, have been ported to, or interact with Galaxy | 2012 | | [+Cloud](https://www.zotero.org/groups/galaxy/items/tag/+Cloud/) | Publications referencing / extending / discussing Galaxy in a cloud context. | 2013 | -| [+RefPublic](https://www.zotero.org/groups/galaxy/items/tag/+RefPublic/) | References a [publicly accessible Galaxy instance](/src/use/index.md) or a [Galaxy service](/src/use/index.md). This is distinct from the *+UsePublic* tag. | 2013 | +| [+RefPublic](https://www.zotero.org/groups/galaxy/items/tag/+RefPublic/) | References a [publicly accessible Galaxy instance](/use/) or a [Galaxy service](/use/). This is distinct from the *+UsePublic* tag. | 2013 | | [+Unknown](https://www.zotero.org/groups/galaxy/items/tag/+Unknown/) | Publications that we know refer to Galaxy, but we aren't sure how because they are behind a paywall we don't have access to. These are revisited periodically. | 2013 | | [+UseCloud](https://www.zotero.org/groups/galaxy/items/tag/+UseCloud/) | Uses a custom built cloud based instance of Galaxy in its methods. | 2013 | | [+UseLocal](https://www.zotero.org/groups/galaxy/items/tag/+UseLocal/) | Uses a local installation of Galaxy in its methods. | 2013 | -| [+UseMain](https://www.zotero.org/groups/galaxy/items/tag/+UseMain/) | Uses the project's public server, [usegalaxy.org](https://usegalaxy.org/) (a.k.a. [Main](/src/main/index.md), in its methods. | 2013 | -| [+UsePublic](https://www.zotero.org/groups/galaxy/items/tag/+UsePublic/) | Uses a [publicly accessible Galaxy instance](/src/use/index.md) or a [Galaxy service](/src/use/index.md) in its methods. | 2013 | +| [+UseMain](https://www.zotero.org/groups/galaxy/items/tag/+UseMain/) | Uses the project's public server, [usegalaxy.org](https://usegalaxy.org/) (a.k.a. [Main](/main/), in its methods. | 2013 | +| [+UsePublic](https://www.zotero.org/groups/galaxy/items/tag/+UsePublic/) | Uses a [publicly accessible Galaxy instance](/use/) or a [Galaxy service](/use/) in its methods. | 2013 | | [+Visualization](https://www.zotero.org/groups/galaxy/items/tag/+Visualization/) | Publications referencing Galaxy in a visualization and/or visual analytics context. | 2013 | | [+Education]() | Papers referencing Galaxy in a training or education context. | 2019 | @@ -686,7 +686,7 @@ With the move to Zotero we added two new sets of tags. The first set is used to ## Platform tags -The second set of new tags show which [public Galaxy platform](/src/use/index.md) is used or discussed in publications. These are tagged with the platform's name, preceded by a ">". For example, the [>RepeatExplorer](https://www.zotero.org/groups/1732893/galaxy/tags/%3ERepeatExplorer) tag lists all papers that use or reference the [RepeatExplorer](/src/use/repeatexplorer/index.md) public server. +The second set of new tags show which [public Galaxy platform](/use/) is used or discussed in publications. These are tagged with the platform's name, preceded by a ">". For example, the [>RepeatExplorer](https://www.zotero.org/groups/1732893/galaxy/tags/%3ERepeatExplorer) tag lists all papers that use or reference the [RepeatExplorer](/src/use/repeatexplorer/index.md) public server. ## Publisher Tags diff --git a/content/blog/2021-09-hub2/content-dir-static-inserts.svg b/content/blog/2021-09-hub2/content-dir-static-inserts.svg index 72da947e90..b48f45bbc4 100644 --- a/content/blog/2021-09-hub2/content-dir-static-inserts.svg +++ b/content/blog/2021-09-hub2/content-dir-static-inserts.svg @@ -645,7 +645,7 @@ x="-209.80302" y="273.19214" style="font-size:6.74271393px;fill:#a86b24;fill-opacity:1;stroke-width:0.34331468" - id="tspan13455">Galaxy's free public server [Main](/src/main/index.md).Galaxy's free public server [Main](/main/).• [Galaxy Application Programming Interface (API)](#application-programming-interface-api)
• [Cloud](#cloud)
• [Data Managers](#data-managers)
• [DataSource Tools](#datasource-tools)
• [External Display Applications](#external-display-applications)
• [Interactive Environments](#interactive-environments)
• [Reproducibility](#reproducibility)
• [ToolShed](#toolshed)
• [Training & Education](#training-education) | | **Referencing a Galaxy web resource other than those above** | See [Citing Medicine: NLM Style Guide for Authors, Editors, and Publishers](http://www.ncbi.nlm.nih.gov/books/NBK7256/) for how to cite [web pages](http://www.ncbi.nlm.nih.gov/books/NBK7274/), [wikis](http://www.ncbi.nlm.nih.gov/books/NBK7266/#A61262), and just about everything else. | @@ -18,7 +18,7 @@ So, how can you do that? It depends on your research: # Which Galaxy? -If you *used* Galaxy in your methods, please specify which instances of Galaxy were used: Was it [usegalaxy.org](https://usegalaxy.org/), one of the [other public Galaxy servers, cloud sevices, VMs or containers](/src/use/index.md) (and see each resource's page for citation info), or a local install? +If you *used* Galaxy in your methods, please specify which instances of Galaxy were used: Was it [usegalaxy.org](https://usegalaxy.org/), one of the [other public Galaxy servers, cloud sevices, VMs or containers](/use/) (and see each resource's page for citation info), or a local install? Some excellent examples (*emphasis added*): @@ -26,7 +26,7 @@ Some excellent examples (*emphasis added*): "The sequencing data were uploaded to the Galaxy web platform, and *we used the public server at usegalaxy.org to analyze the data ([Afgan et al. 2016](http://www.g3journal.org/content/7/9/2979#ref-1))*." -* Used a [public server](/src/use/index.md): from [Bhargava, *et al.*](https://www.nature.com/articles/s41598-017-07791-8): +* Used a [public server](/use/): from [Bhargava, *et al.*](https://www.nature.com/articles/s41598-017-07791-8): "RAW files generated directly from the mass spectrometer *were imported into Galaxy-P platform[53](https://www.nature.com/articles/s41598-017-07791-8#ref-CR53) for protein identification and quantification[25](https://www.nature.com/articles/s41598-017-07791-8#ref-CR25), [51](https://www.nature.com/articles/s41598-017-07791-8#ref-CR51).*" diff --git a/content/cloud/index.md b/content/cloud/index.md index 7d6039b01e..4e9d5e2f34 100644 --- a/content/cloud/index.md +++ b/content/cloud/index.md @@ -5,13 +5,13 @@ Researchers' compute requirements vary widely over time and formerly required ei The *cloud* provides another option for this situation that can be cost-effective and efficient. Cloud infrastructures are elastic and dynamic. You only allocate resource when you need them, and you are able to dynamically scale up and down your allocated resources as your needs change over time. Furthermore, compute clouds are maintained by outside providers - you don't need to install your own hardware, or need to have access to a research compute cluster at your institution. -Cloud infrastructures are just [one of the many ways that Galaxy is available](/src/use/index.md). +Cloud infrastructures are just [one of the many ways that Galaxy is available](/use/). # CloudMan -
CloudMan
+
CloudMan
-[CloudMan](/src/cloudman/index.md) is a software package that abstracts the interface to cloud infrastructure, allowing users to take advantage of the power of cloud infrastructure without having to learn much of the underlying details of any particular infrastructure. CloudMan supports elastic, dynamic resource scaling and works with Galaxy out of the box. Cloudman can launch a customized Galaxy instance using the simple [launch page](https://launch.usegalaxy.org/launch). It is also integrated with [CloudBioLinux](http://cloudbiolinux.org/). CloudMan works with multiple cloud infrastructures including [Amazon Web Services](http://aws.amazon.com), [OpenStack](http://www.openstack.org/), and [OpenNebula](http://opennebula.org). +[CloudMan](/cloudman/) is a software package that abstracts the interface to cloud infrastructure, allowing users to take advantage of the power of cloud infrastructure without having to learn much of the underlying details of any particular infrastructure. CloudMan supports elastic, dynamic resource scaling and works with Galaxy out of the box. Cloudman can launch a customized Galaxy instance using the simple [launch page](https://launch.usegalaxy.org/launch). It is also integrated with [CloudBioLinux](http://cloudbiolinux.org/). CloudMan works with multiple cloud infrastructures including [Amazon Web Services](http://aws.amazon.com), [OpenStack](http://www.openstack.org/), and [OpenNebula](http://opennebula.org). See the CloudMan page for more. @@ -33,7 +33,7 @@ Galaxy can store user data on a cloud-based storage, and can also download data [OpenStack](http://openstack.org) -Both CloudMan and [Globus Genomics](/src/cloud/index.md#globus-genomics) use [Amazon Web Services](http://aws.amazon.com). CloudMan can also run on any cloud provider that supports the [OpenStack](http://openstack.org) or [OpenNebula](http://opennebula.org) cloud management protocols. This covers the vast majority of commercial cloud providers. +Both CloudMan and [Globus Genomics](/cloud/#globus-genomics) use [Amazon Web Services](http://aws.amazon.com). CloudMan can also run on any cloud provider that supports the [OpenStack](http://openstack.org) or [OpenNebula](http://opennebula.org) cloud management protocols. This covers the vast majority of commercial cloud providers. You can also set up your own Galaxy server using any cloud provider, but not CloudMan. In this situation you handle the Galaxy installation and the cloud aspects of the install. diff --git a/content/cloud/jetstream/ssh/index.md b/content/cloud/jetstream/ssh/index.md index b35f37e357..f66ca029bf 100644 --- a/content/cloud/jetstream/ssh/index.md +++ b/content/cloud/jetstream/ssh/index.md @@ -19,11 +19,11 @@ From here, you can perform any administrative task. You will be logged in as the ## Changing Galaxy settings -Galaxy has an extensive set of administrative [configuration options](/src/admin/index.md). The most common changes to Galaxy are performed by editing *galaxy.ini* file. On the Jetstream image, this file is located in */opt/galaxy/galaxy-app/config/galaxy.ini* and it must be edited as *galaxy* system user. You can edit the file using [nano](http://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/) or [vim](https://www.linux.com/learn/vim-101-beginners-guide-vim) editors. The most current list of available options is always available in the [galaxy.ini.sample](https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample) file; any missing options can be added of the existing ones can be modified. If adding new options to the file, make sure that you are adding them under the right section of the file, most likely under *[app:main]* header. Note that after changing this file, it is necessary to restart Galaxy. +Galaxy has an extensive set of administrative [configuration options](/admin/). The most common changes to Galaxy are performed by editing *galaxy.ini* file. On the Jetstream image, this file is located in */opt/galaxy/galaxy-app/config/galaxy.ini* and it must be edited as *galaxy* system user. You can edit the file using [nano](http://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/) or [vim](https://www.linux.com/learn/vim-101-beginners-guide-vim) editors. The most current list of available options is always available in the [galaxy.ini.sample](https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample) file; any missing options can be added of the existing ones can be modified. If adding new options to the file, make sure that you are adding them under the right section of the file, most likely under *[app:main]* header. Note that after changing this file, it is necessary to restart Galaxy. ### Adding Galaxy Admin user -To be able to add new tools or reference data, it is necessary to become Galaxy Admin user and use the [admin panel](/src/admin/index.md). This is done by editing Galaxy settings (see above section) and adding a line like the following under the *[app:main]* section: *admin_users = *. Save the file and restart Galaxy process. +To be able to add new tools or reference data, it is necessary to become Galaxy Admin user and use the [admin panel](/admin/). This is done by editing Galaxy settings (see above section) and adding a line like the following under the *[app:main]* section: *admin_users = *. Save the file and restart Galaxy process. ## Restarting Galaxy diff --git a/content/cloudman/aws/capacity-planning/index.md b/content/cloudman/aws/capacity-planning/index.md index b17e65c28a..65788f0f8f 100644 --- a/content/cloudman/aws/capacity-planning/index.md +++ b/content/cloudman/aws/capacity-planning/index.md @@ -5,7 +5,7 @@ title: Capacity Planning
Instructors Greg Von Kuster, Penn State University
Björn Grüning, University of Freiburg
Peter Cock, James Hutton Institute 		Greg Von Kuster, Penn State University
Björn Grüning, University of Freiburg
Peter Cock, James Hutton Institute
Content
3:00-3:25 TT10: The first biomedical AppStore: Galaxy Tool Shed, Greg von Kuster, Penn State University TT10: The first biomedical AppStore: Galaxy Tool Shed, Greg von Kuster, Penn State University Slides
- +
Galaxy CloudMan CapacityPlanning for Amazon Web Services
Galaxy CloudMan CapacityPlanning for Amazon Web Services
 http://aws.amazon.com/
@@ -18,7 +18,7 @@ This page offers advice on how much cloud infrastructure you will need to [run y # Amazon Web Services -[CloudMan](/src/cloudman/index.md) was initially developed for the [Amazon Web Services (AWS)](http://aws.amazon.com/) cloud platform. Before we cover AWS, we'll need to introduce some terminology: +[CloudMan](/cloudman/) was initially developed for the [Amazon Web Services (AWS)](http://aws.amazon.com/) cloud platform. Before we cover AWS, we'll need to introduce some terminology: ## Terminology diff --git a/content/cloudman/aws/getting-started/index.md b/content/cloudman/aws/getting-started/index.md index 18bd155226..fcb04419d1 100644 --- a/content/cloudman/aws/getting-started/index.md +++ b/content/cloudman/aws/getting-started/index.md @@ -8,7 +8,7 @@ title: Getting Started with Galaxy CloudMan -This page provides a step-by-step instructions on how to start your own instance of Galaxy on [Amazon Web Services (AWS)](http://aws.amazon.com/) [Elastic Compute Cloud (EC2)](http://aws.amazon.com/ec2/). More general information and instructions about Galaxy CloudMan can be found [here](/src/cloudman/index.md). +This page provides a step-by-step instructions on how to start your own instance of Galaxy on [Amazon Web Services (AWS)](http://aws.amazon.com/) [Elastic Compute Cloud (EC2)](http://aws.amazon.com/ec2/). More general information and instructions about Galaxy CloudMan can be found [here](/cloudman/). ## Screencast @@ -104,7 +104,7 @@ All of these inbound rules are necessary for proper functioning of CloudMan and ** This step is required every time a new cloud instance of Galaxy is desired.** -[CloudMan](/src/cloudman/index.md) works in a master-worker fashion: the master is used to control all of the needed services as well as worker instances. Worker instances are needed to run analysis jobs submitted through Galaxy that runs on the master instance (for a more detailed description of running Galaxy in cluster environments, see the [cluster performance page](/src/admin/config/performance/cluster/index.md)). So, in order to start a Galaxy CloudMan cluster, we need to start a master instance. +[CloudMan](/cloudman/) works in a master-worker fashion: the master is used to control all of the needed services as well as worker instances. Worker instances are needed to run analysis jobs submitted through Galaxy that runs on the master instance (for a more detailed description of running Galaxy in cluster environments, see the [cluster performance page](/src/admin/config/performance/cluster/index.md)). So, in order to start a Galaxy CloudMan cluster, we need to start a master instance. 1. Go to the [AWS Management Console for EC2](https://console.aws.amazon.com/ec2/home) and click **Launch Instance** diff --git a/content/cloudman/building/index.md b/content/cloudman/building/index.md index f602f84278..82875288f2 100644 --- a/content/cloudman/building/index.md +++ b/content/cloudman/building/index.md @@ -4,7 +4,7 @@ title: Building Galaxy CloudMan components -Launching a default version of [CloudMan](http://usecloudman.org/) and [Galaxy on the Cloud](/src/cloudman/index.md) is a pretty straightforward process. [The underlying system](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full), however, is more complex and consists of a number of components. This page describes the steps required to build your own version of the components and deploy the system. You may want to do this if you are deploying the system on your own Cloud. If you would just like to have a custom version of the existing system on AWS, perhaps [cluster sharing & cloning](/src/cloudman/sharing/index.md) can help? +Launching a default version of [CloudMan](http://usecloudman.org/) and [Galaxy on the Cloud](/cloudman/) is a pretty straightforward process. [The underlying system](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full), however, is more complex and consists of a number of components. This page describes the steps required to build your own version of the components and deploy the system. You may want to do this if you are deploying the system on your own Cloud. If you would just like to have a custom version of the existing system on AWS, perhaps [cluster sharing & cloning](/src/cloudman/sharing/index.md) can help? ## Overview diff --git a/content/cloudman/capacity-planning/index.md b/content/cloudman/capacity-planning/index.md index eec70f67a6..bed20f447d 100644 --- a/content/cloudman/capacity-planning/index.md +++ b/content/cloudman/capacity-planning/index.md @@ -15,7 +15,7 @@ There are many reasons why you may want to run Galaxy on the cloud. This page a ## Scenario 1: Light usage -Scenario 1 is characterized by **light usage paired with the desire to avoid system administration.** In this case you want to use Galaxy for relatively lightweight processing tasks, but you don't want to use a [shared Galaxy server](/src/use/index.md), or install your own copy. Galaxy's cloud images come with more tools and datasets preinstalled than does [Main](/src/main/index.md), and far more than a [locally installed Galaxy](/src/admin/get-galaxy/index.md). You may also not want to put your data on a public server. +Scenario 1 is characterized by **light usage paired with the desire to avoid system administration.** In this case you want to use Galaxy for relatively lightweight processing tasks, but you don't want to use a [shared Galaxy server](/use/), or install your own copy. Galaxy's cloud images come with more tools and datasets preinstalled than does [Main](/main/), and far more than a [locally installed Galaxy](/src/admin/get-galaxy/index.md). You may also not want to put your data on a public server. ## Scenario 2: Occasional but heavy usage diff --git a/content/cloudman/faq/index.md b/content/cloudman/faq/index.md index 523fc1469c..0e510a0e55 100644 --- a/content/cloudman/faq/index.md +++ b/content/cloudman/faq/index.md @@ -3,7 +3,7 @@ title: Frequently Asked Questions for CloudMan --- -See [Learn/FAQ](/src/learn/faq/index.md) for questions about using any Galaxy instance and [CloudMan](/src/cloudman/index.md) page for general information about CloudMan. +See [Learn/FAQ](/src/learn/faq/index.md) for questions about using any Galaxy instance and [CloudMan](/cloudman/) page for general information about CloudMan. ---- diff --git a/content/cloudman/index.md b/content/cloudman/index.md index 405f0d4cc3..e413571357 100644 --- a/content/cloudman/index.md +++ b/content/cloudman/index.md @@ -7,7 +7,7 @@ title: Galaxy CloudMan -There are several choices for using Galaxy. This page describes using Galaxy on a *[cloud infrastructure](https://www.tcnp3.com/home/cloud-technology/what-is-cloud-computing-infographic/)* using CloudMan (see below). For other options, see the [Galaxy Platform Directory](/src/use/index.md) and [Cloud](/src/cloud/index.md). +There are several choices for using Galaxy. This page describes using Galaxy on a *[cloud infrastructure](https://www.tcnp3.com/home/cloud-technology/what-is-cloud-computing-infographic/)* using CloudMan (see below). For other options, see the [Galaxy Platform Directory](/use/) and [Cloud](/cloud/). ## About Galaxy CloudMan diff --git a/content/cloudman/openstack/index.md b/content/cloudman/openstack/index.md index ba5ebf3042..dac58d2596 100644 --- a/content/cloudman/openstack/index.md +++ b/content/cloudman/openstack/index.md @@ -1,5 +1,5 @@ -Details on running [CloudMan](/src/cloudman/index.md) on OpenStack-based cloud infrastructures. This is an active area of development for the [CloudMan Team](/src/cloudman/team/index.md). +Details on running [CloudMan](/cloudman/) on OpenStack-based cloud infrastructures. This is an active area of development for the [CloudMan Team](/src/cloudman/team/index.md). [John Chilton](/people/john-chilton/) has made available [a set of scripts and config files](https://github.com/jmchilton/cloudman_openstack_bootstrap) he uses to setup customized CloudMan instances on OpenStack. They do not represent a turn-key solution and would require significant modification, but it is a potential place to start looking for ideas on this topic. diff --git a/content/cloudman/services/galaxy/index.md b/content/cloudman/services/galaxy/index.md index 6983911fb5..23f627adc0 100644 --- a/content/cloudman/services/galaxy/index.md +++ b/content/cloudman/services/galaxy/index.md @@ -24,7 +24,7 @@ sh run.sh --pid-file=main.pid --log-file=main.log --daemon ``` -Additional Galaxy configuration options can be found on the [Galaxy Admin page](/src/admin/index.md). +Additional Galaxy configuration options can be found on the [Galaxy Admin page](/admin/). #### Adding a custom Tool Shed diff --git a/content/cloudman/userdata/index.md b/content/cloudman/userdata/index.md index 463d5166a3..c810d470f8 100644 --- a/content/cloudman/userdata/index.md +++ b/content/cloudman/userdata/index.md @@ -3,7 +3,7 @@ -[CloudMan](/src/cloudman/index.md) supports the notion of User Data when instantiating an instance. User Data allows individual instances of CloudMan to be customized for a given user. Some of the User Data fields are required while others allow further customization of one's instance. This page describes the available User Data fields. User Data is specified at the time of instance request in [YAML format](http://en.wikipedia.org/wiki/YAML), for example: +[CloudMan](/cloudman/) supports the notion of User Data when instantiating an instance. User Data allows individual instances of CloudMan to be customized for a given user. Some of the User Data fields are required while others allow further customization of one's instance. This page describes the available User Data fields. User Data is specified at the time of instance request in [YAML format](http://en.wikipedia.org/wiki/YAML), for example: ```bash cluster_name: password: diff --git a/content/community/galaxy-admins/index.md b/content/community/galaxy-admins/index.md index cccb53e014..b984f33219 100644 --- a/content/community/galaxy-admins/index.md +++ b/content/community/galaxy-admins/index.md @@ -13,4 +13,4 @@ This community currently continues on [Galaxy Project Gitter "Admins"](https://g ## Meetups -The group used to [meet up](/src/community/galaxy-admins/meetups/index.md) the third Thursday of every two month (starting February) unless otherwise notified, and irregularly at [Galaxy-related events](/src/events/index.md), such as [GCC2016](https://web.archive.org/web/http://gcc2016.iu.edu/). The final in person gathering under this name was during [GCCBOSC 2018](https://gccbosc2018.sched.com/event/FMQW/bof-galaxyadmins). +The group used to [meet up](/src/community/galaxy-admins/meetups/index.md) the third Thursday of every two month (starting February) unless otherwise notified, and irregularly at [Galaxy-related events](/events/), such as [GCC2016](https://web.archive.org/web/http://gcc2016.iu.edu/). The final in person gathering under this name was during [GCCBOSC 2018](https://gccbosc2018.sched.com/event/FMQW/bof-galaxyadmins). diff --git a/content/community/galaxy-admins/meetups/2012-07-09/index.md b/content/community/galaxy-admins/meetups/2012-07-09/index.md index 00000da0b5..5635cda0d6 100644 --- a/content/community/galaxy-admins/meetups/2012-07-09/index.md +++ b/content/community/galaxy-admins/meetups/2012-07-09/index.md @@ -30,7 +30,7 @@ Ann proposed this generic agenda for future calls * 20 min: Galaxy in Our Town. Presentation from a local galaxy institution on what they are doing or a problem they are troubleshooting - or have someone walk through their use cases and pain points. * 20 min: Galaxy Today/Tomorrow. - Presentation on a galaxy coding item. Either from [Galaxy Team](/galaxy-team/), or from [someone](/src/community/index.md) working on a new feature or customization. + Presentation on a galaxy coding item. Either from [Galaxy Team](/galaxy-team/), or from [someone](/community/) working on a new feature or customization. * 20 mins: Open Mic Discussion & make point to point connections. Organize smaller breakouts if someone wants to host a call specific to an issue, ... diff --git a/content/community/galaxy-admins/meetups/2012-11-14/index.md b/content/community/galaxy-admins/meetups/2012-11-14/index.md index 06b9ca300d..26c1ea1cab 100644 --- a/content/community/galaxy-admins/meetups/2012-11-14/index.md +++ b/content/community/galaxy-admins/meetups/2012-11-14/index.md @@ -36,7 +36,7 @@ Curtis Hendrickson of the [University of Alabama Birmingham's Center for Clinica

-*We also bid farewell to [Ann Black-Ziegelbein of the University of Iowa](https://www.linkedin.com/pub/ann-blackziegelbein/a/166/117).* Ann has been the driving force behind launching the [GalaxyAdmins](/src/community/index.md) group and has guided it through its first (wildly successful!) 6 months of existence. Ann is handing over the reigns to her fellow U Iowa colleague Srinivas Maddhi, whose day job is getting Iowa's Galaxy server into production. +*We also bid farewell to [Ann Black-Ziegelbein of the University of Iowa](https://www.linkedin.com/pub/ann-blackziegelbein/a/166/117).* Ann has been the driving force behind launching the [GalaxyAdmins](/community/) group and has guided it through its first (wildly successful!) 6 months of existence. Ann is handing over the reigns to her fellow U Iowa colleague Srinivas Maddhi, whose day job is getting Iowa's Galaxy server into production. We thank Ann profusely for her contributions, and Srinivas for taking this on. diff --git a/content/community/galaxy-admins/meetups/2013-11-20/index.md b/content/community/galaxy-admins/meetups/2013-11-20/index.md index 8a632b1615..75c8d962be 100644 --- a/content/community/galaxy-admins/meetups/2013-11-20/index.md +++ b/content/community/galaxy-admins/meetups/2013-11-20/index.md @@ -48,7 +48,7 @@ Action items from BoF: Draft implementations of the first two are in place: * Community/Deployments hub page -* Community/Logs hub page (since moved to the [Galaxy Blog](/src/blog/index.md) +* Community/Logs hub page (since moved to the [Galaxy Blog](/blog/) What do people think of this approach? The use of *boxes* on the right side is used to create much more informative lists of deployments and logs on their hub pages, using the [http://moinmo.in/MacroMarket/DictColumns](http://moinmo.in/MacroMarket/DictColumns) macro. diff --git a/content/community/galaxy-admins/meetups/index.md b/content/community/galaxy-admins/meetups/index.md index 7ac567ae44..19b805e569 100644 --- a/content/community/galaxy-admins/meetups/index.md +++ b/content/community/galaxy-admins/meetups/index.md @@ -55,7 +55,7 @@ The [GalaxyAdmins](/src/community/galaxy-admins/meetups/index.md) group has bi-m * 2014/06/30-2014/07/02: [GalaxyAdmins BoF](/src/events/gcc2014/bofs/galaxy-admins/index.md) at [GCC2014](/src/events/gcc2014/index.md) * Meet in person at [GCC2014](/src/events/gcc2014/index.md) to discuss [the future of GalaxyAdmins](/src/community/galaxy-admins/future/index.md). * [2013-11-20 Web Meetup](/src/community/galaxy-admins/meetups/2013-11-20/index.md) - * GCC2013 discussion followup, and [Main](/src/main/index.md) moves to TACC. + * GCC2013 discussion followup, and [Main](/main/) moves to TACC. **2013** diff --git a/content/community/index.md b/content/community/index.md index 420e71f4a8..56a6e7eb05 100644 --- a/content/community/index.md +++ b/content/community/index.md @@ -1,7 +1,7 @@ --- title: The Galaxy Community --- -A vibrant community of contributors is the reason this project exists. The [Galaxy team](/galaxy-team/) alone cannot possibly [maintain enough servers](/src/use/index.md), [wrap enough tools](https://toolshed.g2.bx.psu.edu/), [teach enough workshops](/src/events/index.md), implement [all needed features](https://github.com/galaxyproject), or [answer every question](/src/support/index.md) on its own. This is why community is vital to our core mission - enabling reproducible research in data-rich sciences and beyond. Members within the Galaxy community are located all around the world and often form subgroups that differ in size (small versus large) and degree of privacy (public versus private). This page highlights these groups. +A vibrant community of contributors is the reason this project exists. The [Galaxy team](/galaxy-team/) alone cannot possibly [maintain enough servers](/use/), [wrap enough tools](https://toolshed.g2.bx.psu.edu/), [teach enough workshops](/events/), implement [all needed features](https://github.com/galaxyproject), or [answer every question](/support/) on its own. This is why community is vital to our core mission - enabling reproducible research in data-rich sciences and beyond. Members within the Galaxy community are located all around the world and often form subgroups that differ in size (small versus large) and degree of privacy (public versus private). This page highlights these groups.
@@ -14,7 +14,7 @@ A vibrant community of contributors is the reason this project exists. The [Gala -In 2010 the National Science Foundation initiated a yearly gathering of Galaxy users and developers by providing the project with a grant supplement. Since then this gathering has grown into an annual event known as the **[Galaxy Community Conference (GCC)](/src/gcc/index.md)**. GCC alternates between North America and elsewhere, and provides a forum for sharing knowledge and building collaborations. There have been over 200 participants every year since 2012. +In 2010 the National Science Foundation initiated a yearly gathering of Galaxy users and developers by providing the project with a grant supplement. Since then this gathering has grown into an annual event known as the **[Galaxy Community Conference (GCC)](/gcc/)**. GCC alternates between North America and elsewhere, and provides a forum for sharing knowledge and building collaborations. There have been over 200 participants every year since 2012. # Working Groups and Project Governance @@ -25,7 +25,7 @@ In 2010 the National Science Foundation initiated a yearly gathering of Galaxy u # IUC: Keepers of Galaxy Tools -The [Intergalactic Utilities Commission](/src/iuc/index.md) (IUC) was established in 2012 to enable the pervasive use of the main Galaxy Tool Shed by ensuring the repositories available include contents that are functionally correct and optimized for installation into local Galaxies. When appropriate, the group provides guidance to Galaxy tool developers so that they can improve the quality of their repositories. +The [Intergalactic Utilities Commission](/iuc/) (IUC) was established in 2012 to enable the pervasive use of the main Galaxy Tool Shed by ensuring the repositories available include contents that are functionally correct and optimized for installation into local Galaxies. When appropriate, the group provides guidance to Galaxy tool developers so that they can improve the quality of their repositories.
diff --git a/content/data-libraries/index.md b/content/data-libraries/index.md index e50f087b64..8f913e3abd 100644 --- a/content/data-libraries/index.md +++ b/content/data-libraries/index.md @@ -45,13 +45,13 @@ Select folders to be imported. You can choose whether to `preserve directory str # Administration -Every library has to be created (and deleted) by an [admin](/src/admin/index.md) user but subsequently can be filled with datasets and folders by anyone with permissions. It has multiple levels of access control for the data inside ranqing from 'public' to 'one person only'. +Every library has to be created (and deleted) by an [admin](/admin/) user but subsequently can be filled with datasets and folders by anyone with permissions. It has multiple levels of access control for the data inside ranqing from 'public' to 'one person only'.