diff --git a/config.json b/config.json index ebe2717c3c..4ac1f28278 100644 --- a/config.json +++ b/config.json @@ -83,7 +83,7 @@ "name": "GenOuest" }, "elixir-it": { - "name": "ELIXIR-IT/Laniakea" + "name": "ELIXIR-IT" }, "ifb": { "name": "ELIXIR-FR/IFB" diff --git a/content/elixir-it/cite/index.md b/content/elixir-it/cite/index.md new file mode 100644 index 0000000000..fbc2cc71da --- /dev/null +++ b/content/elixir-it/cite/index.md @@ -0,0 +1,61 @@ +--- +title: Cite us +--- + +

If UseGalaxy.it and/or Laniakea helped you, please do not forget to cite us.

+
+ +

Publications

+ +
+ +

2024

+
    + +
  1. Tangaro,M.A. et al. (2024) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. NAR Genomics and Bioinformatics, 2024, 6(4), lqae140. DOI: 10.1093/nargab/lqae140.
    2. +
    +
  2. The Galaxy Community (2024) The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Nucleic Acids Research, 2024, 52(W1), pp. W83–W94. DOI: 10.1093/nar/gkae410.
    3. +
+ + +

2023

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    +
  1. Tangaro,M.A. et al. (2023) The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. Communications in Computer and Information Science, 2023, 1668 CCIS, pp. 179–191. DOI: 10.1007/978-3-031-25380-5_14.
    2. +
    +
  2. Mandreoli,P. et al. (2023) Using “Galaxy-rCASC”: A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis. Methods in Molecular Biology, 2023, 2584, pp. 311–335. DOI: 10.1007/978-1-0716-2756-3_16.
    3. +
+ + +

2022

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    +
  1. The Galaxy Community (2024) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Nucleic Acids Research, 2022, 50(W1), pp. W345–W351. DOI: 10.1093/nar/gkac247.
    2. +
+ + +

2021

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    +
  1. Tangaro,M.A. et al. (2021) Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinformatics, 2021, 22, 544. DOI: 10.1186/s12859-021-04401-3.
    2. +
    +
  2. Zambelli,F. et al. (2021) aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals. Journal of Molecular Biology, 2021, 433(11), 166829. DOI: 10.1016/j.jmb.2021.166829.
    3. + +
+ + +

2020

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    +
  1. Chiara,M. et al. (2020) VINYL: Variant prIoritizatioN by survivaL analysis. Bioinformatics, 2020, 36(24), pp. 5590–5599. DOI: 10.1093/bioinformatics/btaa1067.
    2. +
    +
  2. Chiara,M. et al. (2020) CorGAT: A tool for the functional annotation of SARS-CoV-2 genomes. Bioinformatics, 2020, 36(22-23), pp. 5522–5523. DOI: 10.1093/bioinformatics/btaa1047.
    3. +
    +
  3. Castrignanò,T. et al. (2020) ELIXIR-IT HPC@CINECA: High performance computing resources for the bioinformatics community. BMC Bioinformatics, 2020, 21, 352. DOI: 10.1186/s12859-020-03565-8.
    4. +
    +
  4. Tangaro,M.A. et al. (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. GigaScience, 2020, 9(4), giaa033. DOI: 10.1093/gigascience/giaa033.
    5. +
+ + +

2019

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    +
  1. Zanardi,N. et al. (2019) PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data. Scientific Reports, 2019, 9(1), 17550. DOI: 10.1038/s41598-019-53155-9.
    2. +
+
+ diff --git a/content/elixir-it/events/archive/main.md b/content/elixir-it/events/archive/main.md index fbb3550448..1bd0646e21 100644 --- a/content/elixir-it/events/archive/main.md +++ b/content/elixir-it/events/archive/main.md @@ -1,6 +1,6 @@ --- -title: ELIXIR-IT/Laniakea Galaxy Event Archive +title: Galaxy Italy Event Archive --- -Old events relevant to the ELIXIR-IT/Laniakea Galaxy community. +Old events relevant to the Italian Galaxy community. diff --git a/content/elixir-it/events/main.md b/content/elixir-it/events/main.md index dc4f1522dc..5ca3eff538 100644 --- a/content/elixir-it/events/main.md +++ b/content/elixir-it/events/main.md @@ -1,10 +1,10 @@ --- -title: ELIXIR-IT/Laniakea Event Horizon +title: Galaxy Italy Event Horizon --- events -Upcoming (and past) events with content relevant to the ELIXIR-IT/Laniakea Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/). +Upcoming (and past) events with content relevant to the Italian Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/). ### Advertise your event! diff --git a/content/elixir-it/lead.md b/content/elixir-it/lead.md.off similarity index 100% rename from content/elixir-it/lead.md rename to content/elixir-it/lead.md.off diff --git a/content/elixir-it/lead1.md b/content/elixir-it/lead1.md new file mode 100644 index 0000000000..12643926b9 --- /dev/null +++ b/content/elixir-it/lead1.md @@ -0,0 +1,8 @@ +
+ +
+ +[![](/images/logos/usegalaxy-it.png)](https://usegalaxy.it) + +
+
diff --git a/content/elixir-it/lead2.md b/content/elixir-it/lead2.md new file mode 100644 index 0000000000..e9eb9b8dc5 --- /dev/null +++ b/content/elixir-it/lead2.md @@ -0,0 +1,3 @@ +**Galaxy** is a user-friendly open-source web platform designed to facilitate accessible, reproducible, and transparent computational research. It provides access to a vast collection of free-to-use, well-documented and maintained tools. + +**Galaxy Italy** provides Elixir Italy users and beyond compute and storage resources for running several tools in different research domains. For more information, issues and suggestions please contact us by mail. diff --git a/content/elixir-it/lower.md b/content/elixir-it/lower.md new file mode 100644 index 0000000000..ed97d539c0 --- /dev/null +++ b/content/elixir-it/lower.md @@ -0,0 +1 @@ +--- diff --git a/content/elixir-it/lower1.md b/content/elixir-it/lower1.md.off similarity index 100% rename from content/elixir-it/lower1.md rename to content/elixir-it/lower1.md.off diff --git a/content/elixir-it/lower2.md b/content/elixir-it/lower2.md.off similarity index 100% rename from content/elixir-it/lower2.md rename to content/elixir-it/lower2.md.off diff --git a/content/elixir-it/main1.md b/content/elixir-it/main1.md new file mode 100644 index 0000000000..fb2fa346db --- /dev/null +++ b/content/elixir-it/main1.md @@ -0,0 +1,11 @@ +--- +title: Galaxy Italy +subtitle: The homepage of the Italian Galaxy community +--- +
+
+

The Italian Galaxy server

+

The Italian Galaxy server UseGalaxy.it is maintained primarily by ELIXIR-ITALY, in collaboration with many academic groups across Italy. Please check our Terms of Use before using the server.

+

The following Institutions are actively providing resource to usegalaxy.it: CNR, INFN, University of Bari, Consortium GARR, CINECA and University of Milan.

+
+
diff --git a/content/elixir-it/main2.md b/content/elixir-it/main2.md new file mode 100644 index 0000000000..f96fd648af --- /dev/null +++ b/content/elixir-it/main2.md @@ -0,0 +1,67 @@ +--- +title: Galaxy Italy +subtitle: The homepage of the Italian Galaxy community +--- + + + + +
+
+
+

Contact

+

Ask for help, tools, or temporary increase of quota on our support forum

+
+ qsupport +



+ Contact support +
+
+
+
+
+

Get information

+

Be updated on the Italian Galaxy community activities! Subscribe to our mailing list.

+
+ training +


+ Newsletter +
+
+
+
+
+

Laniakea

+

Need to deploy your own Galaxy instance? Have a look to Laniakea.

+
+ Laniakea +



+ Get access +
+
+
+
+
+

Citation

+

Have you used the Italian Galaxy server or Laniakea for your data analysis?

+
+
+ citation +


+ Cite us! +
+
+
+
+
+

Elixir Italy

+

For any questions regarding ELIXIR-Italy initiatives, please contact us.

+

+
+ team +

+ Web site +
+
+
+
diff --git a/content/elixir-it/main3.md b/content/elixir-it/main3.md new file mode 100644 index 0000000000..8ee3e15b18 --- /dev/null +++ b/content/elixir-it/main3.md @@ -0,0 +1,29 @@ +--- +title: Galaxy Italy +subtitle: Data policy +--- + +# Our Data Policy + + + + + + + + + + +
Registered UsersUnregistered UsersGDPR Compliance
User data on UseGalaxy.it (i.e. datasets, histories) will be available as long as they are not deleted by the user. + Once marked as deleted the datasets will be permanently removed within 14 days. If the user "purges" the dataset in the + Galaxy, it will be removed immediately, permanently. + In special cases, an extended quota can be requested + for a limited time period.. + Processed data will only be accessible during one browser session, using a + cookie to identify your data. This cookie is not used for any other purposes + (e.g. tracking or analytics). + If UseGalaxy.it service is not accessed for 90 days, those datasets will be + permanently deleted. + The Galaxy service complies with the EU General Data Protection Regulation + (GDPR). You can read more about this on our + Terms and Conditions.
diff --git a/content/elixir-it/main.md b/content/elixir-it/main4.md similarity index 70% rename from content/elixir-it/main.md rename to content/elixir-it/main4.md index 540748841e..4cd483b9e5 100644 --- a/content/elixir-it/main.md +++ b/content/elixir-it/main4.md @@ -1,13 +1,18 @@ --- -title: Laniakea@ReCaS +title: Galaxy Italy +subtitle: Laniakea on-demand platform --- +# Laniakea@ReCaS +
-The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks. +The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster-backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks. + +For more information about Laniakea, please subscribe to our mailing list. -[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-secondary .trim-p} +[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-primary .trim-p}
diff --git a/content/elixir-it/main5.md b/content/elixir-it/main5.md new file mode 100644 index 0000000000..69a9da30ca --- /dev/null +++ b/content/elixir-it/main5.md @@ -0,0 +1,62 @@ +--- +title: Galaxy Italy +subtitle: Laniakea on-demand platform +--- + +# Communities: Laniakea's public servers + +
+
+
+

Vinyl

+

VINYL (Variant prIoritizatioN bY survivaL analysis) integrates an innovative method for variant prioritization, along with a highly curated collection of databases and resources for the annotation of human genetic variants.

+
+
+ Vinyl +


+ Vinyl +
+
+
+
+
+

CorGAT

+

CorGAT, the Coronavirus Genome Analysis Tool, is a novel, highly effective and user-friendly approach for the functional annotation of SARS-CoV-2 genomes based on Galaxy.

+
+

+ CorGAT +


+ CorGAT +
+
+
+
+
+

ITSoneWB

+

ITSoneWB (ITSone WorkBench) collects and integrates the high-quality ITS1 reference collection in ITSoneDB with DNA metabarcoding well-established analysis pipelines and new tools in an easy-to-use service addressing the eukaryotic domain of life.

+
+ ITSoneWB +


+ ITSoneWB +
+
+
+
+
+
+
+

PIPE-T

+

PIPE-T is the first Galaxy tool for parsing, filtering, normalising, imputing, and analysing RT-qPCR data. PIPE-T integrates the functionalities implemented in various R packages, such as HTqPCR, impute, and RankProd, in a simple, transparent, accessible, reproducible, and user-friendly environment.

+
+
+ Vinyl +

+ Pipe-T +
+
+
+
+
+
+
+
diff --git a/content/elixir-it/navbar.yml b/content/elixir-it/navbar.yml index b1a4c92a13..e5621de53c 100644 --- a/content/elixir-it/navbar.yml +++ b/content/elixir-it/navbar.yml @@ -1,5 +1,6 @@ style: color: "#2c81bb" + #lightBg: true left: - label: News relativeTo: subsite @@ -8,7 +9,11 @@ left: relativeTo: subsite target: events/ - label: People - target: https://usegalaxy-eu.github.io/elixir-it/people + relativeTo: subsite + target: people/ + - label: Cite + relativeTo: subsite + target: cite/ right: - label: Help contents: diff --git a/content/elixir-it/news/main.md b/content/elixir-it/news/main.md index 2e9659adfd..6034938e37 100644 --- a/content/elixir-it/news/main.md +++ b/content/elixir-it/news/main.md @@ -1,5 +1,5 @@ --- -title: ELIXIR-IT/Laniakea Galaxy News +title: Galaxy Italy News --- news diff --git a/content/elixir-it/people/index.md b/content/elixir-it/people/index.md new file mode 100644 index 0000000000..c036ddf8bd --- /dev/null +++ b/content/elixir-it/people/index.md @@ -0,0 +1,50 @@ +--- +title: Galaxy Italy Team +--- + +
+ +
+ +
+

Federico Zambelli

+

ELIXIR-Italy technical coordinator and Galaxy Italy team leader

+ + + +
+
+ +
+ +
+

Marco Antonio Tangaro

+

UseGalaxy.it and Laniakea lead developer

+ + + +
+
+ +
+ +
+

Luigi Mansi

+

UseGalaxy.it and Laniakea developer

+ +
+
+ +
+ +
+

Gaetanomaria De Sanctis

+

UseGalaxy.it and Laniakea developer

+ +
+
+ + + +
diff --git a/content/elixir-it/site-footer.md b/content/elixir-it/site-footer.md index 6c1d93cf38..134182c94b 100644 --- a/content/elixir-it/site-footer.md +++ b/content/elixir-it/site-footer.md @@ -1,13 +1,32 @@ +

+ +
+ +[![](https://raw.githubusercontent.com/Laniakea-elixir-it/resources/master/logos/elixir_italy_white_background.png)](https://elixir-italy.org/) +[![](https://raw.githubusercontent.com/Laniakea-elixir-it/resources/refs/heads/master/logos/logo_CNR_compatto.png)](https://www.cnr.it/en) +[![](https://github.com/Laniakea-elixir-it/resources/blob/master/logos/INFN.png?raw=true)](https://www.ba.infn.it/it/) +[![](https://github.com/Laniakea-elixir-it/resources/blob/master/logos/ReCaS-Bari.png?raw=true)](https://www.recas-bari.it/index.php/en/) +[![](https://work.unimi.it/aree_protette/cataloghi/ATENEO/MARCHI/jpg/ATENEO-09.jpg)](https://www.unimi.it/en) +[![](https://www.uniba.it/it/dati-homepage/logo_UNIBA.png)](https://www.uniba.it/en) +[![](https://www.garr.it/it/news-e-eventi/pubblicazioni/materiale-informativo/loghi/3955-logo-garr-png/file)](https://www.garr.it/en/) +[![](https://www.cineca.it/sites/default/files/2024-07/logo-cineca.png)](https://www.cineca.it/en) + +
+ +
+
-[Laniakea](https://laniakea-elixir-it.github.io) has been developed in the framework of the [INDIGO-Datacloud](https://www.indigo-datacloud.eu) project funded by the European Commision H2020 research and innovation program under grant agreement RIA 653549. +[UseGalaxy.it](https://usegalaxy.it) has been developed in the framework of the [EuroScienceGateway](https://galaxyproject.org/projects/esg/) funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. + +The [UseGalaxy.it](https://usegalaxy.it) service is provided with the support of [ELIXIR-ITALY](https://elixir-italy.org), [ReCaS-Bari](https://www.recas-bari.it), [](), [Consortium GARR](https://www.garr.it/en/), [CINECA](https://www.cineca.it/en) and [University of Milan](https://www.unimi.it/en). -The development of Laniakea continues in the framework of [EOSC-Pillar](https://www.eosc-pillar.eu) (Grant agreement ID: 857650) and [EOSC-Life](https://www.eosc-life.eu) (Grant agreement ID: 824087) H2020 projects. +[Laniakea](https://laniakea-elixir-it.github.io) has been developed in the framework of the [INDIGO-Datacloud](https://www.indigo-datacloud.eu) project funded by the European Commision H2020 research and innovation program under grant agreement RIA 653549. The development of Laniakea continued in the framework of [EOSC-Pillar](https://www.eosc-pillar.eu) (Grant agreement ID: 857650) and [EOSC-Life](https://www.eosc-life.eu) (Grant agreement ID: 824087) H2020 projects. The [Laniakea@ReCaS](https://laniakea-elixir-it.github.io/laniakea_at_recas) service is provided with the support of [ELIXIR-ITALY](https://elixir-italy.org) and [ReCaS-Bari](https://www.recas-bari.it). [](){: .fab .fa-github style="color: #777"} [Edit this page on GitHub](https://github.com/galaxyproject/galaxy-hub/blob/master/content/bare/elixir-it/galaxy/index.md)   -[](){: .fa .fa-envelope style="color: #777"} [laniakea.helpdesk@gmail.com](mailto:laniakea.helpdesk@gmail.com)   +[](){: .fab .fa-github style="color: #777"} [UseGalaxy-it](https://github.com/usegalaxy-it/)   [](){: .fab .fa-github style="color: #777"} [Laniakea-elixir-it](https://github.com/Laniakea-elixir-it)   [](){: .fa .fa-rss style="color: #777"} Subscribe [via RSS (UseGalaxy.eu Feed)](/eu/feed.atom) diff --git a/content/images/logos/usegalaxy-it.png b/content/images/logos/usegalaxy-it.png new file mode 100644 index 0000000000..a0ad98c20f Binary files /dev/null and b/content/images/logos/usegalaxy-it.png differ