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index-proteomics.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Australia</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The Australian Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://usegalaxy-au.github.io/index-proteomics.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Australia" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
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</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><br />
<img src="/assets/media/GalaxyP_logo.png" height="200px" alt="GalaxyP logo" /></p>
<h1 id="welcome-to-galaxy-proteomics">Welcome to <strong>Galaxy Proteomics</strong></h1>
<p><em>This European Galaxy branches off from the main <a href="https://usegalaxy.eu" target="_blank">usegalaxy.eu</a> server and focuses on one specific domain: Proteomics.</em></p>
<p><strong>Galaxy Proteomics</strong> is a multiple ‘omics’ data analysis platform with particular emphasis on mass spectrometry-based proteomics. It is hosted by GalaxyEU and maintained by the <a href="http://galaxyp.org" target="_blank">GalaxyP team</a> from the University of Minnesota, MN, USA.</p>
<p>Feel free to check out another server maintained by the GalaxyP team: <a href="http://galaxyp-proteogenomics.duckdns.org" target="_blank">Proteogenomics Gateway</a>.</p>
<h1 id="get-started">Get started</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take <a href="https://proteomics.usegalaxy.eu/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<div class="row" id="carousel-eu-container">
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<li data-target="#splash-box" data-slide-to="0" class="active"></li>
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</ol>
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<div class="item carousel-item jumbotron active">
<h2 class="display-3">Data Driven Reseach for Everyone</h2>
<div class="col-md-6">
<p>Galaxy is an <strong>open, web-based</strong> platform for accessible, reproducible, and transparent computational biological research.</p>
<ul>
<li><strong>Accessible:</strong> Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.</li>
<li><strong>Reproducible:</strong> Galaxy captures all the metadata from an analysis, making it completely reproducible.</li>
<li><strong>Transparent:</strong> Users share and publish analyses via interactive pages that can enhance analyses with user annotations.</li>
<li><strong>Scalable:</strong> Galaxy can run on anything, from a laptop, to large clusters, to the cloud</li>
</ul>
<!-- <button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://usegalaxy.org.au')">UseGalaxy.org.au</button>
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<h2 class="display-3">Training Infrastructure as a Service</h2>
<div class="col-md-6">
<p>
We want to help you conduct your training seminars. You provide the
training, we provide you training infrastructure <i>at no cost.</i>
</p>
<div>
<p>Why use UseGalaxy.eu training infrastructure?</p>
<ul>
<li>Free</li>
<li>Private queue, no wait times</li>
<li>No Galaxy Maintenance</li>
<li>No Galaxy Administration</li>
</ul>
</div>
</div>
<div class="col-md-6">
<p>
Simply fill out the infrastructure request form and we'll get back to you shortly.
</p>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://docs.google.com/forms/d/e/1FAIpQLSdoPRDhpYwNFuZSlGRNQj3dDWwfsdemP5yntAdcqhN3YHbqLA/viewform')">Request Training Infrastructure</button>
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<h2 class="display-3">UseGalaxy.org.au: The Australian Galaxy instance</h2>
<div class="col-md-6" style="padding: 1em;">
<ul>
<li><i class="fa fa-cogs"></i> Thousands of documented and maintained tools</li>
<li><i class="fa fa-user-plus"></i> Free to use</li>
<li><i class="fa fa-hdd-o"></i> 600 GB for Australian based users (100GB for others)</li>
<li><i class="fa fa-graduation-cap"></i> On demand training capacity</li>
</ul>
<p>And even more!</p>
<!-- <button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://usegalaxy.org.au')">Try it on UseGalaxy.org.au</button>
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<h3>Maintained by:</h3>
<div class="row eu-image-box">
<a href="https://www.qcif.edu.au/" target="_blank">
<img src="/assets/media/QFAB_logo_2020.png" class="img-responsive eu-image" alt="QCIF Logo" />
</a>
<a href="https://melbournebioinformatics.org.au/" target="_blank">
<img src="/assets/media/melbourne_bio.png" class="img-responsive eu-image" alt="Melbourne Bioinformatics Logo" />
</a>
<a href="https://rcc.uq.edu.au/" target="_blank">
<img src="/assets/media/uq_rcc_logo.png" class="img-responsive eu-image" alt="UQ RCC Logo" />
</a>
</div>
<h3>Sponsors/Funding:</h3>
<div class="row eu-image-box">
<a href="https://bioplatforms.com" target="_blank">
<img src="/assets/media/BioplatformsAustralia.png" class="img-responsive eu-image" alt="Bioplatforms Logo" />
</a>
<a href="https://ardc.edu.au" target="_blank">
<img src="/assets/media/ardc_built-1.png" class="img-responsive eu-image" alt="ARDC Logo" />
</a>
<a href="https://www.biocommons.org.au/" target="_blank" style="max-width:22%">
<img src="/assets/media/AustralianBiocommons.png" class="img-responsive eu-image" alt="Biocommons Logo" />
</a>
<a href="https://www.education.gov.au/national-collaborative-research-infrastructure-strategy-ncris" target="_blank">
<img src="/assets/media/ncris.png" class="img-responsive eu-image" alt="NCRIS Logo" />
</a>
</div>
</div>
</div>
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<div class="row">
<h2 class="display-3">Supported projects</h2>
<p class="lead"></p>
<p>The UseGalaxy.eu team supports many projects in the Galaxy community:</p>
</div>
<div class="row eu-image-box">
<a href="http://galaxyp.org/" target="_blank">
<img src="/assets/media/GalaxyP_logo.png" class="img-responsive eu-image" alt="Galaxy-P Logo" />
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</a>
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</a>
</div>
<div class="row">
<p class="lead"></p>
<p>and also:</p>
<ul>
<li><a href="https://hicexplorer.usegalaxy.eu/">Galaxy HiCExplorer</a> to process, analyse and visualize Hi-C data</li>
</ul>
</div>
</div>
</div>
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<div class="item carousel-item jumbotron">
<h2 class="display-3">Training Materials</h2>
<div class="col-md-6">
<p>The Galaxy Community maintains a wide variety of training materials at <a href="https://training.galaxyproject.org">https://training.galaxyproject.org</a>
</p>
<p>
Topics include: variant analysis, transcriptomics, metagenomics, epigenetics, and many more!
</p>
<p>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://galaxy-au-training.github.io/tutorials/')">Galaxy Australia Training Material</button>
</p>
<p>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://training.galaxyproject.org')">Galaxy Training Network</button>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://www.sciencedirect.com/science/article/pii/S2405471218302308')">View Publication</button>
</p>
</div>
<div class="col-md-6">
<img src="/assets/media/training.png" alt="Galaxy training materials page" style="max-width: 90%;" />
</div>
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<div class="item carousel-item jumbotron">
<h2 class="display-3">Acknowledgements</h2>
<p>We are aiming to maintain high competency and provide high quality data analysis
services to all our Galaxy users.</p>
<p>Therefore we request that you acknowledge this service by including the
members of the Australian Galaxy Team as co-authors if they have made a
significant intellectual and/or organizational contribution to the work
described (conceptualization, design, data analysis, data interpretation
and/or input into drafting, revising or writing any portion of the manuscript).</p>
<p>If you use Galaxy Australia in your research, please cite the GVL paper:</p>
<blockquote>
<!--<p>Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. PLoS One. 2015 Oct 26;10(10):e0140829.
</p> -->
<p>Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko, <i>The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update</i>, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W395–W402, <a href="https://doi.org/10.1093/nar/gkaa434">https://doi.org/10.1093/nar/gkaa434</a>
</p>
</blockquote>
<p>Additional funding of projects and/or provision of material expenses are welcome as well, to help
support our growing Galaxy community in Australia.</p>
<p style="padding-bottom: 3em" />
</div>
<div class="item carousel-item jumbotron">
<h2 class="display-3">Downtime Notifications</h2>
<div class="col-md-6">
<p>
We want you to feel that usegalaxy.org.au is a reliable service, so we are
promising to give you advanced warning (when possible) about upcoming
downtimes or any events that might degrade the availability.
</p>
<ul>
<li>This is a best effort, we will try and give as much warning as we possibly can</li>
<li>But we cannot make any promise regarding downtime notices as some will be out of our control</li>
<li>The numbers we provide here are rough estimates</li>
</ul>
</div>
<div class="col-md-6">
For any planned downtime events:
<table class="table table-striped">
<thead>
<tr>
<th>Downtime</th><th>Advanced Notice</th>
</tr>
</thead>
<tbody>
<tr>
<td><5 minutes</td><td>possibly without notice</td>
</tr>
<tr>
<td>1 hour</td><td>1 day</td>
</tr>
<tr>
<td>1 day</td><td>1 week</td>
</tr>
<tr>
<td>1 week</td><td>1 month</td>
</tr>
</tbody>
</table>
</div>
<p style="padding-bottom: 3em" />
</div>
<!-- <div class="item carousel-item jumbotron">
<h2 class="display-3">Our Data Retention Policy</h2>
<p>
<h3>Registered Users</h3>
<p>
User data on UseGalaxy.org.au (i.e. datasets, histories) will be available for a
minimum of 1 year (52 weeks) as long as they are not deleted by the user. Once
marked as deleted the datasets will be permanently removed within 5 days. If
the user "purges" the dataset in the Galaxy, it will be removed immediately,
permanently.</p>
<p>
Registered users are allocated a 100GB disk quota to begin with. Registered
users with an Australian research institute are allocated 600GB.</p>
<p>
An extended quota can be <a href="https://docs.google.com/forms/d/e/1FAIpQLSeiw6ajmkezLCwbXc3OFQEU3Ai9hGnBd967u9YbQ8ANPgvatA/viewform" target="_blank">requested</a>
for a limited time period in special cases. </p>
<h3>Unregistered Users</h3>
<p>
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.)</p>
<p>
If UseGalaxy.org.au service is not accessed for 5 days, those datasets will be
permanently deleted.</p>
<h3>Full Data Policy</h3>
<p>
<a href="/galaxy/data-policy.html">Our full data policy can be found here.</a>
</p>
<p>
Instructions for Downloading and deletion of data from Galaxy Australia can be found here: <a href="https://galaxy-au-training.github.io/tutorials/modules/galaxy-data/">https://galaxy-au-training.github.io/tutorials/modules/galaxy-data/</a>
</p>
</p>
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<h2 class="display-3">Service Administration</h2>
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Galaxy Australia is administered by a team of academics from the Universities of Queensland and Melbourne. We work very closely with our colleagues from Galaxy Europe and the U.S. Galaxy Team. Galaxy Australia is a part of the usegalaxy.* ecosystem of shared resources and collaborations.
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We make <i>every effort</i> to provide high uptime.
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our control, our service is temporarily inaccessible.
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<h2 class="display-3">Domain-specific European Galaxies</h2>
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<p>UseGalaxy.eu hosts several domain specific versions of the usegalaxy.eu server. You can access any of these servers and find all of your data, with a set of tools focused on one specific domain.</p>
<table class="table table-striped">
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<th>Instance</th><th>Description</th>
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<td><a href="https://metagenomics.usegalaxy.eu">metagenomics.usegalaxy.eu</a></td>
<td>An instance focused on metagenomics tools like Mothur and Qiime</td>
</tr>
<tr>
<td><a href="https://proteomics.usegalaxy.eu">proteomics.usegalaxy.eu</a></td>
<td>An instance focused around proteomics.</td>
</tr>
<tr>
<td><a href="https://hicexplorer.usegalaxy.eu">hicexplorer.usegalaxy.eu</a></td>
<td>The place to go for all of your HiC analyses</td>
</tr>
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<h2><a href="news">News</a></h2>
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<a class="list-group-item border-freiburg" href="/posts/2022/03/23/tool-updates/">
<p class="list-group-item-text">Mar 23, 2022</p>
<h4 class="list-group-item-heading">
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Galaxy Australia tool updates 2022-03-23
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</a>
<a class="list-group-item border-freiburg" href="/posts/2022/03/16/tool-updates/">
<p class="list-group-item-text">Mar 16, 2022</p>
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<i class="fa fa-wrench" aria-hidden="true"></i>
Galaxy Australia tool updates 2022-03-16
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<a class="list-group-item border-freiburg" href="/posts/2022/03/08/tool-updates/">
<p class="list-group-item-text">Mar 8, 2022</p>
<h4 class="list-group-item-heading">
<i class="fa fa-wrench" aria-hidden="true"></i>
Galaxy Australia tool updates 2022-03-08
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<a class="list-group-item border-freiburg" href="/posts/2022/03/01/tool-updates/">
<p class="list-group-item-text">Mar 1, 2022</p>
<h4 class="list-group-item-heading">
<i class="fa fa-wrench" aria-hidden="true"></i>
Galaxy Australia tool updates 2022-03-01
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</a>
<a class="list-group-item border-freiburg" href="/posts/2022/02/22/tool-updates/">
<p class="list-group-item-text">Feb 22, 2022</p>
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<i class="fa fa-wrench" aria-hidden="true"></i>
Galaxy Australia tool updates 2022-02-22
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<a class="list-group-item border-freiburg" href="/posts/2022/02/15/tool-updates/">
<p class="list-group-item-text">Feb 15, 2022</p>
<h4 class="list-group-item-heading">
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Galaxy Australia tool updates 2022-02-15
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<h2><a href="events">Events and Workshops</a></h2>
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<a class="list-group-item border-freiburg" href="https://gallantries.github.io/posts/2021/12/14/smorgasbord2-tapas/?utm_source=eu-website&utm_medium=web&utm_campaign=smorgasbord2">
<p class="list-group-item-text">
Mar 14, 2022 - Mar 18, 2022
</p>
<h4 class="list-group-item-heading">
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<i class="fa fa-calendar" aria-hidden="true"></i>
GTN Smörgåsbord 2
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</a>
<a class="list-group-item border-freiburg" href="https://galaxyproject.org/events/2022-01-papercuts/">
<p class="list-group-item-text">
Jan 20, 2022
</p>
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<i class="fa fa-calendar" aria-hidden="true"></i>
Galaxy Papercuts CoFest Day
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<a class="list-group-item border-freiburg" href="https://galaxyproject.org/events/2021-11-papercuts/">
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Nov 18, 2021
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Galaxy Paper Cuts
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<a class="list-group-item border-freiburg" href="/event/2021-09-26-galaxy_workshops_october/">
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Oct 7, 2021
</p>
<h4 class="list-group-item-heading">
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<i class="fa fa-calendar" aria-hidden="true"></i>
WORKSHOP: Hybrid de novo genome assembly - October 2021
</h4>
</a>
<a class="list-group-item border-freiburg" href="https://galaxyproject.org/events/2021-09-papercuts/">
<p class="list-group-item-text">
Sep 16, 2021
</p>
<h4 class="list-group-item-heading">
<i class="fa fa-calendar" aria-hidden="true"></i>
Galaxy Paper Cuts
</h4>
</a>
<a class="list-group-item border-freiburg" href="/event/2021-08-21-galaxy_workshops_september/">
<p class="list-group-item-text">
Sep 9, 2021
</p>
<h4 class="list-group-item-heading">
<i class="fa fa-graduation-cap" aria-hidden="true"></i>
<i class="fa fa-calendar" aria-hidden="true"></i>
WORKSHOP: Online data analysis for biologists - September 2021
</h4>
</a>
</div>
</div>
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<h2>Our Data Policy</h2>
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<p><strong>Galaxy Australia</strong> is designed for data analysis and not for
long term storage of data.</p>
<br />
<p>Use Galaxy Australia to host your input data only for the period required for
analysis. Also, remember to export/download your analysed data as this also
will not be stored beyond the limits set out below.</p>
<p>It is <u>your responsibility</u> as a user of the system to manage your own data
and routinely remove both your input and output data from this community system
to enable capacity for other users. Any data that is not removed by you within
a defined time period (see below) will be automatically and permanently deleted.
</p>
<p>Galaxy Australia maintains a collection of frequently used reference genomes
and annotation datasets. The inclusion of additional reference genomes and/or
annotation data on the system for community use can be <a href="https://docs.google.com/forms/d/e/1FAIpQLSdXuarvkzFA5kRqoCfO8uiUGAB0PplfR4yvAfpCPSpdMcehmA/viewform">
requested</a>. Galaxy Australia's hosting of all reference and annotation data
does not count to your quota and it is the best way to access
reference/annotation data.</p>
<h3>Data storage quotas and retention periods</h3><br />
<center>
<table>
<tr>
<th></th>
<th>Storage quota</th>
<th>Data retention period</th>
</tr>
<tr>
<td><strong>Registered Australian researchers</strong></td><td>600GB</td><td>1 year (52 weeks)</td>
</tr>
<tr>
<td><strong>Other registered users</strong></td><td>100GB</td><td>1 year (52 weeks)</td>
</tr>
<tr>
<td><strong>Unregistered users</strong></td><td>5GB</td><td>NA</td>
</tr>
</table>
</center>
<h3>Registered Users</h3>
<ul>
<li><u>Registered Australian Researchers</u> are defined by registration
Email from:
<ul>
<li>@domain.edu.au</li>
<li>@domain.org.au</li>
<li>@domain.edu - only in the case of known Australian Universities
not on the .au domain</li>
</ul>
</li>
<li><u>Other Registered Users</u> are defined as any registration Email
from all other @domains</li>
<li>Please contact us ([email protected]) if your institution does not
conform to this rule but you understand it should be defined as
performing publicly funded Australian research</li>
</ul>
<p>Registered users from Australian publicly funded research organisations have
a 600GB data storage quota. Other registered users have a 100GB quota. An
increased data storage quota can be <a href="https://docs.google.com/forms/d/e/1FAIpQLSeiw6ajmkezLCwbXc3OFQEU3Ai9hGnBd967u9YbQ8ANPgvatA/viewform">
requested</a> for a limited time period in special cases.</p>
<p>Registered User's data (i.e. datasets, histories) will be available on the
system for 1 year (52 weeks) from the point of upload or creation. Within this period,
any data marked by a Registered User as "deleted" will be permanently removed
within 5 days. If a registered user "purges" the dataset, it will be removed
immediately and permanently.</p>
<h3>Unregistered Users</h3>
<p>Processed data will only be accessible during one browser session, using a
browser cookie to identify an Unregistered User's data. This cookie is not used
for any other purposes (e.g. tracking or analytics.)</p>
<h3>What does it mean when I go over quota?</h3>
<p>You data and histories are still accessible, but you not be able to run new
jobs or import more data. If you know in advance then take advantage of
<a href="https://docs.google.com/forms/d/e/1FAIpQLSeiw6ajmkezLCwbXc3OFQEU3Ai9hGnBd967u9YbQ8ANPgvatA/viewform">
requesting</a> more analysis storage or downloading and deleting old, unwanted data.</p>
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<p>UseGalaxy.org.au is maintained largely by the <a href="/people">Australian Galaxy Team</a> including staff from QCIF, UQ-RCC and Melbourne Bioinformatics.
All content on this site is available under <a href="https://creativecommons.org/share-your-work/public-domain/cc0/" target="_blank">CC0-1.0</a>, unless otherwise specified.
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