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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
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<body>
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<p><br /></p>
<p><img src="/assets/media/logo_eirene_black_200.png" height="83px" width="200px" alt="EIRENE-RI logo" /></p>
<h1 class="no_toc" id="welcome-to-usegalaxyeu-eirene">Welcome to <strong>UseGalaxy.EU EIRENE</strong></h1>
<p>Environmental Exposure Assessment Research Infrastructure (EIRENE) aims to fill the gap in the European infrastructural landscape and to pioneer the first EU infrastructure on human exposome. EIRENE RI was designed as a geographically balanced network of distributed research infrastructures.</p>
<p>For more information see the official <a href="https://www.eirene-ri.eu/about">EIRENE Website</a>.</p>
<hr />
<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="/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<ol>
<li><a href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html">A short introduction to Galaxy</a> and the <a href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html">Galaxy 101 for everyone</a> to get a first hang on using Galaxy for your data analysis.</li>
<li><a href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html">Data handling</a> is an important part of using Galaxy, so we also recommend this tutorial.</li>
</ol>
<hr />
<h1 id="training">Training</h1>
<p>Want to learn more? Check out the following tutorials from the <a href="https://galaxyproject.github.io/training-material/" target="_blank">Galaxy Trainings Network</a>:</p>
<ul>
<li><a href="https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html#chemical-collections">Management of chemical data in Galaxy</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html">Peak detection and preprocessing with XCMS</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html">GC-EI+-MS data processing</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html">LC-MS data processing</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/tutorial.html">LC-MS data analysis</a></li>
</ul>
<hr />
<h1 id="gateways">Gateways</h1>
<p>Other national EIRENE Galaxy servers:</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Servers</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://umsa.cerit-sc.cz">EIRENE-CZ</a></td>
</tr>
</tbody>
</table>
<hr />
<h1 id="news-and-events">News and Events</h1>
<div class="row" id="carousel-eu-container">
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<h2 class="display-3">Data Driven Research 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 or the cloud.</li>
</ul>
</div>
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<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://usegalaxy.eu')">UseGalaxy.eu</button>
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<div class="item carousel-item jumbotron">
<h2 class="display-3">UseGalaxy.eu: The European 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 registration</li>
<li><i class="fa fa-hdd-o"></i> 250 GB per user (500 GB for ELIXIR members)</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.eu')">Try it on UseGalaxy.eu</button>
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<div class="item carousel-item jumbotron active">
<h2 class="display-3">Domain-specific European Galaxies</h2>
<div class="col-md-12">
<p>UseGalaxy.eu hosts several domain-specific versions of the usegalaxy.eu server. You can access any of these servers and find data and tools focused on the following research areas:</p>
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<b>africa</b>.usegalaxy.eu
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<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>materials</b>.usegalaxy.eu
</div>
</a>
<a href="https://metabolomics.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>metabolomics</b>.usegalaxy.eu
</div>
</a>
<a href="https://metagenomics.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>metagenomics</b>.usegalaxy.eu
</div>
</a>
<a href="https://microbiome.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>microbiome</b>.usegalaxy.eu
</div>
</a>
<a href="https://microgalaxy.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>microgalaxy</b>.usegalaxy.eu
</div>
</a>
<a href="https://ml.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>ml</b>.usegalaxy.eu
</div>
</a>
<a href="https://nanopore.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>nanopore</b>.usegalaxy.eu
</div>
</a>
<a href="https://nubri.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>nubri</b>.usegalaxy.eu
</div>
</a>
<a href="https://phage.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>phage</b>.usegalaxy.eu
</div>
</a>
<a href="https://plants.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>plants</b>.usegalaxy.eu
</div>
</a>
<a href="https://proteomics.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>proteomics</b>.usegalaxy.eu
</div>
</a>
<a href="https://rna.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>rna</b>.usegalaxy.eu
</div>
</a>
<a href="https://singlecell.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>singlecell</b>.usegalaxy.eu
</div>
</a>
<a href="https://spatialomics.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>spatialomics</b>.usegalaxy.eu
</div>
</a>
<a href="https://ssh.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>ssh</b>.usegalaxy.eu
</div>
</a>
<a href="https://streetscience.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>streetscience</b>.usegalaxy.eu
</div>
</a>
<a href="https://virology.usegalaxy.eu" target="_blank" rel="noopener">
<div class="col-xs-6 col-sm-6 col-md-4 domain-button">
<b>virology</b>.usegalaxy.eu
</div>
</a>
</div>
</div>
</div>
<div class="item carousel-item jumbotron">
<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>
<li>Official Galaxy Training Materials guaranteed to work</li>
</ul>
</div>
</div>
<div class="col-md-6">
<img src="/assets/media/tiaas-logo.png" style="padding-bottom: 3em" />
<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://galaxyproject.eu/tiaas')">Find out more</button>
</div>
</div>
<div class="item carousel-item jumbotron">
<h2 class="display-3">Training</h2>
<p class="lead"></p>
<div class="col-md-6">
<p>
We regularly provide workshops
</p>
<p>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('')">See the Calendar</button>
</p>
<p>
But we cannot always meet capacity, so we've put all of our training
materials online. This has become a community project with people from all
over the world contributing training materials.
</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://training.galaxyproject.org')">Visit the Training Material</button>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296361/')">View Publication</button>
</p>
</div>
<div class="col-md-6 hidden-xs">
<img src="/assets/media/training.png" alt="Galaxy training materials page" style="max-width: 90%;" />
</div>
</div>
<!-- <div class="item carousel-item jumbotron">
<div class="container">
<div class="row">
<h2 class="display-3"></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" />
</a>
<a href="http://asaim.readthedocs.io/en/latest/" target="_blank">
<img src="/assets/media/asaim_logo.png" class="img-responsive eu-image" alt="ASaiM Logo" />
</a>
<a href="http://training.galaxyproject.org/" target="_blank">
<img src="/assets/media/gtn_logo.png" class="img-responsive eu-image" alt="GTN Logo" />
</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>
-->
<!-- <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 Freiburg 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>Individuals who have contributed to the project, but whose contributions
do not rise to the level justifying authorship, can be recognized in the
acknowledgements section of the manuscript as follows:</p>
<blockquote>
<p>The authors acknowledge the support of the Freiburg Galaxy Team:
Person X and Prof. Rolf Backofen, Bioinformatics, University of Freiburg,
Germany funded by <a href="http://www.sfb992.uni-freiburg.de">Collaborative
Research Centre 992 Medical Epigenetics</a> (<a href="http://www.dfg.de">DFG</a>
grant SFB 992/1 2012) and the German Federal Ministry of Education and Research
(<a href="http://www.bmbf.de/">BMBF</a> grant 031 A538A <a href="https://www.denbi.de">de.NBI</a>-RBC).
</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 Freiburg.</p>
<p style="padding-bottom: 3em" />
</div> -->
<div class="item carousel-item jumbotron">
<h2 class="display-3">Service Administration</h2>
<div class="col-md-6">
<p>
The maintenance and administration of UseGalaxy.eu is done primarily by the
Freiburg Galaxy Team in collaboration with other academic
groups across Europe and with the US Galaxy team.
<br />
<br />
We make a <i>best effort</i> to provide high uptime. Please see our <a href="https://status.galaxyproject.org" target="_blank">status page</a> for more information.
<br />
<br />
The Freiburg Team tries to maintain a balance between service uptime and
<a href="https://github.com/hexylena/presentations/blob/master/2018-04-retreat/main.pdf" target="_blank">the health of the administrators behind the service.</a>
<br />
<br />
Sometimes we are able to achieve this, sometimes due to factors outside
our control, our service is temporarily inaccessible.
</p>
</div>
<div class="col-md-6">
<a href="https://github.com/hexylena/presentations/blob/master/2018-04-retreat/main.pdf" target="_blank">
<img src="/assets/media/hxr-empathy-presentation.png" />
</a>
</div>
</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.eu 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 of useGalaxy.eu.
</p>
<ul>
<li>This is a best effort, as much warning as we possibly can.</li>
<li>But we cannot make any regarding downtime notices.</li>
<li>The numbers we provide here are rough estimates.</li>
</ul>
</div>
<div class="col-md-6">
For any planned downtime events:
<br />
<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>
<table class="table table-striped">
<thead>
<tr>
<th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th>
</tr>
</thead>
<tbody>
<tr>
<td>User data on UseGalaxy.eu (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.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
</td>
<td>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.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
</td>
<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
</td>
<td>The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td>
</tr>
</tbody>
</table>
<!-- <h4>Registered Users</h4>
User data on UseGalaxy.eu (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.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
<h4>Unregistered Users</h4>
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.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
<h4>FTP Data</h4>
Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
-->