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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</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 European 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://galaxyproject.eu/index-metabolomics.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 Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
<script src="/assets/js/jquery-3.2.1.slim.min.js" integrity="sha256-k2WSCIexGzOj3Euiig+TlR8gA0EmPjuc79OEeY5L45g=" crossorigin="anonymous"></script>
<script src="/assets/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><br /></p>
<h1 class="no_toc" id="welcome-to-usegalaxyeu-metabolomics">Welcome to <strong>UseGalaxy.EU Metabolomics</strong></h1>
<p><strong>Metabolomics.UseGalaxy.eu</strong> is a community driven metabolomics Galaxy service. The main aim is to give people a public space to discover and run metabolomics tools. If there is something that should be added, please let us know on <a href="https://gitter.im/usegalaxy-eu/Lobby">Gitter</a>.</p>
<p>During the <a href="https://galaxyproject.org/events/gcc2019/">2019 Galaxy Community Conference</a> (GCC2019) metabolomics users and developers are invited to meet during a Birds of a Feather (BoF) event to plan the aims of this service.</p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#training" id="markdown-toc-training">Training</a></li>
<li><a href="#available-tools" id="markdown-toc-available-tools">Available Tools</a> <ol>
<li><a href="#workflow4metabolomics-tools" id="markdown-toc-workflow4metabolomics-tools">Workflow4Metabolomics Tools</a></li>
<li><a href="#workflow4metabolomics-related-tools" id="markdown-toc-workflow4metabolomics-related-tools">Workflow4Metabolomics Related Tools</a></li>
</ol>
</li>
<li><a href="#gateways" id="markdown-toc-gateways">Gateways</a></li>
<li><a href="#news-and-events" id="markdown-toc-news-and-events">News and Events</a></li>
<li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li>
</ol>
<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>
<h1 id="training">Training</h1>
<p>Want to learn more about metabolomics? Check out the following lesson tutorials from the <a href="https://galaxyproject.github.io/training-material/topics/metabolomics/" target="_blank">Galaxy Trainings Network</a>:</p>
<table class="table table-striped">
<thead>
<tr>
<th>Lesson</th>
<th>Slides</th>
<th>Hands-on</th>
<th>Input dataset</th>
<th>Workflows</th>
<th>Galaxy tour</th>
</tr>
</thead>
<tbody>
<tr>
<td>Introduction to Metabolomics</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/metabolomics/slides/introduction.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Mass spectrometry imaging: Examining the spatial distribution of analytes</td>
<td> </td>
<td><a href="https://galaxyproject.github.io/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/484496" target="_blank"><i class="fa fa-topic" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Mass spectrometry imaging: Finding differential analytes</td>
<td> </td>
<td><a href="https://galaxyproject.github.io/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/2628280" target="_blank"><i class="fa fa-topic" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Mass spectrometry: LC-MS analysis</td>
<td> </td>
<td><a href="https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/3244991" target="_blank"><i class="fa fa-topic" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/metabolomics/tutorials/lcms/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
</tbody>
</table>
<hr />
<h1 id="available-tools">Available Tools</h1>
<h2 id="workflow4metabolomics-tools">Workflow4Metabolomics Tools</h2>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Descirption</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_xcmsset</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_group</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_retcor</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/tool-bank-lipidmaps.git">lipidmaps_textsearch</a></td>
<td>[W4M][LC-MS] LIPID MAPS Structure Database (LMSD) - Annotation - Returns annotation results from LIPID MAPS Structure Database and its Text/Ontology-based search engine.</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/mmonsoor/probmetab">probmetab</a></td>
<td>[W4M][LC-MS] ProbMetab - automatic probabilistic LC-MS based metabolome annotation</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/profia.git">profia</a></td>
<td>[W4M][FIA-HRMS] Preprocessing of Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) data.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_fillpeaks</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/lecorguille/camera_annotate">camera_annotate</a></td>
<td>[W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results (isotope peaks, adducts and fragments)</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_merge</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - Merge individual xcmsSet outputs</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/melpetera/generic_filter">generic_filter</a></td>
<td>[W4M][Utils] Filtering according to specific variables</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/xcms">xcms_summary</a></td>
<td>[W4M][LC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS and CAMERA analysis</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/mmonsoor/camera_combinexsannos">camera_combinexsannos</a></td>
<td>[W4M][LC-MS] CAMERA R Package - Annotation - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/batchcorrection.git">batchcorrection</a></td>
<td>[W4M][LC-MS] Correction of data intensities for signal drift and batch-effects.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/qualitymetrics.git">qualitymetrics</a></td>
<td>[W4M][LC-MS] Metrics and graphics to check the quality of the data.</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/fgiacomoni/hmdb_ms_search">hmdb_ms_search</a></td>
<td>[W4M][LC-MS] HMDB database MS Search Package - Annotation - Returns annotation results (adducts and metabolites) from The Human Metabolome Database.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/univariate.git">univariate</a></td>
<td>[W4M][LC-MS][GC-MS][NMR] Univariate statistics.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/lcmsmatching.git">lcmsmatching</a></td>
<td>[W4M][LC-MS] Annotate LCMS spectrum using an in-house spectra database.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/biosigner.git">biosigner</a></td>
<td>[W4M][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/multivariate.git">multivariate</a></td>
<td>[W4M][LC-MS][GC-MS][NMR] Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA).</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/metaMS">metams_rungc</a></td>
<td>[W4M][GC-MS] metaMS R Package - GC-MS data preprocessing using metaMS package</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics">withinvariation</a></td>
<td>[W4M][Statistics] mixOmics R package withinVariation function for repeated mesurement design</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/marie-tremblay-metatoul/nmr_preprocessing">nmr_preprocessing</a></td>
<td>[W4M][NMR] NMR Preprocessing - Preprocessing (from FID to baseline correction)</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/nmr_alignment">nmr_alignment</a></td>
<td>[W4M][NMR] NMR Alignment - Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/nmr_bucketing">nmr_bucketing</a></td>
<td>[W4M][NMR] NMR Bucketing - Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/nmr_normalization">nmr_normalization</a></td>
<td>[W4M][NMR] NMR Normalization - Normalization (operation applied on each individual spectrum) of bucketed and integrated NMR data</td>
</tr>
<tr>
<td><a href="https://toolshed.g2.bx.psu.edu/view/marie-tremblay-metatoul/normalization">normalization</a></td>
<td>Normalization (operation applied on each individual spectrum) of preprocessed data</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/transformation.git">transformation</a></td>
<td>[W4M][LC-MS][GC-MS][NMR] Transforms the dataMatrix intensity values.</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/tool-bank-golm-lib_search.git">golm_ws_lib_search</a></td>
<td>[W4M][GC-MS] Golm Metabolome Database search spectrum</td>
</tr>
<tr>
<td><a href="https://github.com/workflow4metabolomics/checkformat.git">checkformat</a></td>
<td>[W4M][LC-MS][GC-MS][NMR] Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files.</td>
</tr>
</tbody>
</table>
<h2 id="workflow4metabolomics-related-tools">Workflow4Metabolomics Related Tools</h2>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Descirption</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master">w4mclassfilter</a></td>
<td>Filter W4M data by values or metadata</td>
</tr>
<tr>
<td><a href="https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master">w4mjoinpn</a></td>
<td>Join positive- and negative-mode W4M datasets</td>
</tr>
<tr>
<td><a href="https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master">w4mcorcov</a></td>
<td>OPLS-DA Contrasts of Univariate Results</td>
</tr>
</tbody>
</table>
<hr />
<h1 id="gateways">Gateways</h1>
<p>Other metabolomics specialized Galaxy servers:</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Servers</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://workflow4metabolomics.org/">Workflow4Metabolomics</a></td>
</tr>
<tr>
<td><a href="https://portal.phenomenal-h2020.eu/home">PhenoMeNal</a></td>
</tr>
</tbody>
</table>
<hr />
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<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>
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<h2 class="display-3">UseGalaxy.eu: The European Galaxy instance</h2>
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<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>
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<p>And even more!</p>
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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 data and tools focused on the following research areas:</p>
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<a href="https://africa.usegalaxy.eu" target="_blank" rel="noopener">
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<b>africa</b>.usegalaxy.eu
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<b>annotation</b>.usegalaxy.eu
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<b>cancer</b>.usegalaxy.eu
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<b>climate</b>.usegalaxy.eu
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<h2 class="display-3">Training Infrastructure as a Service</h2>
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<p>
We want to help you conduct your training seminars. You provide the
training, we provide you training infrastructure <i>at no cost.</i>
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<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>
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<p>
Simply fill out the infrastructure request form and we'll get back to you shortly.
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<button type="button" class="btn btn-primary btn-lg" onclick="window.open('https://galaxyproject.eu/tiaas')">Find out more</button>
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<h2 class="display-3">Training</h2>
<p class="lead"></p>
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<p>
We regularly provide workshops
</p>
<p>
<button type="button" class="btn btn-primary btn-lg" onclick="window.open('')">See the Calendar</button>
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<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>
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<p>The UseGalaxy.eu team supports many projects in the Galaxy community:</p>
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<a href="http://galaxyp.org/" target="_blank">
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</a>
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<p>and also:</p>
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<li><a href="https://hicexplorer.usegalaxy.eu/">Galaxy HiCExplorer</a> to process, analyse and visualize Hi-C data</li>
</ul>
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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 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> -->
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<h2 class="display-3">Service Administration</h2>
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<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>