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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-plants.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">
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</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><img src="/assets/media/logo_plants.png" alt="Plant Analysis on Galaxy" class="sc-intro-left" /></p>
<h1 class="no_toc" id="welcome-to-galaxy-for-plant-biology">Welcome to Galaxy for Plant Biology</h1>
<p><br />
The <strong>Plant Anaylsis Workbench</strong> is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the <a href="https://galaxyproject.org" target="_blank">Galaxy framework</a>,
which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.</p>
<p><br /></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> <ol>
<li><a href="#workshops" id="markdown-toc-workshops">Workshops</a></li>
<li><a href="#training-material" id="markdown-toc-training-material">Training material</a></li>
</ol>
</li>
<li><a href="#partners" id="markdown-toc-partners">Partners</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 <a href="https://plants.usegalaxy.eu/tours/core.galaxy_ui" target="_blank"><strong>guided tour</strong></a> through Galaxy’s user interface.</p>
<h1 id="training">Training</h1>
<p>We are working in close collaboration with the <a href="https://training.galaxyproject.org" target="_blank"><strong>Galaxy Training Network (GTN)</strong></a> to develop training materials of data analyses based on Galaxy. If you want to know more about the GTN or how to become part of the Galaxy community, check the videos below!</p>
<p><br /></p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/lDqWxzWNk1k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="">
</iframe>
<iframe width="560" height="315" src="https://www.youtube.com/embed/-1MPdxmRs8U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
<p><br /></p>
<h2 id="workshops">Workshops</h2>
<ul>
<li><a href="https://docs.google.com/document/d/1Y5MqYmMxFCy7PDImYYuHLhgCKVV7MjoGMr22G2U68Ec/preview#"><strong>Plant Transcriptome Analysis Workshop</strong></a>, April 19-23, 2021.</li>
</ul>
<p><br /></p>
<h2 id="training-material">Training material</h2>
<p>All relevant materials for <a href="https://training.galaxyproject.org/training-material/search?query=plant">plant-related data analysis</a> can also be found within the GTN.</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 History</th>
</tr>
</thead>
<tbody>
<tr>
<td>Welcome and introduction to Galaxy</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://training.galaxyproject.org/training-material/videos/watch.html?v=introduction/tutorials/galaxy-intro-short/slides" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>An Introduction to Transcriptomics</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/transcriptomics/slides/introduction.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://youtu.be/qKkS_tztw_Q" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Quality Control</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://youtu.be/BWonTPS4zB8" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://youtu.be/QJRlX2hWDKM" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.61771" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/gallardoalba/h/quality-control" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Mapping</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://youtu.be/7FhHb8EV3EU" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://youtu.be/1wm-62E2NkY" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1324070" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/gallardoalba/h/mapping" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>miRNA data analysis</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://training.galaxyproject.org/training-material/videos/watch.html?v=transcriptomics/tutorials/mirna-target-finder/slides" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=TyWCXxzHZak" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/4606701#.YHrzd66xWV4" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/gallardoalba/h/mirna-data-analysis" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>mRNA data analysis and miRNA target prediction</td>
<td> </td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html#mrna-data-analysis" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=4Xpd25T6ziw" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/4606701#.YHrzd66xWV4" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/videmp/h/arabidopsis-transcriptome-analysis" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>An introduction to single-cell RNA-seq data analysis</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/scrna-intro/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=D3qvYWZMFa0" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Understanding Barcodes</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/scrna-plates-batches-barcodes/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://training.galaxyproject.org/training-material/videos/watch.html?v=transcriptomics/tutorials/scrna-plates-batches-barcodes/slides" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-umis/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=AJ17BicjmYU" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/2573177" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/workflows/run?id=d7aa4c258e2edc95" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/mehmet-tekman/h/understanding-barcodes" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Pre-processing of 10X Single-Cell RNA Datasets</td>
<td> </td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://youtu.be/vNBNFkF0L4U" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/3457880" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/workflows/run?id=d79309343e2a5d62" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/mehmet-tekman/h/pre-processing-of-10x-single-cell-rna-star-278a" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Clustering 3K PBMCs with ScanPy</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=nefB35Bi1l4" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/3581213" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/workflows/run?id=921cab3e6faf30be" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/mehmet-tekman/h/clustering-3k-pbmcs-with-scanpy" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Analysis of plant scRNA-Seq data using ScanPy</td>
<td> </td>
<td><a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-plant/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://www.youtube.com/watch?v=yKlJ5ESri7o" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/4597857" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/workflows/run?id=d70dc4cfeedb690b" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://plants.usegalaxy.eu/u/mehmet-tekman/h/analysis-of-plant-scrna-seq-data-with-scanpy" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
</tbody>
</table>
<h1 id="partners">Partners</h1>
<p>This service is a joint project between different groups from the <a href="https://nfdi4plants.github.io/" target="_blank">DataPLANT Consortium</a>, the <a href="https://portal.biodaten.info/" target="_blank">BioDATEN project</a>, <a href="https://vib.be/vib-ugent-center-plant-systems-biology" target="_blank">VIB</a>, <a href="https://www.ipk-gatersleben.de/" target="_blank">IPK</a>, and the <a href="https://galaxyproject.eu/freiburg/" target="_blank">University of Freiburg</a>.
The service is part of the European Galaxy server and is maintained by the <a href="https://www.denbi.de/network/rna-bioinformatics-center-rbc" target="_blank">RNA Bioinformatics Center (RBC)</a> as part of <a href="https://www.denbi.de" target="_blank">de.NBI</a> and <a href="http://elixir-europe.org" target="_blank">ELIXIR</a>.</p>
<table border="0"><tr><td width="20%">
<img alt="DataPLANT" src="/assets/media/DataPLANT_logo_colour.svg" />
</td>
<td with="2%"></td>
<td width="15%">
<img alt="BioDATEN" src="/assets/media/biodaten_logo.png" />
</td>
<td with="2%"></td>
<td width="15%">
<img alt="VIB" src="/assets/media/vib_rf_plant_systems_biology_rgb_pos.png" />
</td>
<td with="2%"></td>
<td width="15%">
<img alt="Technische Universität Kaiserslautern" src="/assets/media/tu_kaiserslautern.svg" />
</td>
<td with="2%"></td>
<td width="15%">
<img alt="Forschungszentrum Jülich" src="/assets/media/juelich_logo.svg" />
</td>
<td with="2%"></td>
<td width="15%">
<img alt="IPK" src="/assets/media/ipklogo.png" />
</td></tr></table>
<h2>Our Data Policy</h2>
<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>.
-->
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<div class="col-md-12">
</div>
</section>
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