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<title>ECCB 2014 T01</title>
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<a href="#"><h2 class="label label-green">Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets</h2></a>
</div>
<div class="clearer"> </div>
</div>
<div class="navigation" id="sub-nav">
<ul class="tabbed">
<li class="current-tab"><a href="index.html">Home</a></li>
<li ><a href="session1.html">Session1:Web site</a></li>
<li><a href="session2.html">Session2:Command line</a></li>
<li><a href="session3.html">Session3:SOAP Web services</a></li>
</ul>
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<div class="clearer"> </div>
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</div>
<div class="main" id="main-two-columns">
<div class="left" id="main-content">
<h2 id="contents"> ECCB 2014 tutorial T01 </h2>
<p/>
<h4>Access</h4>
<table>
<tr>
<td>Tutorial announcement</td>
<td><a target='_blank' href='http://www.eccb14.org/program/tutorials/cis-r'>http://www.eccb14.org/program/tutorials/cis-r</a></td>
</tr>
<tr>
<td>Location</td>
<td>
Faculté de Médecine, Building Forum, Room 4, rue Kirschleger, 67085 Strasbourg
<br><a target='_blank' href='http://goo.gl/maps/hNsF2'>Map</a></td>
</tr>
<tr>
<td>Access instructions (in French)</td>
<td><a target='_blank' href='http://med.unistra.fr/fre/La-faculte/Localisation/Acces-au-Campus-Medecine'>http://med.unistra.fr/fre/La-faculte/Localisation/Acces-au-Campus-Medecine</a></td>
</tr>
<tr>
<td>Maps of the buildings</td>
<td><a target='_blank' href='http://med.unistra.fr/fre/La-faculte/Les-plans-des-Amphitheatres-et-des-salles-de-cours'>http://med.unistra.fr/fre/La-faculte/Les-plans-des-Amphitheatres-et-des-salles-de-cours</td>
</tr>
</table>
<h4>Requirements for hands-on</h4>
<ul>
<li><b>Hardware</b>
<p>Participants are expected to bring their laptop for the
practical sessions.</p>
</li>
<li><b>Software to install before the tutorial</b></li>
<table>
<tr>
<td><b>Putty </b>(only for Windows)
</td><td>
secure shell connection. Only required for Windows, since Linux and Mac OSX have ssh included in the terminal.
Will be used for command-line use of RSAT: ssh connection for Window users.
</td>
<td><a href="http://www.putty.org/" target="_blank">http://www.putty.org/</a>
</td>
</tr>
<tr>
<td><b>Filezilla</b>
</td><td>
Secured file transfer (graphical user interface). Will be used for command-line use of RSAT: retrieve the result files and folders.
</td>
<td>
<a href="https://filezilla-project.org/" target="_blank">https://filezilla-project.org/</a>
<!-- <a href="http://filezilla.fr/" target="_blank">http://filezilla.fr/</a>-->
</td>
</tr>
<tr>
<td>
<b>Python
version 2.7 </b> (not 3)
</td><td>
Programming language. Will be used for Web services: run the client script.
</td>
<td><a href="https://www.python.org/download/" target="_blank">https://www.python.org/download/</a>
</td>
</tr>
<tr>
<td>
<b>Code editor (for the programming session) </b>
</td><td>
Will be used for Web services to edit the client scripts.
</td>
<td><a href="http://www.sublimetext.com/" target="_blank">Sublime text</a> or
<a href="http://www.notepad-plus-plus.org/" target="_blank">Notepad++</a>
</td>
</tr>
</table>
</ul>
<p/>
<h4>Schedule</h4>
<table>
<tr>
<td>08:00-09:00</td>
<td><b>Registration and configuration of participants' laptops (network
access)</b>
<ol>
<li>Laptop configuration.</li>
<li>Checking your access to the <a target='_blank' href='https://cloud.france-bioinformatique.fr/'>IFB cloud</a>
<br>(<b>ideally</b>: account should have been obtained before
the tutorial).</li>
<li>Opening your own RSAT server on the <a target='_blank' href='https://cloud.france-bioinformatique.fr/'>IFB cloud</a>.</li>
<li>Installing an RSAT Virtual Machine on your
computer <br>(<b>optional</b>, only for participants who wish to hold
an RSAT VM on their own laptop).</li>
</ol>
</td>
</tr>
<tr>
<td>09:00-10:30</td>
<td><a href="session1.html">Session 1: Analysis of cis-regulatory
elements with the Regulatory Sequence Analysis Tools (RSAT):
methods and website utilization</a> (http://www.rsat.eu/).
<ol>
<li>Retrieving sequences from a set of peak coordinates (<i>fetch-sequences</i>)</li>
<li>Discovering motifs from peak sequences (<i>peak-motifs</i>)</li>
<li>Visualizing the sites in the context of genome annotations (UCSC genome browser)</li>
<li>Measure the enrichment of peaks for the expected motif (<i>matrix-quality</i>)</li>
<li>A quick tour of utility tools on RSAT</li>
</ol>
</td>
</tr>
<tr>
<td>10:30-10:45</td>
<td>Coffee break</td>
</tr>
<tr>
<td>10:45-12:00</td><td>Session 1 (continued)</td>
</tr>
<tr><td>12:00-13:30</td><td>Lunch</td></tr>
<tr><td>13:30-16:00</td><td><a href="session2.html">Session 2: Using RSAT in command-line (Unix terminal via ssh connection) </a>
<ol>
<li>Technical overview (Access modes for RSAT)</li>
<li>First RSAT command-line ((<i>fetch-sequences</i>)</li>
<li>Motif scanning in peaks (<i>matrix-scan</i>)</li>
<li>Testing the tools with negative controls (<i>random-seq, random-genomic-fragments</i>)</li>
</ol>
</td></tr>
<tr><td>16:00-16:20</td><td>Coffee break </td></tr>
<tr><td>16:20-18:00</td><td><a href="session3.html">Session 3: programming SOAP/WSDL clients for RSAT </a>
<ol>
<li>Fetching sequences corresponding to peak coordinates (<i>fetch-sequences</i>)</li>
<li>Motif scanning in peaks (<i>matrix-scan</i>)</li>
</ol></td></tr>
</table>
</div>
<!-- SIDE BAR -->
<div class="right sidebar" id="sidebar">
<img src="logos/RSAT.png" height=50/>
<p/>
<h5>Organizers</h5>
<ul>
<li><a href="http://jacques.van-helden.perso.luminy.univ-amu.fr/" target="_blank">Jacques van Helden</a></li>
<li><a href="http://morgane.bardiaux.fr" target="_blank">Morgane Thomas-Chollier</li>
</ul>
<h5>Teaching team</h5>
<ul>
<li><a href="http://www.epernicus.com/am27" target="_blank">Alejandra Medina-Rivera</a></li>
<li><a href="http://biologie.univ-mrs.fr/carlherrmann/home.html" target="_blank">Carl Herrmann</a></li>
<li><a href="https://www.researchgate.net/profile/Celine_Hernandez" target="_blank">Céline Hernandez</a></li>
</ul>
<p/>
<h5>Support</h5>
<a href="http://www.allbioinformatics.eu" target="_blank">
<img width="150" src="logos/allbiologo_23.png"></a>
<a href="http://www.france-bioinformatique.fr/" target="_blank">
<img width="150" src="logos/ifb-logo-s.png"></a>
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<p>© 2014 Morgane Thomas-Chollier. All rights Reserved</p>
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