Commit 88319a83 authored by root's avatar root

Mise a jour de la page Aide et Home avec dataset Roux et al.

parent c8ea9ac8
../web/resources/zip/Roux_et_al_2015.zip
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<h2 class="portal-title">Screen Casts</h2>
<div class="starter-template">
<h3>Manage</h3>
<div style="display: table; width:100%; display:table-row">
<div style="display: table; width:100%; display:table-row">
<div style="display: table-cell; width:30%; ">
<h3>Analyse raw proteomes (without InterProScan data)</h3>
<small>Analyse raw proteomes (without InterProScan data)</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/8T3IR8ufmx4" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Fast launch (using an archive containing all raw data)</h3>
<small>Fast launch (using an archive containing all raw data)</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/NzYZLz_O5u8" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Share/Download/Delete</h3>
<small>Share/Download/Delete</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/QegiXGtDmu0" frameborder="0" allowfullscreen></iframe>
</div>
</div>
<br>
<h3>Search</h3>
<div style="display: table; width:100%; display:table-row">
<div style="display: table-cell; width:25%; ">
<h3>Browse analysis results</h3>
<small>Browse analysis results</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/WHur7_H1gL4" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:25%; ">
<h3>Blast search</h3>
<small>Blast search</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/m35fhrtIs1s" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:25%; ">
<h3>Keyword search</h3>
<small>Keyword search</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/1Vxif-QshXc" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:25%; ">
<h3>Search groups containing proteins from X proteomes and not Y proteomes</h3>
<small>Search groups containing proteins from X proteomes and not Y proteomes</small><br>
<iframe width="330" height="215" src="https://www.youtube.com/embed/p36fs3WvPbg" frameborder="0" allowfullscreen></iframe>
</div>
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</div>
<h2 class="portal-title">Test datasets</h2>
<div class="alert alert-info">Demo (small) dataset</div>
<ul>
<li><a href="resources/zip/Xbbric_dataset.zip">3 proteomes of about 400 proteins each annotated with InterPro 51.0</a></li>
<li><a href="http://family-companion.toulouse.inra.fr/?view=6W81Zwy2xR&owner=bbric.family.companion@gmail.com">Test dataset analyses results (OrthoMCL with hight coverage parameter - pvmatch cut off = 80)</a></li>
</ul>
<div style="display: table-cell; width:30%; ">
<h3>Test Dataset</h3>
<a href="resources/zip/Xbbric_dataset.zip">3 proteomes of about 400 proteins each annotated with InterPro 51.0</a>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Results</h3>
<a href="https://bbric-pipelines.toulouse.inra.fr/family-companion?view=WpepkHiCXx&owner=sebastien.carrere@toulouse.inra.fr">Test dataset analyses results (OrthoMCL with hight coverage parameter - pvmatch cut off = 80)</a>
</div>
<div class="alert alert-info"><i>Realworld</i> dataset</div>
<ul>
<li><a href="resources/zip/Roux_et_al_2015.zip">13 Xanthomonas proteomes each annotated with InterPro</a>
<p>
<small><b>Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome.</b><br>
Roux B, Bolot S, Guy E, Denancé N, Lautier M, Jardinaud MF, Fischer-Le Saux M, Portier P, Jacques MA, Gagnevin L, Pruvost O, Lauber E, Arlat M, Carrère S, Koebnik R, Noël LD.<br>
<i>BMC Genomics. 2015 Nov 18;16:975. doi: 10.1186/s12864-015-2190-0.</i>
</small>
</p>
</li>
<li><a href="http://family-companion.toulouse.inra.fr/?view=CC_d80y9Jh&owner=bbric.family.companion@gmail.com">Roux et al. dataset analyses results</a></li>
</ul>
</div>
</body>
</html>
<html>
<head>
<link href="resources/css/home.css" rel="stylesheet">
<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.0/spacelab/bootstrap.min.css" rel="stylesheet">
<link href="css/portal.css" rel="stylesheet">
<link href="css/wb.css" rel="stylesheet">
</head>
<body>
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<div class="container">
<div class="starter-template">
<h1>Perform protein family analyses, browse, visualise and share the results!</h1>
<h1 class="portal-title">Family-Companion, a web server dedicated to the computation, the analysis and the exploration of homology groups. </h1>
<p style="text-align:left;">
Nowadays, comparative genomics is a classical tool for biologists to address various scientific questions such as pathogeny determinism, bacteria host specificity, duplication and gene family expansion in a species.<br>
The large number of available finished or draft genome sequences associated with the full automatisation of structural annotation pipelines leads to an era of high throughput comparative genomics. <br>
Tools like <b>OrthoMCL</b> provide an easy way to compare tens of species at a time and build homologous gene families.<br>
However, output results, classically a matrix with groups as lines and genes as columns, remains too raw to be interpreted by an end user without programming skills.<br>
In order to help users in the post process of these data, we developed a web user interface that automatically extract frequently asked datasets such as core and pan proteomes, specific proteins, abundance and presence/absence matrix (aka. phylogenetic profiles). <br>
Providing optional InterPro annotation will also lead to build tables and charts representing terms (eg : PFAM, GO) count in each previously described datasets.<br>
Our tool uses standard formats as input and outputs to ease post-process analyses.
Family-Companion offers a user-friendly interface to launch and share private analyses, and interactive solutions to visualise proteome intersections Venn diagrams, phylogenetic trees, alignments and query (blast, search by keywords) the results .
Family-Companion allows biologists to easily perform and share proteome comparison analyzes and provides them interpretation tools to address the most common questions in this kind of approach.
Family-Companion provides powerful, interactive and user-friendly web solutions to visualise and explore the inferred homology groups (alignments, trees, phylogenetic profiles, Venn diagrams, summary charts).
</p>
<hr>
<div style="display: table-cell; width:30%; ">
<h3>Test Dataset</h3>
<a href="resources/zip/Xbbric_dataset.zip">3 proteomes of about 400 proteins each annotated with InterPro 51.0</a>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Results</h3>
<a href="https://bbric-pipelines.toulouse.inra.fr/family-companion?view=WpepkHiCXx&owner=sebastien.carrere@toulouse.inra.fr">Test dataset analyses results (OrthoMCL with hight coverage parameter - pvmatch cut off = 80)</a>
</div>
<hr>
<a href="../cgi/index.cgi?account=1"><button type="button" class="btn btn-danger">Ask for an account</button></a>
</div>
<!--
<div class="starter-template">
<div style="display: table; width:100%;" display:table-row">
<div style="display: table-cell; width:30%; ">
<h3>Analyse raw proteomes</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/MorXJ4Find8" frameborder="0" allowfullscreen></iframe>
<a href="resources/zip/Xbbric_dataset.zip">
<button type="button" class="btn btn-default" style="width:80%;">
<strong>Test Dataset</strong><br>
3 proteomes of about 400 proteins each annotated with InterPro
</button>
</a>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Analyse annotated proteomes</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/62mfNok7f8A" frameborder="0" allowfullscreen></iframe>
<a href="http://family-companion.toulouse.inra.fr/?view=6W81Zwy2xR&owner=bbric.family.companion@gmail.com">
<button type="button" class="btn btn-default" style="width:80%;">
<strong>Results</strong><br>
Test dataset analyses results
</button>
</a>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Browse</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/qOeN2a-2q-E" frameborder="0" allowfullscreen></iframe>
</div>
</div>
<br><br>
<div style="display: table; width:100%;" display:table-row">
<div style="display: table-cell; width:30%; ">
<h3>Share</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/wqyXtyC-5Ic" frameborder="0" allowfullscreen></iframe>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Delete</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/mzEPKvkocjI" frameborder="0" allowfullscreen></iframe>
<hr>
<div style="display: table-cell; width:30%; ">
<a href="resources/zip/Roux_et_al_2015.zip">
<button type="button" class="btn btn-default" style="width:80%;">
<strong><i>Realworld</i> dataset</strong><br>
13 <i>Xanthomonas</i> proteomes (Roux et al., BMC Genomics 2015)
</button>
</a>
</div>
<div style="display: table-cell; width:30%; ">
<h3>Fast launch</h3>
<iframe width="330" height="215" src="https://www.youtube.com/embed/Hs_tdS0NbaM" frameborder="0" allowfullscreen></iframe>
<a href="http://family-companion.toulouse.inra.fr/?view=CC_d80y9Jh&owner=bbric.family.companion@gmail.com">
<button type="button" class="btn btn-default" style="width:80%;">
<strong><i>Realworld</i> dataset results</strong><br>
Roux et al. <i>Xanthomonas</i> proteomes analyses
</button>
</a>
</div>
<hr>
<a href="../cgi/index.cgi?account=1"><button type="button" class="btn btn-danger">Ask for an account</button></a>
</div>
</div>
-->
<footer class="footer">
<div style="display: table; width:100%;" display:table-row">
<div style="display: table-cell; width:50%; align:left;">
<a href="https://bbric.toulouse.inra.fr/hub/cgi/hub.cgi" target="_blank"><img src="resources/images/bbric.png" style="height: 70px;" /></a>
<p>Martial Briand, Sébastien Carrère, Ludovic Cottret, Corinne Rancurel</p>
<p>Ludovic Cottret, Martial Briand, Corinne Rancurel and Sebastien Carrere</p>
</div>
<div style="display: table-cell; width:25%;align:left;">
<a href="http://www.orthomcl.org/orthomcl/" target="_blank"><img src="resources/images/orthomcl.png" style="max-height: 100px; max-width: 200px" /></a>
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