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documentation_users.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>User Documentation</title>
<meta name="description" content="Cytoscape documents for end-users">
<meta name="author" content="Keiichiro Ono">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.4.min.js"></script>
<link rel="stylesheet" href="https://netdna.bootstrapcdn.com/bootstrap/3.1.0/css/bootstrap.min.css">
<script src="https://netdna.bootstrapcdn.com/bootstrap/3.1.0/js/bootstrap.min.js"></script>
<link href="css/main.bootstrap.css" rel="stylesheet">
</head>
<body>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-sm-4">
<h1>User Links</h1>
<img src="images/logo/cy3logoOrange.svg" height="150px" />
</div>
<div class="col-sm-8">
<br />
<h2>Have a Question?</h2>
<h3>Technical Help</h3>
<p>
<a href="https://bioinformatics.stackexchange.com/questions/tagged/cytoscape?sort=newest">
<big>Bioinformatics StackExchange</big></a>
-- Search and ask questions about software installation, operation and troubleshooting. On this forum, you can also ask questions about data anaysis and visualization, including recommended apps, databases and workflows. Be sure to tag your question with "cytoscape" so we can find it!
</p>
</div>
<div class="col-xs-12 col-md-6">
<h2>Tutorials & Demos</h2>
<ul>
<li>
<a href="https://cytoscape.github.io/cytoscape-tutorials/protocols/tour-of-cytoscape/#/">
Quick tour of Cytoscape
</a>
</li>
<li>
<a href="https://github.com/cytoscape/cytoscape-tutorials/wiki#categories">
tutorials.cytoscape.org
</a>
</li>
<li>
<a href="https://www.youtube.com/channel/UCv6auk9FK4NgXiXiqrDLccw">
Cytoscape YouTube channel
</a>
</li>
<li>
<a href="https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)&report=imagesdocsum&dispmax=100">
Published figures using Cytoscape
</a>
</li>
</ul>
<h2>Automation and Scripting</h2>
<ul>
<li>
<a href="https://github.com/cytoscape/cytoscape-automation/wiki">
automation.cytoscape.org
</a>
</li>
</ul>
<h3>Readings about Cytoscape</h3>
<ul>
<li>
<a href="http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html">
Nature Protocols sample workflow paper
</a> by Cytoscape Consortium - a quick overview of Cytoscape functions.
</li>
<li>
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1758-4">
Cytoscape Automation
</a> by Cytoscape Consortium - empowering workflow-based network analysis.
</li>
<li>
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23132118">Nature Methods paper</a> by Cytoscape Consortium - a quick overview of Cytoscape App (Plugin) universe.
</li>
<li>
<a href="http://www.genome.org/cgi/content/full/13/11/2498">Original Cytoscape paper (2003)</a>
</li>
</ul>
</div>
<div class="col-xs-12 col-md-6">
<h3>User Manual</h3>
<ul>
<li>
<a href="https://manual.cytoscape.org/en/stable/">Latest</a>
</li>
<li><a href="manual">Manuals for older versions</a></li>
</ul>
<h3>Presentations</h3>
<ul>
<li>
<a href="http://www.slideshare.net/keiono/introduction-to-biological-network-analysis-and-visualization-with-cytoscape-part1">Introduction to Cytoscape (Latest)</a>
</li>
<li>
<a href="http://www.slideshare.net/keiono/introduction-to-cytoscape-bioinformatics-summit-2014">Introduction to Cytoscape</a>
</li>
<li>
<a href="http://www.slideshare.net/keiono/cytoscape-tutorial-session-1-at-utkbrin-bioinformatics-summit-2014-4112014">Basic Tutorial</a>
</li>
<li>
<a href="http://www.slideshare.net/keiono/cytoscape-tutorial-session-2-at-utkbrin-bioinformatics-summit-2014-4112014">Advanced Tutorial</a>
</li>
<li>
<a href="http://wiki.cytoscape.org/InternationalConferenceOnSystemsBiologyDemos">
International Conference on Systems Biology Demos
</a>
</li>
<li>
Cytoscape presentation slides at <a href="https://speakerdeck.com/cytoscape">Speaker Deck</a>
</li>
</ul>
<h4><a href="http://www.biostars.org/show/tag/cytoscape/" target="_blank">User FAQ at Biostar</a></h4>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-6">
<h3>Data Sources</h3>
<h4>Biological Networks</h4>
<ul>
<li><a href="http://www.pathguide.org/">Pathguide</a> - Comprehensive list of pathway/interaction databases
</li>
<li><a href="http://code.google.com/p/psicquic/">PSICQUIC</a> - Standardized web service supported by most of the major data providers
</li>
</ul>
<h4>Social Science</h4>
<p>
Social networking services are good data sources. You can write simple web crawler using scripting languages and save it as standard data format such as GML, GraphML, or simple tab-delimited text. Cytoscape supports many standard graph file formats.
</p>
</div>
<div class="col-xs-12 col-md-6">
<h3>Community Resources</h3>
<p>Check out the other <a href="community.html">community resources for Cytoscape</a>.</p>
<br/>
<div class="important">
<h4>Tips for Asking Questions</h4>
<ul>
<li>Be specific: write down steps to reproduce your issues or details about new feature you want.
</li>
<li>Write information about your platform: OS/Java version, memory size, etc.</li>
<li>Add example files: network/attribute files</li>
</ul>
</div>
</div>
</div>
</div>
</div>
<footer></footer>
<script src="js/setup_page.js"></script>
</body>
</html>