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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://stackoverflow.com/questions/tagged/cytoscape?sort=newest">
<big>StackOverflow</big></a>
-- Search and ask questions about software installation, operation and troubleshooting. Be sure to tag your question with "cytoscape" so we can find it!
</p>
<h3>Biology and Bioinformatics Help</h3>
<p>
<a href="https://www.biostars.org/t/cytoscape">
<big>BioStars</big></a>
-- Search and 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>