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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization</title>
<meta name="description" content="Cytoscape Official Web Site" />
<meta name="author" content="Keiichiro Ono" />
<meta name="keywords" content="Cytoscape,visualization,interaction network,
software,genetic,gene,expression,protein interaction,graph,bioinformatics,
computational biology,UCSD,Whitehead Institute,Institute for Systems Biology,
microarray analysis,clustering,pathways,integration,algorithm,
statistical analysis,gene regulation,complex networks,social networks" />
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You are using an <strong>outdated, ancient</strong> browser.
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<h1>
<img src="images/logo/cy3logoOrange.svg" style="height: 150px; padding-bottom: 0" /> Cytoscape
</h1>
<h4>Network Data Integration, Analysis, and Visualization in a Box</h4>
<div class="row">
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<a class="btn btn-block" href="what_is_cytoscape.html">
Introduction
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Download
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Cytoscape version 3.9.1 addresses the limited vulnerability to log4shell of prior versions.
<br/>Please update immediately.
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Click <a class="warning-link" href="https://cytoscape.org/common_issues.html#log4shell">here</a>
for more information.
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<div class="form-group blue-border-focus" style="margin-bottom: 10px">
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<a href="https://www.ndexbio.org" target="_blank"> <img style="border: 0px; margin: 0px; margin-top: 0px; float: right; height: 45px" src="https://home.ndexbio.org/img/poweredbyNDEx.png" title="Visit the NDEx Public Server"></a>
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document.getElementById('openGeneSetButton').disabled = true;
document.getElementById('openGeneSetButton').addEventListener('click', function(e) {
var geneSet = document.getElementById("geneSet_input").value;
geneSet = geneSet.replace(/\s/g, ",")
console.log(geneSet)
var baseUrl = 'https://www.ndexbio.org/iquery?genes=';
console.log(baseUrl + encodeURIComponent(geneSet));
window.open(baseUrl + encodeURIComponent(geneSet));
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<p class="lead">
Cytoscape is an <a href="download.html">open source</a> software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of <a href="http://apps.cytoscape.org/"><i>Apps</i></a> are
available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. <a href="what_is_cytoscape.html">Learn more...</a>
</p>
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Release Notes
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Sample Visualizations
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Cytoscape Tutorials
</a>
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<p>
<a class="btn btn-primary btn-lg btn-block" href="https://github.com/cytoscape/cytoscape/wiki/Cytoscape-3.0-App-Development" target="_new">
App Developers Docs
</a>
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<h3>NRNB and Cytoscape</h3>
<p>
<iframe width="100%" src="https://www.youtube.com/embed/_nbqSe4Zaps?rel=0" frameborder="0" allowfullscreen>
</iframe>
</p>
<p>
<a href="https://nrnb.org" target="blank">Introduction to the National Resource for Network Biology</a>
</p>
<h3>How to Cite Cytoscape</h3>
<p>
<h4 class="warn">Cytoscape project needs your support!</h4>
Please cite the original Cytoscape paper when you use Cytoscape. This is critical to sustaining our federal funding.
</p>
<div class="thumbnail snow-white">
<p>
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
</p>
<h4>Cytoscape: a software environment for integrated models of biomolecular interaction networks</h4>
<p>
Genome Research 2003 Nov; 13(11):2498-504
</p>
<p>
<a href="https://www.genome.org/cgi/content/full/13/11/2498"> [Abstract] </a>
<a href="https://www.genome.org/cgi/reprint/13/11/2498"> [PDF] </a>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/14597658"> [PubMed entry] </a>
</p>
</div>
<p>
For automation usage and implementation leveraging CyREST, Commands or our R and Python libraries, please cite:
<i> Otasek, et al., <b>Cytoscape Automation: empowering workflow-based network analysis</b> Genome Biology, 20:185 (2019)</i>
<br /><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1758-4"> [Abstract] </a>
<a href="https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-019-1758-4"> [PDF] </a>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/31477170"> [PubMed entry] </a>
</p>
<p>
Other articles and papers about Cytoscape are available <a href="documentation_users.html">here</a>.
</p>
<h3>How to Donate to Cytoscape</h3>
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<font style="display:inline-block; font-size:9px; line-height:1.4;">This is a tax deductible donation to a 501(c)(3) nonprofit organization, <br />The Cytoscape Consoritum, Tax ID: 20-4909879.</font>
<br /><br />
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<h3>What Can You Do With Cytoscape?</h3>
<div class="panel-group" id="accordion">
<div class="panel panel-default">
<div class="panel-heading">
<h2 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#biologyPanel">
Biology
</a>
</h2>
</div>
<div id="biologyPanel" class="panel-collapse collapse in">
<div class="panel-body">
<p>
Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics:
</p>
<ul>
<li>
Load molecular and genetic <a href="http://www.imexconsortium.org/">interaction data
sets</a> in <a href="http://manual.cytoscape.org/en/latest/Supported_Network_File_Formats.html">many standards
formats</a>
</li>
<li>
Project and integrate global datasets and functional annotations
</li>
<li>
Establish powerful visual mappings across these data
</li>
<li>
Perform advanced analysis and modeling using <a href="http://apps.cytoscape.org/">Cytoscape Apps</a>
</li>
<li>
Visualize and analyze human-curated pathway datasets such as
<a href="http://www.wikipathways.org/index.php/WikiPathways">WikiPathways</a>,
<a href="http://www.reactome.org/">Reactome</a>, and <a href="http://www.genome.jp/kegg/pathway.html">KEGG</a>.
</li>
</ul>
<p>
<a class="fancybox-button" rel="fancybox-button" href="images/screenshots/visualMapping1.png" title="Visual Mapping for Microarray Data">
<img src="images/screenshots/visualMapping1_380px.png" alt="Visual Mapping" /></a>
<a class="fancybox-button" rel="fancybox-button" href="images/screenshots/kegg1.png" title="KEGG pathway data visualization by KGMLReader App">
<img src="images/screenshots/kegg1_380px.png" alt="KEGG pathway data import" /></a>
</p>
</div>
</div>
</div>
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<div class="panel-heading">
<h3 class="panel-title">
<a data-toggle="collapse" data-parent="#accordion" href="#socialPanel">
Social Science
</a>
</h3>
</div>
<div id="socialPanel" class="panel-collapse collapse">
<div class="panel-body">
Cytoscape is used by social scientists to:
<ul>
<li>
Visualize and analyze large social networks of interpersonal relationships
</li>
<li>
Assemble social networks from tables and forms
</li>
<li>
Gather social interactions from the web by variety of
<a href="https://www.programmableweb.com/apis/directory/1?apicat=social">
web service APIs
</a> with scripting languages and save it in standard data file formats.
<a href="http://manual.cytoscape.org/en/latest/Supported_Network_File_Formats.html">
Cytoscape supports most of the standard file formats
</a>.
</li>
<li>
Calculate network statistics using Apps
</li>
<li>
Use with other tools, such as <a href="https://www.r-project.org/">R</a> with <a href="http://erzuli.ss.uci.edu/R.stuff/">sna</a>/<a href="http://igraph.sourceforge.net/">
igraph</a> package or <a href="https://networkx.github.io/">NetworkX</a>, for more advanced analysis
</li>
</ul>
</div>
<p>
<a class="fancybox-button" rel="fancybox-button" href="images/screenshots/twitterVisualization1.png" title="Twitter Social Network Visualization">
<img src="images/screenshots/twitterVisualization1_380px.png" alt="Twitter Visualization" /></a>
</p>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">
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General Complex Network Analysis
</a>
</h3>
</div>
<div id="complexNetworkPanel" class="panel-collapse collapse">
<div class="panel-body">
Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general.
<ul>
<li>
Calculate statistics for networks by Apps such as <a href="http://med.bioinf.mpi-inf.mpg.de/netanalyzer/">NetworkAnalyzer</a> or <a href="http://profs.sci.univr.it/~scardoni/centiscape/centiscapepage.php">CentiScaPe</a>
</li>
<li>
Find shortest path
</li>
<li>
<a href="http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.html">Find clusters by various
kinds of algorithms</a>
</li>
<li>
Use with other tools for more advanced analysis
</li>
<li>
Perform advanced network analysis in popular tools, including <a href="http://igraph.sourceforge.net/">igraph</a>, <a href="http://vlado.fmf.uni-lj.si/pub/networks/pajek/">Pajek</a>, or <a href="http://www.graphviz.org/">GraphViz</a> and import it to Cytoscape as standard file formats like
<a href="http://graphml.graphdrawing.org/">GraphML</a>
</li>
</ul>
<a class="fancybox-button" rel="fancybox-button" href="images/screenshots/networkAnalyzer1.png" title="Analyze network with NetworkAnalyzer">
<img src="images/screenshots/networkAnalyzer1_380px.png" alt="NetworkAnalyzer" /></a>
</div>
</div>
</div>
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App Development
</a>
</h3>
</div>
<div id="appPanel" class="panel-collapse collapse">
<div class="panel-body">
Cytoscape is expandable and extensible. Cytoscape has a vibrant App developer community and over a hundred Apps developed by third parties.
<ul>
<li>
Source code is available on <a href="https://github.com/cytoscape">GitHub</a>
</li>
<li>
Running on <a href="http://felix.apache.org/">OSGi framework</a>
</li>
<li>
Develop simple and complex Apps in
<a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">Java</a>
</li>
<li>
Clean, Rich Cytoscape Application Programming Interface (
<a href="https://cytoscape.org/javadoc/3.10.0">API</a>)
</li>
<li>
<a href="https://groups.google.com/group/cytoscape-app-dev">Active developer community</a>
</li>
<li>
Automate Cytoscape with any scripting language, see <a href="https://automation.cytoscape.org/">automation docs</a>.
</li>
</ul>
<a title="OSGi" href="https://www.osgi.org/Main/HomePage"> <img src="images/logo/osgi_380px.png" />
</a>
<a title="Hosted on github" href="https://github.com/cytoscape"> <img src="images/logo/github_380px.png" />
</a>
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<h2>
Featured Video Demos
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data-layout="default" data-count="hidden"></div>
</h2>
<p>
<iframe width="560" height="315"
src="https://www.youtube.com/embed/videoseries?list=PLFQS98nmv__zUUAIfU_dGXFi-qZP90VVQ"
frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</p>
</div>
</div>
<!-- Tumblr -->
<div class="row">
<div class="col-sm-12">
<h2>
Publications using Cytoscape
</h2>
<p>Browse published figures referencing Cytoscape at <a href="https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)&report=imagesdocsum&dispmax=100" target="_blank">PubMed Central</a>.</p>
<p>
<a href="https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)&report=imagesdocsum&dispmax=100" target="_blank">
<img src="images/CytoscapePublicationsImagesPMC_grid.png" width="700"></a>
</p>
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<h2>
<a href="https://www.cytoscapeconsortium.org/">Cytoscape Consortium</a>
</h2>
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<a href="https://www.ucsf.edu/"><img src="images/logo/ucsf_logo_web.png" /></a>
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<a href="https://www.ucsd.edu/"><img src="images/logo/ucsd_logo_web.png" /></a>
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