Cytoscape 3.0 Beta

Cytoscape 3 beta version is ready for testing. Try it now!

Cytoscape Workshop 2012 San Francisco

December 13-14 at Gladstone Institutes (UCSF)

Cytoscape New Features

Cytoscape supports custom graphics, functions, and commands.

Module Finding

Cytoscape supports nested network structure. You can easily visualize relationship of modules in the network.

Large Scale Data Visualization

With Cytoscape and modern workstations, you can handle large scale networks such as human interactome or social network datasets.

Custom Graphics 1

From Cytoscape 2.8.0, you can map up to nine images per node.

Custom Graphics 2

Mapping charts to node is one of the most common usecase of Custom Graphics. You can map charts generated web services such as Google Chart API.

Network Data Integration, Analysis, and Visualization in a Box

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

NRNB and Cytoscape

Introduction to the National Resource for Network Biology

How to Cite Cytoscape

Cytoscape project needs your support! Please cite either of the following papers when you use Cytoscape in your publications, which is very important to sustain our federal funding.

Michael Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker
Cytoscape 2.8: new features for data integration and network visualization
Bioinformatics. 2011 February 1; 27(3): 431–432.Published online 2010 December 12.
[PubMed entry]
Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, et al.
Integration of biological networks and gene expression data using Cytoscape
Nature Protocols 2, 2366 - 2382 (2007) Published online: 27 September 2007 | doi:10.1038/nprot.2007.324
[PubMed entry]
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504
[Abstract] [PDF] [PubMed entry]

What Can You Do With Cytoscape?


Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics:

  • Load molecular and genetic interaction data sets in many formats
  • Project and integrate global datasets and functional annotations
  • Establish powerful visual mappings across these data
  • Perform advanced analysis and modeling using Cytoscape plugins
  • Visualize and analyze human-curated pathway datasets such as Reactome or KEGG.

Social Science

Cytoscape is used by social scientists to:
  • Visualize and analyze large social networks of interpersonal relationships
  • Assemble social networks from tables and forms
  • Gather social interactions from the web by variety of web service API and scripted web crawlers within Cytoscape
  • Calculate network statistics using plugins
  • Use with other tools, such as R with sna/ igraph package, for more advanced analysis

Semantic Web

Cytoscape is also a tool of choice for the semantic web community, since the semantic web is encoded and viewed as a network of knowledge and resources.

General Complex Network Analysis

Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general.

Plugin Development

Cytoscape is expandable and extensible. Cytoscape has a vibrant plugin developer community and over a hundred plugins developed by third parties.

Featured Publications

     Let us know if you've published using Cytoscape and we will feature your publication here!

Cytoscape Project is supported by National Resource for Network Biology
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