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 Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. Learn more...

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.

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T.

A travel guide to Cytoscape plugins

Nature Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.

[PubMed entry]

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:

Visual Mapping KEGG pathway data import

Cytoscape is used by social scientists to:

Twitter Visualization

Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general. NetworkAnalyzer
Cytoscape is expandable and extensible. Cytoscape has a vibrant App developer community and over a hundred Apps developed by third parties.

Featured Publications

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

Cytoscape Consortium

Cytoscape project is supported by: