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 the original Cytoscape paper when you use Cytoscape. This is critical to sustaining our federal funding.

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]

For automation usage and implementation leveraging CyREST, Commands or our R and Python libraries, please cite: Otasek, et al., Cytoscape Automation: empowering workflow-based network analysis Genome Biology, 20:185 (2019)
[Abstract] [PDF] [PubMed entry]

Other articles and papers about Cytoscape are available here.

How to Donate to Cytoscape

This is a tax deductible donation to a 501(c)(3) nonprofit organization,
The Cytoscape Consoritum, Tax ID: 20-4909879.

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 Video Demos

Publications using Cytoscape

Browse published figures referencing Cytoscape at PubMed Central.

Cytoscape Consortium

Cytoscape project is supported by:

National Resource for Network Biology