Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization

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?

Biology

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

Load molecular and genetic interaction data sets in many standards formats
Project and integrate global datasets and functional annotations
Establish powerful visual mappings across these data
Perform advanced analysis and modeling using Cytoscape Apps
Visualize and analyze human-curated pathway datasets such as WikiPathways, Reactome, and 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 APIs with scripting languages and save it in standard data file formats. Cytoscape supports most of the standard file formats .
Calculate network statistics using Apps
Use with other tools, such as R with sna/ igraph package or NetworkX, for more advanced analysis

General Complex Network Analysis

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

Calculate statistics for networks by Apps such as NetworkAnalyzer or CentiScaPe
Find shortest path
Find clusters by various kinds of algorithms
Use with other tools for more advanced analysis
Perform advanced network analysis in popular tools, including igraph, Pajek, or GraphViz and import it to Cytoscape as standard file formats like GraphML