An Open Source Platform for Complex Network Analysis and Visualization (original) (raw)

NRNB and Cytoscape

Introduction to the National Resource for Network Biology

How to Cite Cytoscape

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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

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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 asWikiPathways,Reactome, and KEGG.