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

# Cytoscape
### Network Data Integration, Analysis, and Visualization in a Box

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Cytoscape Web 1.0

### Analyze Your Genes With NDEx iQuery

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...

Release Notes Sample Visualizations

Cytoscape Tutorials

App Developers Docs

### 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 Cytoscape Web, please cite:

Ono K, Fong D, Gao C, Churas C, Pillich R, Lenkiewicz J, Pratt D, Pico AR, Hanspers K, Xin Y, Morris J, Kucera M, Franz M, Lopes C, Bader G, Ideker T, Chen J

#### Cytoscape Web: bringing network biology to the browser

Nucleic Acids Research, 2025;, gkaf365


\[Abstract\] \[PDF\]

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

### App Development

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

- Source code is available on GitHub
- Running on OSGi framework
- Develop simple and complex Apps in Java
- Clean, Rich Cytoscape Application Programming Interface ( API)
- Active developer community
- Automate Cytoscape with any scripting language, see automation docs.



## 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

National Human Genome Research Institute