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

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.

Genome Research 2003 Nov; 13(11):2498-504

Other articles and papers about Cytoscape are available here.

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.

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

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

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
Write simple functions with scripting languages, including Ruby, Python, Groovy, and JavaScript

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