NRNB: Cytoscape

Cytoscape

Cytoscape is an open source bioinformatics environment for integration, visualization, and query of biological networks that can be used with a broad variety of data types and customized through the use and development of app extensions.

Documentation

Developer Resources

How to Cite

Cytoscape 2.8: new features for data integration and network visualization. Smoot, et al., Bioinformatics 2011.
A travel guide to Cytoscape plugins. Saito et al., Nature Methods 2012.
Integration of biological networks and gene expression data using Cytoscape. Cline et al., Nature Protocols 2007.
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon et al., Genome Research 2003.

Image Gallery

In addition to these images, also see published figures using Cytoscape.

An arbitrary network demonstrating powerful visual style and layout features in Cytoscape.
An arbitrary network demonstrating versatile edge line coloring and routing in Cytoscape.
An arbitrary network demonstrating custom edge types and nested network visualization in Cytoscape.

An arbitrary network demonstrating the layout of massive networks in Cytoscape.
An arbitraty network demonstrating the use of nested networks to represent protein complexes in Cytoscape.
An arbitrary network demonstrating the use of transparency in representing overlapping node sets in Cytoscape.