Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways.
It enables to integrate these networks with annotations, gene expression profiles and other state data. Cytoscape is most commonly used to construct molecular interaction networks, but it can be used to visualize and analyze network graphs of any kind involving nodes and edges.
Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps that may be developed by anyone using the Cytoscape open API based on Java™ technology.
Cytoscape 3 is the mainstream version of Cytoscape with modular architecture.