From Cytoscape Consortium:
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles, and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java technology and plugin community development is encouraged.