Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. The current version of Cytoscape is v2.4.
Reference: Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, and Ideker T. (2003) "Cytoscape: A software environment for integrated models of biomolecular interaction networks." Genome Research 13:2498-04. Download PDF