Cytoscape: An Open Source Platform for Complex-Network Analysis and Visualization
From the website:
Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Alluded to in: AllegroMCOCE: GPU-accelerated Cytoscape Plugin TM Explorer? but encountering Cytoscape again, decided it needed a separate posting.