Cytoscape
Network Data Integration, Analysis, and Visualization in a Box
Description: Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. (doi:10.1101/gr.1239303)
Citation
Shannon, Paul, et al. "Cytoscape: a software environment for integrated models of biomolecular interaction networks." Genome research 13.11 (2003): 2498-2504.