Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework, applicable to any system of molecular components and interactions. It is particularly powerful alongside large databases of protein-protein, protein-DNA, and genetic interactions available for humans and model organisms, and its software core provides the basic functionality to lay out and query a network, visually integrate it with expression profiles, phenotypes, and other molecular states, and link it to databases of functional annotations.

The Core is extensible through a straightforward plug-in architecture, enabling rapid development of additional computational analyses and features. The paper surveys several such plug-ins as case studies, including a search for interaction pathways correlating with gene expression changes, a study of protein complexes involved in cellular recovery from DNA damage, an inferred combined physical and functional interaction network for Halobacterium, and an interface to detailed stochastic and kinetic gene regulatory models, illustrating the versatility of the platform.