2003 | Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S. Baliga, Jonathan T. Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker
Cytoscape is an open-source software environment designed for integrating biomolecular interaction networks with high-throughput expression data and other molecular states. It is particularly powerful when used with large databases of protein-protein, protein-DNA, and genetic interactions. The core of Cytoscape provides basic functionalities such as network layout, data integration, and visual representation, while its extensible plugin architecture allows for rapid development of additional computational analyses and features. The article discusses three case studies that demonstrate the application of Cytoscape in various biological problems: identifying pathways and protein complexes activated by genetic perturbations, inferring and visualizing a combined physical-functional interaction network for *Halobacterium*, and stochastic simulation of gene regulation using the Systems Biology Markup Language (SBML). The authors also highlight future directions, including direct connections to interaction databases and further exploration of bridging high-level interaction networks with lower-level physico-chemical models.Cytoscape is an open-source software environment designed for integrating biomolecular interaction networks with high-throughput expression data and other molecular states. It is particularly powerful when used with large databases of protein-protein, protein-DNA, and genetic interactions. The core of Cytoscape provides basic functionalities such as network layout, data integration, and visual representation, while its extensible plugin architecture allows for rapid development of additional computational analyses and features. The article discusses three case studies that demonstrate the application of Cytoscape in various biological problems: identifying pathways and protein complexes activated by genetic perturbations, inferring and visualizing a combined physical-functional interaction network for *Halobacterium*, and stochastic simulation of gene regulation using the Systems Biology Markup Language (SBML). The authors also highlight future directions, including direct connections to interaction databases and further exploration of bridging high-level interaction networks with lower-level physico-chemical models.