Abstract

Summary: CytoModeler is an open-source Java application based on the Cytoscape platform. It integrates large-scale network analysis and quantitative modeling by combining omics analysis on the Cytoscape platform, access to deterministic and stochastic simulators, and static and dynamic network context visualizations of simulation results.Availability: Implemented in Java, CytoModeler runs with Cytoscape 2.6 and 2.7. Binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv/cytomodeler/.Contact: julied@iastate.edu; netscape@iastate.eduSupplementary Information: Supplementary data are available at Bioinformatics online.

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