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CellNOpt (CellNetOptimizer)


CellNOpt (from CellNetOptimizer; a.k.a. CNO) is a software used for creating logic-based models of signal transduction networks using different logic formalisms (Boolean, Fuzzy, or differential equations). CellNOpt uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against high-throughput biochemical data to create cell-specific models. CellNOpt is freely available under GPL license in R and Matlab languages. It can be also accessed through a python wrapper, and a Cytoscape plugin called CytoCopter.

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
C. Terfve, T. Cokelaer, D. Henriques, A. MacNamara, E. Goncalves, M.K. Morris, M. van Iersel, D.A. Lauffenburger, J. Saez-Rodriguez (2012)
BMC Syst Biol 6:133 [doi:10.1186/1752-0509-6-133] [pubmed:23079107]