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 provides a graphical user interface. CellNOpt is mainly developed at the Saez-Rodriguez group at the European Bioinformatics Institute (EBI). The project started at the groups of Peter Sorger (Harvard Medical School) and Doug Lauffenburger (M.I.T.). There is a group of CellNOpt developers at different locations.