MaBoSS is a simulation software for continuous time Boolean modeling. The model is described by a network, where nodes have Boolean states. Transitions between the node states are governed by logical equations, with an associated rate (a real number ∈[0,∞[⁠).

CoE: PerMedCoe


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.

CoE: PerMedCoe