CellNOpt

CellNOpt (CellNetOptimiser) is a framework to build predictive logic models of signalling pathways by training a prior knowledge network (PKN) to biochemical data obtained from perturbation experiments. The CellNOpt R packages feature different formalisms ranging from Boolean logic to logic-based ordinary differential equation and they are also available in Bioconductor.

CellNOpt is being maintained and further developed by saezlab. For more details you can check the two related publications (Terfve et.al. 2012 and Gjerga et. al. 2020) as well as it’s dedicated Github page.