A computer modeling system for study of behavior of complex signaling pathways is described. The computer modeling system includes a computer representation of one or more nonlinear models of at least one signaling pathway arrangement involving enzyme cascades and/or allosteric enzymes and feedback. The computer representation of the model is transformed into at least portions of a bilinear dynamical system representation from which a series of Lie bracket operations are computed and the result tested for transitivity conditions of the associated semisimple Lie matrix algebra so as to determine potential instabilities and crosstalk susceptibilities. Also, the computer model can additionally comprise accurate numerical simulations, equilibrium condition analysis tools, and other algebraic structural tools involving graphs and matroids. The computer representation further includes a modular model environment for models to evolve with new discovery, trial of experimental models, combining multiple nonlinear models into more complex models, interactive user environments, crosstalk study, and detailed comparative analysis.
Nonlinear and lie algebra structural analysis system for enzyme cascades, metabolic signal transduction, signaling pathways, catalytic chemical reaction networks, and immunology