DiMSim: a discrete-event simulator of metabolic networks.

A novel, scalable, quantitative, discrete-event simulator of metabolic and more general reaction pathways-DiMSim-has been developed. Rather than being modeled by systems of differential equations, metabolic pathways are viewed as bipartite graphs consisting of metabolites and reactions, linked by unidirectional or bidirectional arcs, and fluxes of metabolites emerge as the product of flows of the metabolites through the individual reactions. If required, DiMSim is able to model reactions involving single molecules up to molar concentrations so it is able to cope with the special characteristics of biochemical systems, including reversible reactions and discontinuous behavior, e.g. due to competition between reactions for limited quantities of reactants, product or allosteric inhibition and highly nonlinear behavior, e.g. due to cascades. It is also able to model membrane-bound compartments and the channels used to transport metabolites between them (both passive diffusion and active transport). While Michaelis-Menten kinetics is supported, DiMSim makes almost no assumptions other than each reaction having a fixed stoichiometry and that each reaction takes a stated amount of time.