Research Seminar - December 15, 2003

DiMSim: A Discrete-Event Simulator of Metabolic Network

Abstract:

Dr Wise is a computational biologist visiting UWA. He will describe a novel, scalable, quantitative, discrete-event simulator of metabolic and more general reaction pathways - DiMSim - developed with Dr Xiao-Qin Xia. Rather than being modelled by systems of differential equations, metabolic pathways are viewed as bipartite graphs consisting of metabolites and reactions, linked by unidirectional or bi-directional arcs; fluxes of metabolites emerge as the product of flows of the metabolites through the individual reactions. DiMSim is able to model reactions involving single molecules, up to molar concentrations. It is able to cope with the special characteristics of biochemical systems, including reversible reactions and discontinuous behaviour, e.g. due to competition between reactions for limited quantities of reactants, product or allosteric inhibition and highly non-linear behaviour, 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. Among other areas, it is anticipated that DiMSim will be find application in in silico toxicology - elucidating the metabolic effects of compounds. A demonstration of the system will accompany the talk.