A Discrete-Event Simulator of Metabolic Networks - Bottom Up Systems Biolog

Speaker: A/Prof Michael Wise
Date : 23rd October 2006
Time : 10:00 – 11:00am
Venue : CSSE Seminar Room 1.24


DiMSim is a novel system for simulating the flows of metabolites through networks of metabolic or more general biochemical reactions. 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; details of metabolite fluxes emerge as the sums of flows of the metabolites through the 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. DiMSim 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 itself makes only two assumptions: each reaction takes an amount of time that is computed on-the-fly or set by the user, and every reaction has a fixed stoichiometry.

DiMSim may therefore also be applied to modelling other, time-dependent processes. DiMSim has enormous potential for application in areas related to drug-target evaluation.



A demonstration of the system will accompany the talk