1. A method comprising: defining one or more biochemical reactions of a system to be modeled, each biochemical reaction having one or more reactants; defining a spatial decomposition of the system by defining a plurality of regions of a space in which the system is to be modeled and by assigning each biochemical reaction to one of the regions, such that the system is spatially heterogeneous; defining relationships for inter-region movement of the reactants of the biochemical reactions; and, modeling the system of the biochemical reactions by modeling the biochemical reactions of each region as a spatially homogenous stochastic Petri-net and by modeling the inter-region movement of the reactants based on the relationships defined.