1. A method, comprising: defining a biochemical reaction of a system, said biochemical reaction occurring between at least two reactants to form a product, said system comprising a space in which each reactant of the at least two reactants is non-uniformly spatially distributed; defining a spatial decomposition of the space by subdividing the space into a plurality of regions, wherein each region of the plurality of regions is a unique three-dimensional sub-space of a three-dimensional space; defining relationships for inter-region movement of the at least two reactants between different regions of the plurality of regions, wherein defining relationships for inter-region movement of the at least two reactants is selected from the group consisting of defining flux-based molecular movement, defining advection-based molecular movement, defining convection-based molecular movement, defining diffusion-based movement, and combinations thereof; modeling the biochemical reaction in each region as a spatially homogenous stochastic Petri-net; modeling the inter-region movement of the at least two reactants between said different regions based on the defined relationships; determining, from said modeling the biochemical reaction in each region and said modeling the inter-region movement of the at least two reactants between said different regions, an identification of the product of the biochemical reaction in each region; and storing the identification of the product of the biochemical reaction in each region in a computer readable medium, wherein said modeling the biochemical reaction comprises modeling the biochemical reaction as occurring in a sequence of time steps, wherein said modeling the biochemical reaction in each region as a spatially homogenous stochastic Petri-net is performed in each time step, and wherein said modeling the inter-region movement of the at least two reactants between said different regions based on the defined relationships is performed between a first time step and a second time step in each pair of successive time steps in the sequence of time steps, and wherein defining relationships for inter-region movement of the at least two reactants is selected from the group consisting of defining flux-based molecular movement, defining advection-based molecular movement, defining convection-based molecular movement, defining diffusion-based movement, and combinations thereof, and wherein said modeling the biochemical reaction in each region, said modeling the inter-region movement of the at least two reactants between said different regions, said determining an identification of the product of the biochemical reaction in each region, and said storing the identification of the product of the biochemical reaction in each region are performed by a computer processor.