Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus


This paper presents a simulation algorithm for the stochastic π-calculus, designed for the efficient simulation of biological systems with large numbers of molecules. The cost of a simulation depends on the number of species, rather than the number of molecules, resulting in a significant gain in efficiency. The algorithm is proved correct with respect to the calculus, and then used as a basis for implementing the latest version of the SPiM stochastic simulator. The algorithm is also suitable for generating graphical animations of simulations, in order to visualise system dynamics.

Computational Methods in Systems Biology (CMSB)