This paper presents a simulation algorithm for the stochastic pi-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.

}, author = {Andrew Phillips and Luca Cardelli}, journal = {Computational Methods in Systems Biology}, month = {September}, pages = {184–199}, publisher = {Springer}, series = {LNCS}, title = {Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus}, url = {http://research.microsoft.com/apps/pubs/default.aspx?id=65223}, volume = {4695}, year = {2007}, }