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

This paper presents a simulation algorithm for the stochastic -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.

• Type: Conference
• Year: 2007
• Where: CMSB
• Authors: Andrew Phillips, Luca Cardelli
• Keywords: Applied Computing, CMSB 2007, Efficient Simulation, Simulation Algorithm, SPiM Stochastic Simulator