Share on Facebook Tweet on Twitter Share on LinkedIn Share by email
Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus

Andrew Phillips and Luca Cardelli

Abstract

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.

Details

Publication typeArticle
Published inComputational Methods in Systems Biology
URLhttp://dx.doi.org/10.1007/978-3-540-75140-3_13
Pages184–199
Volume4695
SeriesLNCS
PublisherSpringer
> Publications > Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus