Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus
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- Phillips A., Cardelli L. (2007) Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus. In: Calder M., Gilmore S. (eds) Computational Methods in Systems Biology. CMSB 2007. Lecture Notes in Computer Science, vol 4695. Springer, Berlin, Heidelberg
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.
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