{"id":148020,"date":"2007-09-01T00:00:00","date_gmt":"2007-09-01T00:00:00","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/msr-research-item\/efficient-correct-simulation-of-biological-processes-in-the-stochastic-pi-calculus\/"},"modified":"2018-10-16T20:00:56","modified_gmt":"2018-10-17T03:00:56","slug":"efficient-correct-simulation-of-biological-processes-in-the-stochastic-pi-calculus","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/efficient-correct-simulation-of-biological-processes-in-the-stochastic-pi-calculus\/","title":{"rendered":"Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus"},"content":{"rendered":"<div class=\"asset-content\">\n<p>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.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>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. 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The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. 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