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

  • Andrew Phillips
  • Luca Cardelli
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4695)

Abstract

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Andrew Phillips
    • 1
  • Luca Cardelli
    • 1
  1. 1.Microsoft Research, 7 JJ Thomson Avenue, CB3 0FB CambridgeUK

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