A Graphical Representation for Biological Processes in the Stochastic pi-Calculus

  • Andrew Phillips
  • Luca Cardelli
  • Giuseppe Castagna
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230)

Abstract

This paper presents a graphical representation for the stochastic π-calculus, which is formalised by defining a corresponding graphical calculus. The graphical calculus is shown to be reduction equivalent to stochastic π, ensuring that the two calculi have the same expressive power. The graphical representation is used to model a couple of example biological systems, namely a bistable gene network and a mapk signalling cascade. One of the benefits of the representation is its ability to highlight the existence of cycles, which are a key feature of biological systems. Another benefit is its ability to animate interactions between system components, in order to visualise system dynamics. The graphical representation can also be used as a front end to a simulator for the stochastic π-calculus, to help make modelling and simulation of biological systems more accessible to non computer scientists.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Andrew Phillips
    • 1
  • Luca Cardelli
    • 1
  • Giuseppe Castagna
    • 2
  1. 1.Microsoft ResearchCambridgeUK
  2. 2.École Normale SupérieureParisFrance

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