The Attributed Pi Calculus

  • Authors:

  • Mathias John;Cédric Lhoussaine;Joachim Niehren;Adelinde M. Uhrmacher

  • Affiliations:

  • University of Rostock, Institute of Computer Science, Modeling and Simulation Group,;University of Lille 1, LIFL, CNRS UMR8022, and BioComputing project, LIFL, Lille,;INRIA, Lille, Mostrare project, and BioComputing project, LIFL, Lille,;University of Rostock, Institute of Computer Science, Modeling and Simulation Group,

  • Venue:
  • CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
  • Year:
  • 2008

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Abstract

The attributed pi calculus $({\phi({\mathcal L})})$ forms an extension of the pi calculus with attributed processes and attribute dependent synchronization. To ensure flexibility, the calculus is parametrized with the language ${\mathcal L}$ which defines possible values of attributes. ${\phi({\mathcal L})}$ can express polyadic synchronization as in pi@ and thus diverse compartment organizations. A non-deterministic and a stochastic semantics, where rates may depend on attribute values, is introduced. The stochastic semantics is based on continuous time Markov chains. A simulation algorithm is developed which is firmly rooted in this stochastic semantics. Two examples underline the applicability of ${\phi({\mathcal L})}$ to systems biology: Euglena's movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda.