The attributed pi-calculus with priorities

  • Authors:

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

  • Affiliations:

  • Institute of Computer Science, Modeling and Simulation Group, University of Rostock;University of Lille 1;Inria, Lille;Institute of Computer Science, Modeling and Simulation Group, University of Rostock

  • Venue:
  • Transactions on Computational Systems Biology XII
  • Year:
  • 2010

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Abstract

We present the attributed π−calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The λ-calculus serves as a constraint language underlying the π−calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a non-deterministic and a stochastic semantics for the attributed π−calculus. We show how to encode the π−calculus with priorities and polyadic synchronization π−@ and thus dynamic compartments, as well as the stochastic π−calculus with concurrent objects spico. We illustrate the usefulness of the attributed π−calculus for modeling biological systems at two particular examples: Euglena's spatial movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda. Furthermore, population-based model is supported beside individual-based modeling. A stochastic simulation algorithm for the attributed π−calculus is derived from its stochastic semantics. We have implemented a simulator and present experimental results, that confirm the practical relevance of our approach.