The Attributed Pi Calculus

John, Mathias and Lhoussaine, Cédric and Niehren, Joachim and Uhrmacher, Adelinde M. (2008) The Attributed Pi Calculus. In: 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, October 12-15, Rostock, Germany. Proceedings,, pp. 83-102.

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The attributed pi calculus (ϕ(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 L which defines possible values of attributes. ϕ(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 ϕ(L) to systems biology: Euglena’s movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda.

Item Type: Conference or Workshop Item (Paper)
Projects: GRK dIEM oSiRiS