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Mathias John, Cédric Lhoussaine, Joachim Niehren, and Adelinde Uhrmacher (2010)

The Attributed Pi-Calculus with Priorities

Transactions on Computational Systems Biology XII, 5945/2010:13-76.

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.

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