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The Attributed Pi Calculus with Priorities

Mathias John 1 Cédric Lhoussaine 2 Joachim Niehren 3, 4, * Adelinde Uhrmacher 1 
* Corresponding author
3 MOSTRARE - Modeling Tree Structures, Machine Learning, and Information Extraction
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
4 BioComputing - Programming Languages for Biological Modeling and Simulation
LIFL - Laboratoire d'Informatique Fondamentale de Lille
Abstract : We present the attributed $\pi$-calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The $\pi$-calculus serves as a constraint language underlying the $\pi$-calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a nondeterministic and a stochastic semantics for the attributed $\pi$-calculus. We show how to encode the $\pi$-calculus with priorities and polyadic synchronization $\pi$@ and thus dynamic compartments, as well as the stochastic $\pi$-calculus with concurrent objects spico. We illustrate the usefulness of the attributed $\pi$-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 $\pi$-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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Mathias John, Cédric Lhoussaine, Joachim Niehren, Adelinde Uhrmacher. The Attributed Pi Calculus with Priorities. Corrado Priami; Rainer Breitling; David Gilbert; Monika Heiner; Adelinde M. Uhrmacher. Transactions on Computational Systems Biology XII: Special Issue on Modeling Methodologies, LNBI-5945, Springer, pp.13-76, 2010, Lecture Notes in Bioinformatics (Journal Subline), 978-3-642-11712-1. ⟨10.1007/978-3-642-11712-1_2⟩. ⟨inria-00422969⟩

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