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Author manuscript, published in "Transactions on Computational Systems Biology XII, 5945 (2010) 13-76" The Attributed Pi-Calculus with Priorities (2009)
BibTeX
@MISC{John09authormanuscript,,
author = {Mathias John and Cédric Lhoussaine and Joachim Niehren and Adelinde M. Uhrmacher and Inria Lille and Biocomputing Group Lifl},
title = {Author manuscript, published in "Transactions on Computational Systems Biology XII, 5945 (2010) 13-76" The Attributed Pi-Calculus with Priorities},
year = {2009}
}
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Abstract
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 nondeterministic 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. 1
Keyphrases
attributed calculus computational system biology xii attributed pi-calculus author manuscript stochastic semantics population-based model dynamic compartment interaction constraint bacteriophage lambda cooperative protein polyadic synchronization constraint language interaction constraint subsume priority present experimental result spatial movement concurrent object stochastic calculus gene regulation global aspect calculus serf biological system practical relevance individual-based modeling concurrent system stochastic simulation algorithm particular example
