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The attributed pi-calculus with priorities. (English) Zbl 1275.92023
Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XII. Special issue on modeling methodologies. Berlin: Springer (ISBN 978-3-642-11711-4/pbk). Lecture Notes in Computer Science 5945. Lecture Notes in Bioinformatics. Journal Subline, 13-76 (2010).
Summary: We present the attributed \(\pi \)-calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The \(\lambda \)-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 non-deterministic 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.
For the entire collection see [Zbl 1204.92037].

MSC:
92C42 Systems biology, networks
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
Software:
Bio-PEPA; SpiCO
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