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The Attributed Pi Calculus

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 : The attributed pi calculus (pi(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. pi(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, the movement processes in the phototaxis of Euglena and the cooperative binding in the gene regulation of the lambda Phage, underline the applicability of pi(L) to systems biology.
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Submitted on : Monday, November 2, 2009 - 10:44:29 AM
Last modification on : Friday, February 4, 2022 - 3:10:52 AM
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  • HAL Id : inria-00308970, version 4


Mathias John, Cédric Lhoussaine, Joachim Niehren, Adelinde Uhrmacher. The Attributed Pi Calculus. Computational Methods in Systems Biology, 6th International Conference CMSB, Oct 2008, Rostock, Germany. pp.83-102. ⟨inria-00308970v4⟩



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