inria-00308970, version 4
The Attributed Pi Calculus
Mathias John 1Cédric Lhoussaine 2Joachim Niehren
3, 4Adelinde Uhrmacher 1
Computational Methods in Systems Biology, 6th International Conference CMSB (2008) 83-102
Résumé : 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.
- 1 : University of Rostock
- University of Rostock
- 2 : Laboratoire d'Informatique Fondamentale de Lille (LIFL)
- CNRS : UMR8022 – INRIA – IRCICA – Université Lille 1 - Sciences et Technologies
- 3 : MOSTRARE (INRIA Lille - Nord Europe)
- INRIA – CNRS : UMR8022 – Université Lille 1 - Sciences et Technologies : EA3588 – Université Charles de Gaulle - Lille III
- 4 : BIOCOMPUTING (LIFL)
- Université Lille 1 - Sciences et Technologies – CNRS : UMR8022
- Domaine : Informatique/Langage de programmation
Informatique/Bio-informatique
Sciences du Vivant/Bio-Informatique, Biologie Systémique - Versions disponibles : v1 (01-09-2008) v2 (25-03-2009) v3 (27-07-2009) v4 (02-11-2009)
- inria-00308970, version 4
- http://hal.inria.fr/inria-00308970
- oai:hal.inria.fr:inria-00308970
- Contributeur : Joachim Niehren
- Soumis le : Lundi 2 Novembre 2009, 10:44:29
- Dernière modification le : Mardi 1 Juin 2010, 15:26:10






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