Biochemical Reaction Rules with Constraints

Mathias John 1 Cédric Lhoussaine 1 Joachim Niehren 1, 2, * Cristian Versari 3
* Corresponding author
1 BioComputing - Programming Languages for Biological Modeling and Simulation
LIFL - Laboratoire d'Informatique Fondamentale de Lille
2 MOSTRARE - Modeling Tree Structures, Machine Learning, and Information Extraction
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : We propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology, that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based programming languages, and further illustrate the high expressiveness of React(C). We present a stochastic simulator for React(C) independently of the choice of the constraint language C. Our simulator must decide for a given reaction rule whether it can be applied to the current biochemical solution. We show that this decision problem is NP-complete for arbitrary constraint systems C, and that it can be solved in polynomial time for rules of bounded arity. In practice, we propose to solve this problem by constraint programming.
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Submitted on : Thursday, February 3, 2011 - 10:43:47 PM
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Mathias John, Cédric Lhoussaine, Joachim Niehren, Cristian Versari. Biochemical Reaction Rules with Constraints. 20th European Symposium on Programming Languages, Mar 2011, Saarbrücken, Germany. pp.338-357. ⟨inria-00544387⟩

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