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Biochemical reaction rules with constraints. (English) Zbl 1326.68050
Barthe, Gilles (ed.), Programming languages and systems. 20th European symposium on programming, ESOP 2011, held as part of the joint European conferences on theory and practice of software, ETAPS 2011, Saarbrücken, Germany, March 26 – April 3, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-19717-8/pbk). Lecture Notes in Computer Science 6602, 338-357 (2011).
Summary: 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 decides 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.
For the entire collection see [Zbl 1213.68027].

MSC:
68N15 Theory of programming languages
68Q17 Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.)
68Q25 Analysis of algorithms and problem complexity
92-08 Computational methods for problems pertaining to biology
92C40 Biochemistry, molecular biology
92C42 Systems biology, networks
Software:
BioNetGen; Dizzy; SpiCO
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