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Attractor Equivalence: An Observational Semantics for Reaction Networks

Guillaume Madelaine 1, 2, * Cédric Lhoussaine 1, 2 Joachim Niehren 1, 3
* Corresponding author
1 BioComputing
CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
3 LINKS - Linking Dynamic Data
Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
Abstract : We study observational semantics for networks of chemical reactions as used in systems biology. Reaction networks without kinetic information, as we consider, can be identified with Petri nets. We present a new observational semantics for reaction networks that we call the attractor equivalence. The main idea of the attractor equivalence is to observe reachable attractors and reachability of an attractor divergence in all possible contexts. The attractor equivalence can support powerful simplifications for reaction networks as we illustrate at the example of the Tet-On system. Alternative semantics based on bisimulations or traces, in contrast, do not support all needed simplifications.
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Submitted on : Thursday, July 9, 2015 - 3:19:27 PM
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  • HAL Id : hal-00990924, version 1

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Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren. Attractor Equivalence: An Observational Semantics for Reaction Networks. First International Conference on Formal Methods in Macro-Biology, Sep 2014, Nouméa, New Caledonia. pp.82-101. ⟨hal-00990924⟩

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