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International Conference on Formal Methods in Macro-Biology

FMMB 2014: Formal Methods in Macro-Biology pp 82–101Cite as

Attractor Equivalence: An Observational Semantics for Reaction Networks

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8738))

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.

This work has been funded by the French National Research Agency research grant Iceberg ANR-IABI-3096.

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Author information

Authors and Affiliations

  1. BioComputing, LIFL Lille (CNRS UMR 8022), France

    Guillaume Madelaine, Cédric Lhoussaine & Joachim Niehren

  2. University of Lille 1, France

    Guillaume Madelaine & Cédric Lhoussaine

  3. INRIA Lille, France

    Joachim Niehren

Authors
  1. Guillaume Madelaine
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  2. Cédric Lhoussaine
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  3. Joachim Niehren
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Editors and Affiliations

  1. Inria,, Bâtiment 8, Domaine de Voluceau, 78150, Rocquencourt, France

    François Fages

  2. Department of Mathematics and Computer Science, University of Udine, Via le Scienze 206, 33100, Udine, Italy

    Carla Piazza

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Madelaine, G., Lhoussaine, C., Niehren, J. (2014). Attractor Equivalence: An Observational Semantics for Reaction Networks. In: Fages, F., Piazza, C. (eds) Formal Methods in Macro-Biology. FMMB 2014. Lecture Notes in Computer Science(), vol 8738. Springer, Cham. https://doi.org/10.1007/978-3-319-10398-3_7

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  • DOI: https://doi.org/10.1007/978-3-319-10398-3_7

  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-319-10398-3

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