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Modeling in Systems Biology pp 253–279Cite as

A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets

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Part of the book series: Computational Biology ((COBO,volume 16))

Abstract

Advances in high-throughput technologies have enabled the delineation of large networks of interactions that control cellular processes. To understand behavioral properties of these complex networks, mathematical and computational tools are required. The multi-valued logical formalism, initially defined by Thomas and coworkers, proved well adapted to account for the qualitative knowledge available on regulatory interactions, and also to perform analyses of their dynamical properties. In this context, we present two representations of logical models in terms of Petri nets. In a first step, we briefly show how logical models of regulatory networks can be transposed into standard (place/transition) Petri nets, and discuss the capabilities of such a representation. In the second part, we focus on logical regulatory modules and their composition, demonstrating that a high-level Petri net representation greatly facilitates the modeling of interconnected modules. Doing so, we introduce an explicit means to integrate signals from various interconnected modules, taking into account their spatial distribution. This provides a flexible modeling framework to handle regulatory networks that operate at both intra- and intercellular levels. As an illustration, we describe a simplified model of the segment-polarity module involved in the segmentation of the Drosophila embryo.

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Notes

  1. 1.

    A multigraph is a graph with possibly several edges between a pair of nodes.

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Acknowledgements

We thank G. Batt, A. Naldi, E. Remy, S. Soliman, D. Thieffry for fruitful discussions. This work was supported by the French Research Agency (project ANR-08-SYSC-003).

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    Authors
    1. Claudine Chaouiya
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    2. Hanna Klaudel
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    3. Franck Pommereau
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    Correspondence to Claudine Chaouiya .

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    Editors and Affiliations

    1. Institute for Computer Science, J.W. Goethe University Frankfurt, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany

      Ina Koch

    2. Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099, Germany

      Wolfgang Reisig

    3. Institute of Computer Science, Martin Luther Univ. Halle-Wittenberg, Von Seckendorff Platz 1, Halle, 06120, Germany

      Falk Schreiber

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    Chaouiya, C., Klaudel, H., Pommereau, F. (2011). A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. In: Koch, I., Reisig, W., Schreiber, F. (eds) Modeling in Systems Biology. Computational Biology, vol 16. Springer, London. https://doi.org/10.1007/978-1-84996-474-6_12

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    • DOI: https://doi.org/10.1007/978-1-84996-474-6_12

    • Publisher Name: Springer, London

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    • Online ISBN: 978-1-84996-474-6

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