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A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets

  • Claudine Chaouiya
  • Hanna Klaudel
  • Franck Pommereau
Part of the Computational Biology book series (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.

Keywords

Regulatory Network Synthetic Biology Regulatory Component Topological Relation Binary Decision Diagram 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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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Copyright information

© Springer-Verlag London Limited 2011

Authors and Affiliations

  • Claudine Chaouiya
    • Hanna Klaudel
      • Franck Pommereau

        There are no affiliations available

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