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A modular, qualitative modelling of regulatory networks using Petri nets

Abstract : Advances in high-throughput technologies have enabled the de-lineation of large networks of interactions that control cellular processes. To understand behavioural properties of these complex networks, mathematical and computational tools are required. The multi-valued logical formalism, initially defined by R. Thomas and co-workers, 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 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 modelling 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 modelling 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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https://hal.archives-ouvertes.fr/hal-02309999
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Hanna Klaudel, Claudine Chaouiya, Franck Pommereau. A modular, qualitative modelling of regulatory networks using Petri nets. Modeling in Systems Biology, pp.253-279, 2011, ⟨10.1007/978-1-84996-474-6_12⟩. ⟨hal-02309999⟩

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