Petri net modelling of biological regulatory networks

@article{citeulike:3574343, abstract = {The complexity of biological regulatory networks often defies the intuition of the biologist and calls for the development of proper mathematical methods to model their structures and to delineate their dynamical properties. One qualitative approach consists in modelling regulatory networks in terms of logical equations (using either Boolean or multi-level discretisations). The Petri Net (PN) formalism offers a complementary framework to analyse the dynamical behaviour of large systems, either from a qualitative or from a quantitative point of view. Our proposal consists in articulating the logical approach with the PN formalism. In a previous work, we have already defined a systematic re-writing of Boolean regulatory models into a standard PN formalism. In this paper, we propose a rigorous and systematic mapping of multi-level logical regulatory models into specific standard Petri nets, called Multi-level Regulatory Petri Nets (MRPNs). We further propose some reduction strategies. Consequently, the resulting models become amenable to the algebraic and computational analyses used by the PN community. To illustrate our approach, we apply it to a multi-level logical model of the genetic switch controlling the lysis-lysogeny decision in the lambda bacteriophage.}, author = {Chaouiya, C. and Remy, E. and Thieffry, D.}, citeulike-article-id = {3574343}, doi = {10.1016/j.jda.2007.06.003}, issn = {15708667}, journal = {Journal of Discrete Algorithms}, keywords = {bacteriophage, genome-level, genomics, modeling, networks, petri-nets, regulation}, month = {June}, number = {2}, pages = {165--177}, posted-at = {2008-11-18 14:10:59}, priority = {5}, title = {Petri net modelling of biological regulatory networks}, url = {http://dx.doi.org/10.1016/j.jda.2007.06.003}, volume = {6}, year = {2008} }

TY - JOUR ID - citeulike:3574343 L3 - citeulike-article-id:3574343 N2 - The complexity of biological regulatory networks often defies the intuition of the biologist and calls for the development of proper mathematical methods to model their structures and to delineate their dynamical properties. One qualitative approach consists in modelling regulatory networks in terms of logical equations (using either Boolean or multi-level discretisations). The Petri Net (PN) formalism offers a complementary framework to analyse the dynamical behaviour of large systems, either from a qualitative or from a quantitative point of view. Our proposal consists in articulating the logical approach with the PN formalism. In a previous work, we have already defined a systematic re-writing of Boolean regulatory models into a standard PN formalism. In this paper, we propose a rigorous and systematic mapping of multi-level logical regulatory models into specific standard Petri nets, called Multi-level Regulatory Petri Nets (MRPNs). We further propose some reduction strategies. Consequently, the resulting models become amenable to the algebraic and computational analyses used by the PN community. To illustrate our approach, we apply it to a multi-level logical model of the genetic switch controlling the lysis-lysogeny decision in the lambda bacteriophage. IS - 2 JF - Journal of Discrete Algorithms SN - 15708667 EP - 177 TI - Petri net modelling of biological regulatory networks VL - 6 SP - 165 KW - bacteriophage KW - genome-level KW - genomics KW - modeling KW - networks KW - petri-nets KW - regulation AU - Chaouiya, C AU - Remy, E AU - Thieffry, D PY - 2008/06// UR - http://dx.doi.org/10.1016/j.jda.2007.06.003 ER -