Petri net modelling of biological regulatory networks
Journal of Discrete Algorithms
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FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Path finding approaches and metabolic pathways
Discrete Applied Mathematics
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IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Rule-based modeling of transcriptional attenuation at the tryptophan operon
Winter Simulation Conference
Petri net representation of multi-valued logical regulatory graphs
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Petri net models for the semi-automatic construction of large scale biological networks
Natural Computing: an international journal
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CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
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CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Qualitative petri net modelling of genetic networks
Transactions on Computational Systems Biology VI
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
An abstraction theory for qualitative models of biological systems
Theoretical Computer Science
Survey: Computational challenges in systems biology
Computer Science Review
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Motivation: The integrated dynamical modelling of mixed metabolic/genetic networks constitutes one of the challenges of systems biology. Furthermore, as most of available data about genetic and metabolic regulations are qualitative, there is a pressing need for rigorous qualitative mathematical approaches. Results: On the basis of two established formalisms, the logical modelling of genetic regulatory networks and the Petri net modelling of metabolic networks, we propose a systematic approach for the modelling of regulated metabolic networks. This approach leans on previous work defining a systematic procedure to translate logical regulatory graphs into standard (discrete) Petri nets (PNs). This approach is illustrated by the qualitative modelling of the biosynthesis of tryptophan (Trp) in Escherichia coli, taking into account two types of regulatory feedbacks: the direct inhibition of the first enzyme of the pathway by the final product of the pathway, and the transcriptional inhibition of the Trp operon by the Trp--repressor complex. On the basis of this integrated PN model, we further indicate how available dynamical analysis tools can be applied to obtain significant insights in the behaviour of the system. Availability: The software GINsim for the logical modelling of genetic regulatory networks together with the PN model of the regulated Trp biosynthesis pathway are available at: http://gin.univ-mrs.fr/GINsim. Contact: chaouiya@ibdm.univ-mrs.fr