Asynchronous Links in the PBC and M-Nets
ASIAN '99 Proceedings of the 5th Asian Computing Science Conference on Advances in Computing Science
AMAST '98 Proceedings of the 7th International Conference on Algebraic Methodology and Software Technology
Maria: Modular Reachability Analyser for Algebraic System Nets
ICATPN '02 Proceedings of the 23rd International Conference on Applications and Theory of Petri Nets
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Semantics of Biological Regulatory Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
ICATPN'00 Proceedings of the 21st international conference on Application and theory of petri nets
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
Petri net models for the semi-automatic construction of large scale biological networks
Natural Computing: an international journal
Modelling and analysing genetic networks: from boolean networks to petri nets
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Compositional reachability analysis of genetic networks
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
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Regulatory networks are at the core of all biological functions from bio-chemical pathways to gene regulation and cell communication processes. Because of the complexity of the interweaving retroactions, the overall behavior is difficult to grasp and the development of formal methods is needed in order to confront the supposed properties of the biological system to the model. We revisit here the tremendous work of R. Thomas and show that its binary and also its multi-valued approach can be expressed in a unified way with high-level Petri nets. A compact modeling of genetic networks is proposed in which the tokens represent gene's expression levels and their dynamical behavior depends on a certain number of biological parameters. This allows us to take advantage of techniques and tools in the field of high-level Petri nets. A developed prototype allows a biologist to verify systematically the coherence of the system under various hypotheses. These hypotheses are translated into temporal logic formulae and the model-checking techniques are used to retain only the models whose behavior is coherent with the biological knowledge.