Petri nets: an introduction
Digital design fundamentals (2nd ed.)
Digital design fundamentals (2nd ed.)
Model checking using net unfoldings
TAPSOFT '93 Selected papers of the colloquium on Formal approaches of software engineering
Classification of random boolean networks
ICAL 2003 Proceedings of the eighth international conference on Artificial life
SARGE: a tool for creation of putative genetic networks
Bioinformatics
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Discrete Mathematics for Computing
Discrete Mathematics for Computing
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Modeling multi-valued genetic regulatory networks using high-level petri nets
ICATPN'05 Proceedings of the 26th international conference on Applications and Theory of Petri Nets
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Control Flow Analysis of Generalised Boolean Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Net-based analysis of event processing networks: the fast flower delivery case
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
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In order to understand complex genetic regulatory networks researchers require automated formal modelling techniques that provide appropriate analysis tools. In this paper we propose a new qualitative model for genetic regulatory networks based on Petri nets and detail a process for automatically constructing these models using logic minimization. We take as our starting point the Boolean network approach in which regulatory entities are viewed abstractly as binary switches. The idea is to extract terms representing a Boolean network using logic minimization and to then directly translate these terms into appropriate Petri net control structures. The resulting compact Petri net model addresses a number of shortcomings associated with Boolean networks and is particularly suited to analysis using the wide range of Petri net tools. We demonstrate our approach by presenting a detailed case study in which the genetic regulatory network underlying the nutritional stress response in Escherichia coli is modelled and analysed.