A petri net application to model metabolic processes
Systems Analysis Modelling Simulation
Modeling dynamic biological systems
Modeling dynamic biological systems
Petri Nets and Grafcet: Tools for Modelling Discrete Event Systems
Petri Nets and Grafcet: Tools for Modelling Discrete Event Systems
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Self-Modifying Nets, a Natural Extension of Petri Nets
Proceedings of the Fifth Colloquium on Automata, Languages and Programming
Modelling and Simulation of Metabolic Networks Petri Nets Approach and Perspective
Proceedings of the 16th European Simulation Multiconference on Modelling and Simulation 2002
Integrating biopathway databases for large-scale modeling and simulation
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
COPASI---a COmplex PAthway SImulator
Bioinformatics
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
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
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
Conservative and aggressive rough SVR modeling
Theoretical Computer Science
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For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. During the last 15 years, Petri nets have attracted more and more attention to help to solve this key problem. Regarding the published papers, it seems clear that hybrid functional Petri nets are the adequate method to model complex biological networks. Today, a Petri net model of biological networks is built manually by drawing places, transitions and arcs with mouse events. Therefore, based on relevant molecular database and information systems biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the application of Petri nets for modeling and simulation of biological networks. Furthermore, we will present a type of access to relevant metabolic databases such as KEGG, BRENDA, etc. Based on this integration process, the system supports semi-automatic generation of the correlated hybrid Petri net model. A case study of the cardio-disease related gene-regulated biological network is also presented. MoVisPP is available at http://agbi.techfak.uni-bielefeld.de/movispp/ .