An analysis of the Petri net based model of the human body iron homeostasis process
Computational Biology and Chemistry
Time Petri Nets for Modelling and Analysis of Biochemical Networks
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Snoopy: a tool to design and animate/simulate graph-based formalisms
Proceedings of the 1st international conference on Simulation tools and techniques for communications, networks and systems & workshops
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
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry
Path finding approaches and metabolic pathways
Discrete Applied Mathematics
DSSZ-MC --- A Tool for Symbolic Analysis of Extended Petri Nets
PETRI NETS '09 Proceedings of the 30th International Conference on Applications and Theory of Petri Nets
Modeling infrastructure interdependency among floodplain infrastructures with extended Petri-Net
ASM '07 The 16th IASTED International Conference on Applied Simulation and Modelling
Hybrid simulation of biochemical systems using hybrid adaptive Petri nets
Proceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools
Ion channel modeling and simulation using hybrid functional Petri net
LSMS/ICSEE'10 Proceedings of the 2010 international conference on Life system modeling and simulation and intelligent computing, and 2010 international conference on Intelligent computing for sustainable energy and environment: Part III
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Natural Computing: an international journal
A discrete Petri net model for cephalostatin-induced apoptosis in leukemic cells
Natural Computing: an international journal
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
Neural system modeling and simulation using hybrid functional Petri net
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Biomodel engineering – from structure to behavior
Transactions on Computational Systems Biology XII
Survey: Computational challenges in systems biology
Computer Science Review
Time Petri Nets for Modelling and Analysis of Biochemical Networks
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Efficient recovery of missing events
Proceedings of the VLDB Endowment
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Motivation: Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and analysis in order to validate the model. The metabolism between sucrose and starch in the potato tuber is of great research interest. Even if the metabolism is one of the best studied in sink organs, it is not yet fully understood. Results: We provide an approach for model validation of metabolic networks using Petri net theory, which we demonstrate for the sucrose breakdown pathway in the potato tuber. We start with hierarchical modelling of the metabolic network as a Petri net and continue with the analysis of qualitative properties of the network. The results characterize the net structure and give insights into the complex net behaviour. Availability: Free availability of the Petri net editor PED, the animator PedVisor via http://www-dssz.informatik.tu-cottbus.de/~wwwdssz, and the analysis tool Integrated Net Analyser (INA) via http://www.informatik.hu-berlin.de/~starke/ina.html Contact: Ina.Koch@tfh-berlin.de