Petri nets: an introduction
A petri net application to model metabolic processes
Systems Analysis Modelling Simulation
Coloured Petri nets: basic concepts, analysis methods and practical use, volume 3
Coloured Petri nets: basic concepts, analysis methods and practical use, volume 3
Petri Net Theory and the Modeling of Systems
Petri Net Theory and the Modeling of Systems
Analysis issues in Petri nets with inhibitor arcs
Theoretical Computer Science
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
Structural Methods to Improve the Symbolic Analysis of Petri Nets
Proceedings of the 20th International Conference on Application and Theory of Petri Nets
Modelling and Simulation of Metabolic Networks Petri Nets Approach and Perspective
Proceedings of the 16th European Simulation Multiconference on Modelling and Simulation 2002
On the integration of delay and throughput measures in distributed processing models
On the integration of delay and throughput measures in distributed processing models
Petri Net Based Descriptions for Systematic Understanding of Biological Pathways
IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences
Recovering metabolic pathways via optimization
Bioinformatics
Biochemistry
Free Choice Petri Nets (Cambridge Tracts in Theoretical Computer Science)
Free Choice Petri Nets (Cambridge Tracts in Theoretical Computer Science)
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)
Petri net modelling of biological regulatory networks
Journal of Discrete Algorithms
Unfoldings: A Partial-Order Approach to Model Checking (Monographs in Theoretical Computer Science. An EATCS Series)
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Towards biopathway modeling and simulation
ICATPN'03 Proceedings of the 24th international conference on Applications and theory of Petri nets
ICATPN'03 Proceedings of the 24th international conference on Applications and theory of Petri nets
Introduction to generalized stochastic Petri nets
SFM'07 Proceedings of the 7th international conference on Formal methods for performance evaluation
From many places to few: automatic abstraction refinement for Petri nets
ICATPN'07 Proceedings of the 28th international conference on Applications and theory of Petri nets and other models of concurrency
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
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
Discrete, Continuous, and Hybrid Petri Nets
Discrete, Continuous, and Hybrid Petri Nets
From petri nets to differential equations – an integrative approach for biochemical network analysis
ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
IDD-based model validation of biochemical networks
Theoretical Computer Science
Preface: Petri nets for Systems and Synthetic Biology
Natural Computing: an international journal
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
Preface: Petri nets for Systems and Synthetic Biology
Natural Computing: an international journal
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
The evolution of higher-level biochemical reaction models
Genetic Programming and Evolvable Machines
Temporal patterns in artificial reaction networks
ICANN'12 Proceedings of the 22nd international conference on Artificial Neural Networks and Machine Learning - Volume Part I
Transactions on Computational Systems Biology XIV
Colouring space - a coloured framework for spatial modelling in systems biology
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
Conservation of Mass Analysis for Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Representing and Comparing Metabolic Pathways as Petri Nets with MPath2PN and CoMeta
Electronic Notes in Theoretical Computer Science (ENTCS)
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In the last 15 years, several research efforts have been directed towards the representation and the analysis of metabolic pathways by using Petri nets. The goal of this paper is twofold. First, we discuss how the knowledge about metabolic pathways can be represented with Petri nets. We point out the main problems that arise in the construction of a Petri net model of a metabolic pathway and we outline some solutions proposed in the literature. Second, we present a comprehensive review of recent research on this topic, in order to assess the maturity of the field and the availability of a methodology for modelling a metabolic pathway by a corresponding Petri net.