SIAM Journal on Scientific Computing
ICATPN'03 Proceedings of the 24th international conference on Applications and theory of 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
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
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
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Analysing Biochemical Oscillation through Probabilistic Model Checking
Electronic Notes in Theoretical Computer Science (ENTCS)
Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network
Fundamenta Informaticae
Quantitative Pathway Logic for Computational Biology
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems 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
Formal cell biology in biocham
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
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
Steady-state solution of biochemical systems, beyond S-systems via T-invariants
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Target driven biochemical network reconstruction based on petri nets and simulated annealing
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Understanding signalling networks as collections of signal transduction pathways
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A comparative study of stochastic analysis techniques
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
IDD-based model validation of biochemical networks
Theoretical Computer Science
A hybrid methodology for pattern recognition in signaling cervical cancer pathways
MCPR'10 Proceedings of the 2nd Mexican conference on Pattern recognition: Advances in pattern recognition
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
Biomodel engineering – from structure to behavior
Transactions on Computational Systems Biology XII
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network
Fundamenta Informaticae
Proceedings of the Winter Simulation Conference
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each perspective adds its contribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how qualitative descriptions are abstractions over stochastic or continuous descriptions, and show that the stochastic and continuous models approximate each other. A key contribution of the paper consists in a precise definition of biochemically interpreted stochastic Petri nets. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks.