Model-checking continuous-time Markov chains
ACM Transactions on Computational Logic (TOCL)
Self-Modifying Nets, a Natural Extension of Petri Nets
Proceedings of the Fifth Colloquium on Automata, Languages and Programming
A Concept of Hierarchical Petri Nets with Building Blocks
Papers from the 12th International Conference on Applications and Theory of Petri Nets: Advances in Petri Nets 1993
Model-Checking Algorithms for Continuous-Time Markov Chains
IEEE Transactions on Software Engineering
A study of the recoverability of computing systems.
A study of the recoverability of computing systems.
Synthetic biology---putting engineering into biology
Bioinformatics
COPASI---a COmplex PAthway SImulator
Bioinformatics
Systems Biology: Properties of Reconstructed Networks
Systems Biology: Properties of Reconstructed Networks
Time Petri Nets for Modelling and Analysis of Biochemical Networks
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
The temporal logic of programs
SFCS '77 Proceedings of the 18th Annual Symposium on Foundations of Computer Science
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
Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases
Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases
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
Executing multicellular differentiation
Bioinformatics
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
Transactions on Computational Systems Biology XI
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
Polynomial algebra of discrete models in systems biology
Bioinformatics
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
Boundedness analysis for open Chemical Reaction Networks with mass-action kinetics
Natural Computing: an international journal
Natural Computing: an international journal
Natural Computing: an international journal
Natural Computing: an international journal
The combinatorics of modeling and analyzing biological systems
Natural Computing: an international journal
Stochastic Petri net models of Ca2+ signaling complexes and their analysis
Natural Computing: an international journal
Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks
Natural Computing: an international journal
Petri net models for the semi-automatic construction of large scale biological networks
Natural Computing: an international journal
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
Biomodel engineering – from structure to behavior
Transactions on Computational Systems Biology XII
Petri nets and integrality relaxations: A view of continuous Petri net models
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Preface: Petri nets for Systems and Synthetic Biology
Natural Computing: an international journal
Snoopy --- a unifying petri net tool
PETRI NETS'12 Proceedings of the 33rd international conference on Application and Theory of Petri Nets
Transactions on Computational Systems Biology XIV
Proceedings of the Modelling of the Physical World Workshop
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
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"How might Petri nets enhance my Systems Biology toolkit?" - this is one of the questions that we get on a regular basis, which motivated us to write an answer in the form of this paper. We discuss the extent to which the Petri net approach can be used as an umbrella formalism to support the process of BioModel Engineering. This includes the facilitation of an active and productive interaction between biomodellers and bioscientists during the construction and analysis of dynamic models of biological systems. These models play a crucial role in both Systems Biology, where they can be explanatory and predictive, and synthetic biology, where they are effectively design templates. In this paper we give an overview of the tools and techniques which have been shown to be useful so far, and describe some of the current open challenges.