A Simple and Fast Algorithm to Obtain All Invariants of a Generalized Petri Net
Selected Papers from the First and the Second European Workshop on Application and Theory of Petri Nets
Automated Trace Analysis of Discrete-Event System Models
IEEE Transactions on Software Engineering
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
QEST '09 Proceedings of the 2009 Sixth International Conference on the Quantitative Evaluation of Systems
Bio-PEPA for Epidemiological Models
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
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
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Verification and testing of biological models
Proceedings of the Winter Simulation Conference
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This paper describes a static analysis for Bio-PEPA models based on the notion of conservation of mass. Failure to obey the law of mass conservation can be an indication that there is an error in the model description. Here we focus on the use of invariant analysis to identify such potential flaws in models. We extend the basic technique to consider open models, in which it is possible to automatically ignore some causes of mass production or consumption that are unlikely to be errors. Our approach is an improvement on direct application of invariant analysis because it does not depend on a deep understanding of the model and prior expectations of the sets of components which should have conserved mass. We demonstrate the use of our technique on a published model from the literature and explain how our analysis can be used to uncover potential problems in the model description. Of course, not all models which fail to conserve mass are flawed. Nevertheless, this represents an important method of model verification which can be applied before the model itself is evaluated - since the analysis does not depend on accurate dynamics it can be undertaken early in the model development process, before the model has been fully parameterised.