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Conservation of Mass Analysis for Bio-PEPA

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http://www.sciencedirect.com/science/article/pii/S157106611300039X
Original languageEnglish
Pages (from-to)107-126
Number of pages20
JournalElectronic Notes in Theoretical Computer Science
Volume296
DOIs
Publication statusPublished - Aug 2013

Abstract

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.

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