Formal methods for checking the consistency of biological models

Clark, Allan, Galpin, Vashti, Gilmore, Stephen, Guerriero, Maria Luisa and Hillston, Jane (2012) Formal methods for checking the consistency of biological models. Adv Exp Med Biol, 736. pp. 461-75. ISSN 0065-2598

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Abstract

Formal modeling approaches such as process algebras and Petri nets seek to provide insight into biological processes by using both symbolic and numerical methods to reveal the dynamics of the process under study. These formal approaches differ from classical methods of investigating the dynamics of the process through numerical integration of ODEs because they additionally provide alternative representations which are amenable to discrete-state analysis and logical reasoning. Backed by these additional analysis methods, formal modeling approaches have been able to identify errors in published and widely-cited biological models. This paper provides an introduction to these analysis methods, and explains the benefits which they can bring to ensuring the consistency of biological models.

Item Type: Article
Uncontrolled Keywords: computational biology,computer simulation,kinetics,models, biological,reproducibility of results,software
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User: Pure Connector
Date Deposited: 20 Jan 2014 15:56
Last Modified: 21 Apr 2020 22:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/46101
DOI: 10.1007/978-1-4419-7210-1_27

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