Formal Methods for Checking the Consistency of Biological Models
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.
KeywordsBiological Model Invariant Analysis Label Transition System Process Algebra Species Definition
Clark, Guerriero, Gilmore, and Hillston are supported by the Centre for Systems Biology at Edinburgh. The Centre for Systems Biology at Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1. The authors benefited from an introduction to invariant generation by Peter Kemper during his time as a SICSA Distinguished Visiting Fellow.
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