Formal methods for checking the consistency of biological models

A. Clark, V. Galpin, S. Gilmore, M.L. Guerriero and J. Hillston

Advances in Systems Biology, Advances in Experimental Medicine and Biology, Vol 736. Springer, 2012


Formal modelling 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 modelling 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. 


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