title: Formal methods for checking the consistency of biological models.
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.
authors.affiliation: Centre for Systems Biology at Edinburgh, The University of Edinburgh, Edinburgh EH9 3JU, Scotland, UK. A.D.Clark@ed.ac.uk
authors.forename: Allan
authors.initials: A
authors.lastname: Clark
authors.forename: Vashti
authors.initials: V
authors.lastname: Galpin
authors.forename: Stephen
authors.initials: S
authors.lastname: Gilmore
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Guerriero
authors.forename: Jane
authors.initials: J
authors.lastname: Hillston
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D015203:Reproducibility of Results; D012984:Software