Formal methods for checking the consistency of biological models

Allan Clark, Vashti Galpin, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)461-75
Number of pages15
JournalAdv Exp Med Biol
Volume736
DOIs
Publication statusPublished - 2012

Keywords

  • Computational Biology
  • Computer Simulation
  • Kinetics
  • Models, Biological
  • Reproducibility of Results
  • Software

Cite this