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Model Checking Approach to the Analysis of Biological Systems

  • Nikola Beneš
  • Luboš Brim
  • Samuel Pastva
  • David ŠafránekEmail author
Chapter
Part of the Computational Biology book series (COBO, volume 30)

Abstract

Formal verification techniques together with other computer science formal methods have been recently tailored for applications to biological and biomedical systems. In contrast to traditional simulation-based approaches, model checking opens an entirely novel way of viewing and analysing the dynamics of such systems. In particular, it can help in system identification and parameter synthesis, in comparison of models with respect to a priori given desired properties, in robustness analysis of systems, in relating models to experimental data, or in globally analysing the bifurcations of systems behaviour with respect to changes in parameters. In this review, we briefly describe the state-of-the-art methods and techniques employing model checking, as one of the most prominent verification techniques, to the analysis of biomedical systems. We demonstrate some of the advantages of using the model checking method by presenting a brief account of the technique itself followed by examples of the application of formal methods based on model checking to three areas related to the analysis of biomedical systems: verification of biological hypotheses, parameters synthesis, and bifurcation analysis. Finally, we discuss several case studies that show how fruitfully the methods can be utilised within the computational systems biology and biomedicine domain.

Notes

Acknowledgements

This work has been partially supported by the Czech Science Foundation grant No. 18-00178S.

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Nikola Beneš
    • 1
  • Luboš Brim
    • 1
  • Samuel Pastva
    • 1
  • David Šafránek
    • 1
    Email author
  1. 1.Systems Biology Laboratory at Faculty of InformaticsMasaryk UniversityBrnoCzech Republic

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