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Model Checking Approach to the Analysis of Biological Systems

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Book cover Automated Reasoning for Systems Biology and Medicine

Part of the book series: Computational Biology ((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.

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Acknowledgements

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

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Authors and Affiliations

  1. Systems Biology Laboratory at Faculty of Informatics, Masaryk University, Botanická 68a, 602 00, Brno, Czech Republic

    Nikola Beneš, Luboš Brim, Samuel Pastva & David Šafránek

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  1. Nikola Beneš
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Correspondence to David Šafránek .

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  1. Department of Computer Science and Technology, University of Cambridge, Cambridge, UK

    Pietro Liò

  2. School of Computing, Newcastle University, Newcastle, UK

    Paolo Zuliani

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Beneš, N., Brim, L., Pastva, S., Šafránek, D. (2019). Model Checking Approach to the Analysis of Biological Systems. In: Liò, P., Zuliani, P. (eds) Automated Reasoning for Systems Biology and Medicine. Computational Biology, vol 30. Springer, Cham. https://doi.org/10.1007/978-3-030-17297-8_1

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