Model Checking Approach to the Analysis of Biological Systems

C 2019

Model Checking Approach to the Analysis of Biological Systems

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK

Basic information

Original name

Model Checking Approach to the Analysis of Biological Systems

Authors

BENEŠ, Nikola (203 Czech Republic, guarantor, belonging to the institution), Luboš BRIM (203 Czech Republic, belonging to the institution), Samuel PASTVA (703 Slovakia, belonging to the institution) and David ŠAFRÁNEK (203 Czech Republic, belonging to the institution)

Edition

Cham, Automated Reasoning for Systems Biology and Medicine, p. 3-35, 33 pp. Computational Biology, 2019

Publisher

Springer, Cham

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

10600 1.6 Biological sciences

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

RIV identification code

RIV/00216224:14330/19:00107592

Organization unit

Faculty of Informatics

ISBN

978-3-030-17296-1

DOI

http://dx.doi.org/10.1007/978-3-030-17297-8_1

UT WoS

000503198000001

Keywords in English

systems biology; model checking

Abstract

V originále

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.

Links

GA18-00178S, research and development project

Name: Diskrétní bifurkační analýza reaktivních systémů

Investor: Czech Science Foundation

MUNI/A/1018/2018, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace VIII.

Investor: Masaryk University, Category A

Citovat

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Model Checking Approach to the Analysis of Biological Systems. Online. In Pietro Liò, Paolo Zuliani. Automated Reasoning for Systems Biology and Medicine. Cham: Springer, Cham, 2019, p. 3-35. Computational Biology. ISBN 978-3-030-17296-1. Available from: https://dx.doi.org/10.1007/978-3-030-17297-8_1.

@inbook{1550299,
   author = {Beneš, Nikola and Brim, Luboš and Pastva, Samuel and Šafránek, David},
   address = {Cham},
   booktitle = {Automated Reasoning for Systems Biology and Medicine},
   doi = {http://dx.doi.org/10.1007/978-3-030-17297-8_1},
   editor = {Pietro Liò, Paolo Zuliani},
   keywords = {systems biology; model checking},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Cham},
   isbn = {978-3-030-17296-1},
   pages = {3-35},
   publisher = {Springer, Cham},
   title = {Model Checking Approach to the Analysis of Biological Systems},
   year = {2019}
}

TY  - CHAP
ID  - 1550299
AU  - Beneš, Nikola - Brim, Luboš - Pastva, Samuel - Šafránek, David
PY  - 2019
TI  - Model Checking Approach to the Analysis of Biological Systems
VL  - Computational Biology
PB  - Springer, Cham
CY  - Cham
SN  - 9783030172961
KW  - systems biology
KW  - model checking
N2  - 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.
ER  -

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Model Checking Approach to the Analysis of Biological Systems. Online. In Pietro Liò, Paolo Zuliani. \textit{Automated Reasoning for Systems Biology and Medicine}. Cham: Springer, Cham, 2019, p.~3-35. Computational Biology. ISBN~978-3-030-17296-1. Available from: https://dx.doi.org/10.1007/978-3-030-17297-8\_{}1.

Detailed Information on Publication Record