High-Performance Symbolic Parameter Synthesis of Biological
Models: A Case Study

D 2016

High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study

DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA, David ŠAFRÁNEK et. al.

Basic information

Original name

High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study

Authors

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

Edition

LNBI 9859. Neuveden, Computational Methods in Systems Biology. CMSB 2016. p. 82-97, 16 pp. 2016

Publisher

Springer International Publishing

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/16:00088099

Organization unit

Faculty of Informatics

ISBN

978-3-319-45176-3

ISSN

DOI

http://dx.doi.org/10.1007/978-3-319-45177-0_6

UT WoS

000460685100006

Keywords in English

model checking; systems biology; Computational Tree Logic; dynamical systems; distributed algorithms

Abstract

V originále

Complex behaviour arising in biological systems is described by highly parameterised dynamical models. Most of the parameters are mutually dependent and therefore it is hard and computationally demanding to find admissible parameter values with respect to hypothesised constraints and wet-lab measurements. Recently, we have developed several high-performance techniques for parameter synthesis that are based on parallel coloured model checking. These methods allow to obtain parameter values that guarantee satisfaction of a given set of dynamical properties and parameter constraints. In this paper, we review the applicability of our techniques in the context of biological systems. In particular, we provide an extended analysis of a genetic switch controlling the regulation in mammalian cell cycle phase transition and a synthetic pathway for biodegradation of a toxic pollutant in E. coli.

Links

GA15-11089S, research and development project

Name: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Czech Science Foundation

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/0945/2015, interní kód MU

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

Investor: Masaryk University, Category A

Citovat

DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. LNBI 9859. Neuveden: Springer International Publishing, 2016, p. 82-97. ISBN 978-3-319-45176-3. Available from: https://dx.doi.org/10.1007/978-3-319-45177-0_6.

@inproceedings{1352261,
   author = {Demko, Martin and Beneš, Nikola and Brim, Luboš and Pastva, Samuel and Šafránek, David},
   address = {Neuveden},
   booktitle = {Computational Methods in Systems Biology. CMSB 2016.},
   doi = {http://dx.doi.org/10.1007/978-3-319-45177-0_6},
   edition = {LNBI 9859},
   editor = {Ezio Bartocci et al.},
   keywords = {model checking; systems biology; Computational Tree Logic; dynamical systems; distributed algorithms},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Neuveden},
   isbn = {978-3-319-45176-3},
   pages = {82-97},
   publisher = {Springer International Publishing},
   title = {High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study},
   year = {2016}
}

TY  - JOUR
ID  - 1352261
AU  - Demko, Martin - Beneš, Nikola - Brim, Luboš - Pastva, Samuel - Šafránek, David
PY  - 2016
TI  - High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study
PB  - Springer International Publishing
CY  - Neuveden
SN  - 9783319451763
KW  - model checking
KW  - systems biology
KW  - Computational Tree Logic
KW  - dynamical systems
KW  - distributed algorithms
N2  - Complex behaviour arising in biological systems is described by highly parameterised dynamical models. Most of the parameters are mutually dependent and therefore it is hard and computationally demanding to find admissible parameter values with respect to hypothesised constraints and wet-lab measurements. Recently, we have developed several high-performance techniques for parameter synthesis that are based on parallel coloured model checking. These methods allow to obtain parameter values that guarantee satisfaction of a given set of dynamical properties and parameter constraints. In this paper, we review the applicability of our techniques in the context of biological systems. In particular, we provide an extended analysis of a genetic switch controlling the regulation in mammalian cell cycle phase transition and a synthetic pathway for biodegradation of a toxic pollutant in E. coli.
ER  -

DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Ezio Bartocci et al. \textit{Computational Methods in Systems Biology. CMSB 2016.}. LNBI 9859. Neuveden: Springer International Publishing, 2016, p.~82-97. ISBN~978-3-319-45176-3. Available from: https://dx.doi.org/10.1007/978-3-319-45177-0\_{}6.

Detailed Information on Publication Record