Detecting Attractors in Biological Models with Uncertain
Parameters

D 2017

Detecting Attractors in Biological Models with Uncertain Parameters

BRIM, Luboš, Jiří BARNAT, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO et. al.

Basic information

Original name

Detecting Attractors in Biological Models with Uncertain Parameters

Authors

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

Edition

LNCS 10545. Cham, Computational Methods in Systems Biology. CMSB 2017, p. 40-56, 17 pp. 2017

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/00216224:14330/17:00094899

Organization unit

Faculty of Informatics

ISBN

978-3-319-67470-4

ISSN

DOI

http://dx.doi.org/10.1007/978-3-319-67471-1_3

UT WoS

000542715600003

Keywords in English

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

Abstract

V originále

Complex behaviour arising in biological systems is typically characterised by various kinds of attractors. An important problem in this area is to determine these attractors. Biological systems are usually described by highly parametrised dynamical models that can be represented as parametrised graphs typically constructed as discrete abstractions of continuous-time models. In such models, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we introduce a novel method for detecting tSCCs in parametrised graphs. The method is supplied with a parallel algorithm and evaluated on discrete abstractions of several non-linear biological models.

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/0992/2016, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Acronym: SKOMU)

Investor: Masaryk University, Category A

Citovat

BRIM, Luboš, Jiří BARNAT, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. Detecting Attractors in Biological Models with Uncertain Parameters. In Jérôme Feret and Heinz Koeppl. Computational Methods in Systems Biology. CMSB 2017. LNCS 10545. Cham: Springer International Publishing, 2017, p. 40-56. ISBN 978-3-319-67470-4. Available from: https://dx.doi.org/10.1007/978-3-319-67471-1_3.

@inproceedings{1387860,
   author = {Brim, Luboš and Barnat, Jiří and Šafránek, David and Beneš, Nikola and Demko, Martin and Pastva, Samuel and Hajnal, Matej},
   address = {Cham},
   booktitle = {Computational Methods in Systems Biology. CMSB 2017},
   doi = {http://dx.doi.org/10.1007/978-3-319-67471-1_3},
   edition = {LNCS 10545},
   editor = {Jérôme Feret and Heinz Koeppl},
   keywords = {model checking; systems biology; Computational Tree Logic; dynamical systems; distributed algorithms;},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Cham},
   isbn = {978-3-319-67470-4},
   pages = {40-56},
   publisher = {Springer International Publishing},
   title = {Detecting Attractors in Biological Models with Uncertain Parameters},
   year = {2017}
}

TY  - JOUR
ID  - 1387860
AU  - Brim, Luboš - Barnat, Jiří - Šafránek, David - Beneš, Nikola - Demko, Martin - Pastva, Samuel - Hajnal, Matej
PY  - 2017
TI  - Detecting Attractors in Biological Models with Uncertain Parameters
PB  - Springer International Publishing
CY  - Cham
SN  - 9783319674704
KW  - model checking
KW  - systems biology
KW  - Computational Tree Logic
KW  - dynamical systems
KW  - distributed algorithms;
N2  - Complex behaviour arising in biological systems is typically characterised by various kinds of attractors. An important problem in this area is to determine these attractors. Biological systems are usually described by highly parametrised dynamical models that can be represented as parametrised graphs typically constructed as discrete abstractions of continuous-time models. In such models, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we introduce a novel method for detecting tSCCs in parametrised graphs. The method is supplied with a parallel algorithm and evaluated on discrete abstractions of several non-linear biological models.
ER  -

BRIM, Luboš, Jiří BARNAT, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. Detecting Attractors in Biological Models with Uncertain Parameters. In Jérôme Feret and Heinz Koeppl. \textit{Computational Methods in Systems Biology. CMSB 2017}. LNCS 10545. Cham: Springer International Publishing, 2017, p.~40-56. ISBN~978-3-319-67470-4. Available from: https://dx.doi.org/10.1007/978-3-319-67471-1\_{}3.

Detailed Information on Publication Record