Parameter Identification and Model Ranking of Thomas Networks

D 2012

Parameter Identification and Model Ranking of Thomas Networks

KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK, Heike SIEBERT et. al.

Basic information

Original name

Parameter Identification and Model Ranking of Thomas Networks

Name in Czech

Identifikace parametrů a clasifikace modelů Thomasových sítí

Authors

KLARNER, Hannes (276 Germany), Adam STRECK (203 Czech Republic, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Juraj KOLČÁK (703 Slovakia, belonging to the institution) and Heike SIEBERT (276 Germany)

Edition

Berlin, Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings, p. 207-226, 20 pp. 2012

Publisher

Springer

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"

References:

URL

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/12:00057781

Organization unit

Faculty of Informatics

ISBN

978-3-642-33635-5

ISSN

DOI

http://dx.doi.org/10.1007/978-3-642-33636-2_13

Keywords in English

Thomas network; parameter identification; model checking

Abstract

V originále

We propose a new methodology for identification and analysis of discrete gene networks as defined by René Thomas, supported by a tool chain: (i) given a Thomas network with partially known kinetic parameters, we reduce the number of acceptable parametrizations to those that fit time-series measurements and reflect other known constraints by an improved technique of coloured LTL model checking performing efficiently on Thomas networks in distributed environment; (ii) we introduce classification of acceptable parametrizations to identify most optimal ones; (iii) we propose two ways of visualising parametrizations dynamics wrt time-series data. Finally, computational efficiency is evaluated and the methodology is validated on bacteriophage \lambda case study.

Links

GAP202/11/0312, research and development project

Name: Vývoj a verifikace softwarových komponent v zapouzdřených systémech (Acronym: Components in Embedded Systems)

Investor: Czech Science Foundation

Citovat

KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK and Heike SIEBERT. Parameter Identification and Model Ranking of Thomas Networks. In Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Berlin: Springer, 2012, p. 207-226. ISBN 978-3-642-33635-5. Available from: https://dx.doi.org/10.1007/978-3-642-33636-2_13.

@inproceedings{1071805,
   author = {Klarner, Hannes and Streck, Adam and Šafránek, David and Kolčák, Juraj and Siebert, Heike},
   address = {Berlin},
   booktitle = {Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings},
   doi = {http://dx.doi.org/10.1007/978-3-642-33636-2_13},
   keywords = {Thomas network; parameter identification; model checking},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Berlin},
   isbn = {978-3-642-33635-5},
   pages = {207-226},
   publisher = {Springer},
   title = {Parameter Identification and Model Ranking of Thomas Networks},
   url = {http://link.springer.com/chapter/10.1007/978-3-642-33636-2_13},
   year = {2012}
}

TY  - JOUR
ID  - 1071805
AU  - Klarner, Hannes - Streck, Adam - Šafránek, David - Kolčák, Juraj - Siebert, Heike
PY  - 2012
TI  - Parameter Identification and Model Ranking of Thomas Networks
PB  - Springer
CY  - Berlin
SN  - 9783642336355
KW  - Thomas network
KW  - parameter identification
KW  - model checking
UR  - http://link.springer.com/chapter/10.1007/978-3-642-33636-2_13
L2  - http://link.springer.com/chapter/10.1007/978-3-642-33636-2_13
N2  - We propose a new methodology for identification and analysis of discrete gene networks as defined by René Thomas, supported by a tool chain: (i) given a Thomas network with partially known kinetic parameters, we reduce the number of acceptable parametrizations to those that fit time-series measurements and reflect other known constraints by an improved technique of coloured LTL model checking performing efficiently on Thomas networks in distributed environment; (ii) we introduce classification of acceptable parametrizations to identify most optimal ones; (iii) we propose two ways of visualising parametrizations dynamics wrt time-series data. Finally, computational efficiency is evaluated and the methodology is validated on bacteriophage \lambda case study.
ER  -

KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK and Heike SIEBERT. Parameter Identification and Model Ranking of Thomas Networks. In \textit{Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings}. Berlin: Springer, 2012, p.~207-226. ISBN~978-3-642-33635-5. Available from: https://dx.doi.org/10.1007/978-3-642-33636-2\_{}13.

Detailed Information on Publication Record