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.

Základní údaje

Originální název

Parameter Identification and Model Ranking of Thomas Networks

Název česky

Identifikace parametrů a clasifikace modelů Thomasových sítí

Autoři

KLARNER, Hannes (276 Německo), Adam STRECK (203 Česká republika, domácí), David ŠAFRÁNEK (203 Česká republika, garant, domácí), Juraj KOLČÁK (703 Slovensko, domácí) a Heike SIEBERT (276 Německo)

Vydání

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

Nakladatel

Springer

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Impakt faktor

Impact factor: 0.402 v roce 2005

Kód RIV

RIV/00216224:14330/12:00057781

Organizační jednotka

Fakulta informatiky

ISBN

978-3-642-33635-5

ISSN

DOI

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

Klíčová slova anglicky

Thomas network; parameter identification; model checking

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 4. 2013 07:21, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

GAP202/11/0312, projekt VaV

Název: Vývoj a verifikace softwarových komponent v zapouzdřených systémech (Akronym: Components in Embedded Systems)

Investor: Grantová agentura ČR, Software Components in Embedded Systems: Development and Verification

Citovat

KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK a 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, s. 207-226. ISBN 978-3-642-33635-5. Dostupné z: 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 a 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, s.~207-226. ISBN~978-3-642-33635-5. Dostupné z: https://dx.doi.org/10.1007/978-3-642-33636-2\_{}13.

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