Timed Modelling of Gene Networks with Arbitrary Expression
Level Discretization

D 2013

Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization

VAN GOETHEM, Simon; Jean-Marie JACQUET; Luboš BRIM a David ŠAFRÁNEK

Základní údaje

Originální název

Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization

Autoři

VAN GOETHEM, Simon (56 Belgie); Jean-Marie JACQUET (56 Belgie); Luboš BRIM (203 Česká republika, domácí) a David ŠAFRÁNEK (203 Česká republika, garant, domácí)

Vydání

Neuveden, Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12), od s. 67-81, 15 s. 2013

Nakladatel

Elsevier

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

elektronická verze "online"

Odkazy

URL

Kód RIV

RIV/00216224:14330/13:00065956

Organizační jednotka

Fakulta informatiky

ISSN

DOI

https://doi.org/10.1016/j.entcs.2013.02.019

UT WoS

000216918000006

Klíčová slova anglicky

timed automata; gene regulatory networks; UPPAAL

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 24. 4. 2014 17:29, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological 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

VAN GOETHEM, Simon; Jean-Marie JACQUET; Luboš BRIM a David ŠAFRÁNEK. Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Online. In Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12). Neuveden: Elsevier, 2013, s. 67-81. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2013.02.019.

@inproceedings{1076398,
   author = {Van Goethem, Simon and Jacquet, JeanandMarie and Brim, Luboš and Šafránek, David},
   address = {Neuveden},
   booktitle = {Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)},
   doi = {https://doi.org/10.1016/j.entcs.2013.02.019},
   keywords = {timed automata; gene regulatory networks; UPPAAL},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Neuveden},
   pages = {67-81},
   publisher = {Elsevier},
   title = {Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization},
   url = {http://www.sciencedirect.com/science/article/pii/S1571066113000212},
   year = {2013}
}

TY  - CONF
ID  - 1076398
AU  - Van Goethem, Simon - Jacquet, Jean-Marie - Brim, Luboš - Šafránek, David
PY  - 2013
TI  - Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
PB  - Elsevier
CY  - Neuveden
KW  - timed automata
KW  - gene regulatory networks
KW  - UPPAAL
UR  - http://www.sciencedirect.com/science/article/pii/S1571066113000212
L2  - http://www.sciencedirect.com/science/article/pii/S1571066113000212
N2  - In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological case study.
ER  -

VAN GOETHEM, Simon; Jean-Marie JACQUET; Luboš BRIM a David ŠAFRÁNEK. Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Online. In \textit{Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)}. Neuveden: Elsevier, 2013, s.~67-81. ISSN~1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2013.02.019.

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