Unfolding of Parametric Boolean Networks

J 2018

Unfolding of Parametric Boolean Networks

KOLČÁK, Juraj, David ŠAFRÁNEK, Paulevé LOIC and Stefan HAAR

Basic information

Original name

Unfolding of Parametric Boolean Networks

Authors

KOLČÁK, Juraj (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Paulevé LOIC (250 France) and Stefan HAAR (276 Germany)

Edition

Electronic Notes in Theoretical Computer Science, Elsevier Science, 2018, 1571-0661

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

RIV identification code

RIV/00216224:14330/18:00100911

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1016/j.entcs.2018.03.009

UT WoS

000430334800005

Keywords in English

asynchronous systems; Boolean networks; concurrency; parameters identification; systems biology

Změněno: 14/5/2020 15:15, RNDr. Pavel Šmerk, Ph.D.

Abstract

V originále

In systems biology, models of cellular regulatory processes such as gene regulatory networks or signalling pathways are crucial to understanding the behaviour of living cells. Available biological data are however often insufficient for full model specification. In this paper, we focus on partially specified models where the missing information is abstracted in the form of parameters. We introduce a novel approach to analysis of parametric logical regulatory networks addressing both sources of combinatoric explosion native to the model. First, we introduce a new compact representation of admissible parameters using Boolean lattices. Then, we define the unfolding of parametric Boolean networks. The resulting structure provides a partial-order reduction of concurrent transitions, and factorises the common transitions among the concrete models. A comparison is performed against state-of-the-art approaches to parametric model analysis

Links

GA15-11089S, research and development project

Name: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Czech Science Foundation

Citovat

KOLČÁK, Juraj, David ŠAFRÁNEK, Paulevé LOIC and Stefan HAAR. Unfolding of Parametric Boolean Networks. Electronic Notes in Theoretical Computer Science. Elsevier Science, 2018, vol. 335, Duben 2018, p. 67-90. ISSN 1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2018.03.009.

@article{1415145,
   author = {Kolčák, Juraj and Šafránek, David and Loic, Paulevé and Haar, Stefan},
   article_number = {Duben 2018},
   doi = {http://dx.doi.org/10.1016/j.entcs.2018.03.009},
   keywords = {asynchronous systems; Boolean networks; concurrency; parameters identification; systems biology},
   language = {eng},
   issn = {1571-0661},
   journal = {Electronic Notes in Theoretical Computer Science},
   title = {Unfolding of Parametric Boolean Networks},
   url = {http://dx.doi.org/10.1016/j.entcs.2018.03.009},
   volume = {335},
   year = {2018}
}

TY  - JOUR
ID  - 1415145
AU  - Kolčák, Juraj - Šafránek, David - Loic, Paulevé - Haar, Stefan
PY  - 2018
TI  - Unfolding of Parametric Boolean Networks
JF  - Electronic Notes in Theoretical Computer Science
VL  - 335
IS  - Duben 2018
SP  - 67-90
EP  - 67-90
PB  - Elsevier Science
SN  - 15710661
KW  - asynchronous systems
KW  - Boolean networks
KW  - concurrency
KW  - parameters identification
KW  - systems biology
UR  - http://dx.doi.org/10.1016/j.entcs.2018.03.009
L2  - http://dx.doi.org/10.1016/j.entcs.2018.03.009
N2  - In systems biology, models of cellular regulatory processes such as gene regulatory networks or signalling pathways are crucial to understanding the behaviour of living cells. Available biological data are however often insufficient for full model specification. In this paper, we focus on partially specified models where the missing information is abstracted in the form of parameters. We introduce a novel approach to analysis of parametric logical regulatory networks addressing both sources of combinatoric explosion native to the model. First, we introduce a new compact representation of admissible parameters using Boolean lattices. Then, we define the unfolding of parametric Boolean networks. The resulting structure provides a partial-order reduction of concurrent transitions, and factorises the common transitions among the concrete models. A comparison is performed against state-of-the-art approaches to parametric model analysis
ER  -

KOLČÁK, Juraj, David ŠAFRÁNEK, Paulevé LOIC and Stefan HAAR. Unfolding of Parametric Boolean Networks. \textit{Electronic Notes in Theoretical Computer Science}. Elsevier Science, 2018, vol.~335, Duben 2018, p.~67-90. ISSN~1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2018.03.009.

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