Modeling biological networks by action languages via answer set programming

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We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage.

Metadaten
Author details:	Steve Dworschak, Susanne Grell, Victoria J. Nikiforova, Torsten H. Schaub ORCiD GND, Joachim Selbig GND
URN:	urn:nbn:de:kobv:517-opus4-429846
DOI:	https://doi.org/10.25932/publishup-42984
ISSN:	1866-8372
Title of parent work (German):	Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
Publication series (Volume number):	Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (843)
Publication type:	Postprint
Language:	English
Date of first publication:	2020/03/10
Publication year:	2008
Publishing institution:	Universität Potsdam
Release date:	2020/03/10
Tag:	action language; answer set programming; biological network model
Issue:	843
Number of pages:	47
Source:	Constraints 13 (2008) 21–65 DOI: 10.1007/s10601-007-9031-y
Organizational units:	Mathematisch-Naturwissenschaftliche Fakultät
DDC classification:	0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik
Peer review:	Referiert
Publishing method:	Open Access
License (German):	Keine öffentliche Lizenz: Unter Urheberrechtsschutz