Constraints

, Volume 13, Issue 1, pp 21–65

Modeling Biological Networks by Action Languages via Answer Set Programming

  • Steve Dworschak
  • Susanne Grell
  • Victoria J. Nikiforova
  • Torsten Schaub
  • Joachim Selbig
Open AccessArticle

DOI: 10.1007/s10601-007-9031-y

Cite this article as:
Dworschak, S., Grell, S., Nikiforova, V.J. et al. Constraints (2008) 13: 21. doi:10.1007/s10601-007-9031-y

Abstract

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.

Keywords

Biological network model Action language Answer set programming 
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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Steve Dworschak
    • 1
  • Susanne Grell
    • 1
    • 2
  • Victoria J. Nikiforova
    • 2
    • 4
  • Torsten Schaub
    • 1
  • Joachim Selbig
    • 1
    • 2
    • 3
  1. 1.Institut für InformatikUniversität PotsdamPotsdamGermany
  2. 2.Max-Planck-Institut für molekulare PflanzenphysiologiePotsdamGermany
  3. 3.Institut für Biologie/BiochemieUniversität PotsdamPotsdamGermany
  4. 4.Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussia