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Modeling Biological Networks by Action Languages via Answer Set Programming |
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| Authors: | Steve Dworschak Susanne Grell Victoria J. Nikiforova Torsten Schaub Joachim Selbig |
| Affiliation: | 1. Institut für Informatik, Universit?t Potsdam, August-Bebel-Str. 89, 14482, Potsdam, Germany 2. Max-Planck-Institut für molekulare Pflanzenphysiologie, 14424, Potsdam, Germany 4. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia 3. Institut für Biologie/Biochemie, Universit?t Potsdam, Postfach?900327, 14439, Potsdam, Germany |
| 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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