, Volume 13, Issue 1-2, pp 21-65,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 25 Mar 2008

Modeling Biological Networks by Action Languages via Answer Set Programming

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.