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. (Proceedings of the twelfth international conference on intelligent systems for molecular biology/third European conference on computational biology (ISMB'04/ECCB'04) (pp. 15-22), 2004). 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.

We elaborate upon the usage of action language C for representing and reasoning about biological models. First, we provide a simple extension of C allowing for variables and show its usefulness in modeling biochemical reactions according to the well-known model of BIOCHAM. Second, we show how the biological action description language C TAID can be mapped onto C. Finally, we describe a toolbox for using action languages, including among them, a compiler mapping C and C TAID to logic programs under answer sets semantics along with a web-service integrating different front-and back-ends for addressing dynamical systems by means of action description languages via answer set programming. This is accompanied by an empirical evaluation with existing systems for processing action description languages.