The System BioC for Reasoning about Biological Models in Action Language C

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.