Answer Set Programming for Systems Biology

Answer Set Programming (ASP) is a declarative problem solving paradigm from the field of Logic Programming combining several computer science areas such as Knowledge Representation and Reasoning, Artificial Intelligence, Databases, Constraints Satisfaction and Combinatorial Optimization, among other.

As a full declarative paradigm, instead of telling a computer how to solve the problem, with ASP one defines what the problem is and leaves its solution to the solver. ASP solvers offer highly efficient inference engines based on Boolean constraint solving technology and can solve hard combinatorial search problems. They can handle complex preferences and multi-criteria optimization guaranteeing the global optimum by reasoning over the complete space of solutions.

We use the ASP grounder gringo which offers native language constructs for applying the guess and check methodology making the problem representation very intuitive and compact. We also use the solver clasp which has proven to be a highly efficient solver compared to the state-of-the-art ASP and SAT solvers. Both belongs to Potassco, the Potsdam Answer Set Solving Collection.

Our aim is to make available the power of ASP for non-expert users from the field of Systems Biology. Towards this end, we have implemented a collection of python applications which encapsulate both, Potassco tools (grounder and solver) and specific ASP encodings for solving several combinatorial search and optimization problems in Systems Biology.

For more details on our software packages and biological applications, visit the section Software & Biological applications. For references publications on ASP applied to System Biology, visit the section References.

For any further information, contact us sending an email to: asp4bio {{at}}