Modeling Protein Interaction Networks with Answer Set Programming

In this paper we propose the use of answer set programming (ASP) to model protein interaction networks. We argue that this declarative formalism rivals the popular boolean networks in terms of ease of use, while at the same time being more expressive. As we demonstrate for the particular case of a fission yeast network, all information present in a boolean network, as well as relevant background assumptions,can be expressed explicitly in an answer set program. Moreover, readily available answer set solvers can then be used to find the stable states of the network.