Logical Modelling of Inhibition and Competition in Biochemical Networks

This paper applies the logic-based formalism of Answer Set Programming (ASP) to the modelling of competition, inhibition and cycles in biochemical networks. In particular, it introduces a generic framework that unifies the competitive and inhibitory mechanisms proposed in the literature along with their complementary approaches to reasoning about loops. We show how the nonmonotonic effects of competition and inhibition can be naturally encoded in the formalism of ASP and that the different ways of handling loops correspond to the computation of stable and supported models. We also show that inhibitory models are currently more general than competitive models and we argue that that both interpretations of loops are justified in some applications.