Integrated regulatory networks (IRNs): Spatially organized biochemical modules

In this paper, we aim at modeling and analyzing the regulation processes in multi-cellular biological systems, in particular, tissues. The modeling framework is a generalization of several existing formalisms. In particular, it can be seen as an extension of logical regulatory networks (à la Thomas) with information about cells’ physical state and environment, e.g., their spatial relationships. The resulting formalisms, called integrated regulatory networks (IRNs) is equipped with a transition systems semantics that preserves the possibility of an enumerative and exhaustive state space exploration. This paper presents the modeling framework, its semantics, as well as a prototype implementation that allowed preliminary experiments on some applications related to biology.