Integrated Regulatory Networks (IRNs): Spatially organized biochemical modules

Jean-Louis Giavitto (1, 2) , Hanna Klaudel (3) , Franck Pommereau (3)

1 Repmus - Représentations musicales
2 MuTant - Synchronous Realtime Processing and Programming of Music Signals
3 IBISC - Informatique, Biologie Intégrative et Systèmes Complexes

In this paper, we aim at modeling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modeling frame- work is a generalization of several existing formalisms. In particular, it can be seen as an extension of logical regulatory networks ('a la Thomas) with information about cells physical state and environment, e.g., their spatial re- lationships. 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.

Keywords: Logical regulatory networks; Topological collections; Enumerable state space; Spatial modeling; Systems biology

Domains: Formal Languages and Automata Theory [cs.FL]; Modeling and Simulation; Bioinformatics [q-bio.QM]; Quantitative Methods [q-bio.QM]; Programming Languages [cs.PL]

Jean-Louis Giavitto, Hanna Klaudel, Franck Pommereau. Integrated Regulatory Networks (IRNs): Spatially organized biochemical modules. Theoretical Computer Science, 2012, 431, pp.219--234. ⟨10.1016/j.tcs.2011.12.054⟩. ⟨hal-00769275⟩