Rule-based programming for integrative biological modeling Application to the modeling of the λ phage genetic switch

Olivier Michel; Antoine Spicher; Jean-Louis Giavitto

doi:10.1007/s11047-008-9105-9

Rule-based programming for integrative biological modeling Application to the modeling of the λ phage genetic switch

Olivier Michel ^{1, *} Antoine Spicher ¹ Jean-Louis Giavitto ²

* Corresponding author

1 LACL - Laboratoire d'Algorithmique Complexité et Logique

2 COSMO

IBISC - Informatique, Biologie Intégrative et Systèmes Complexes

Abstract : Systems biology aims at integrating processes at various time and spatial scales into a single and coherent formal description to allow computer modeling. In this context, we focus on rule-based modeling and its integration in the domain-specific language MGS. Through the notions of topological collections and transformations, MGS allows the modeling of biological processes at various levels of description. We validate our approach through the description of various models of the genetic switch of the lambda phage, from a very simple biochemical description of the process to an individual-based model on a Delaunay graph topology. This approach is a first step into providing the requirements for the emerging field of spatial systems biology which integrates spatial properties into systems biology.

Keywords : Domain-specific languages Rule-based modeling Spatial systems biology

Document type :

Journal articles

Domain :

Computer Science [cs] / Logic in Computer Science [cs.LO]

Computer Science [cs] / Computation and Language [cs.CL]

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