Interaction-Based Simulations for Integrative Spatial Systems Biology

Antoine Spicher (1) , Olivier Michel (1) , Jean-Louis Giavitto (2)

1 LACL - Laboratoire d'Algorithmique Complexité et Logique
2 IBISC - Informatique, Biologie Intégrative et Systèmes Complexes

Systems biology aims at integrating processes at various time and spatial scales into a single and coherent formal description to allow analysis and computer simulation. 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 a synthetic bacteria designed in the context of the iGEM competition, 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: Interaction-Based Simulations; Domain-Specific Languages; RuleBased Modeling; Integrative Spatial Systems Biology; Synthetic Biology; MGS

Domains: Bioinformatics [q-bio.QM]; Quantitative Methods [q-bio.QM]

Antoine Spicher, Olivier Michel, Jean-Louis Giavitto. Interaction-Based Simulations for Integrative Spatial Systems Biology. W. Dubitzky, J Southgate and H. Fuss. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, SpringeVerlag Berlin, Heidelberg, pp.195--231, 2011, ⟨10.1007/978-1-4419-7964-3_10⟩. ⟨hal-00645911⟩