Rule-based programming for integrative biological modeling | Zendy

Olivier Michel | Zendy; Antoine Spicher | Zendy; JeanLouis Giavitto | Zendy

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Rule-based programming for integrative biological modeling

Author(s) -

Olivier Michel,

Antoine Spicher,

JeanLouis Giavitto

Publication year - 2008

Publication title -

natural computing

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.413

H-Index - 40

eISSN - 1572-9796

pISSN - 1567-7818

DOI - 10.1007/s11047-008-9105-9

Subject(s) - computer science , theory of computation , modelling biological systems , theoretical computer science , systems biology , domain (mathematical analysis) , process (computing) , field (mathematics) , context (archaeology) , complex system , simple (philosophy) , artificial intelligence , programming language , computational biology , mathematics , biology , mathematical analysis , paleontology , philosophy , epistemology , pure mathematics

International audienceSystems 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

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