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Rule-based programming for integrative biological modeling

Rule-based programming for integrative biological modeling 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 λ 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Natural Computing Springer Journals

Rule-based programming for integrative biological modeling

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References (51)

Publisher
Springer Journals
Copyright
Copyright © 2008 by Springer Science+Business Media B.V.
Subject
Computer Science; Statistical Physics, Dynamical Systems and Complexity; Artificial Intelligence (incl. Robotics); Processor Architectures; Evolutionary Biology; Theory of Computation
ISSN
1567-7818
eISSN
1572-9796
DOI
10.1007/s11047-008-9105-9
Publisher site
See Article on Publisher Site

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 λ 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.

Journal

Natural ComputingSpringer Journals

Published: Nov 12, 2008

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