title: Modeling the topological organization of cellular processes.
abstract: The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes.
authors.affiliation: LaMI u.m.r. 8042 du CNRS, Université d'Evry Val d'Essone-GENOPOLE, Tour Evry-2, 523 Place des Terasses de l'Agora, 91000 Evry, France. giavitto@lami.univ-evry.fr
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Giavitto
authors.forename: Olivier
authors.initials: O
authors.lastname: Michel
mesh_terms: D000465:Algorithms; D002450:Cell Communication / Q000502:physiology*; D002455:Cell Division; D002462:Cell Membrane / Q000502:physiology*; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D039301:Computers, Molecular; D003205:Computing Methodologies; D004777:Environment; D005110:Extracellular Space / Q000502:physiology; D016247:Information Storage and Retrieval / Q000379:methods; D017136:Ion Transport / Q000502:physiology; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D017711:Nonlinear Dynamics; D011381:Programming Languages; D009626:Terminology as Topic