title: Automatic search for model to simulate the differentiation of T lymphocytes within the thymus.
abstract: The differentiation of T Lymphocytes within the thymus is an important biological phenomenon during which these cell acquire their functions to further control the immune system. Numerous experiments under various conditions have been devised to understand the different mechanisms involved in this complex process. Nevertheless, interpretation of these experiments lead to still contradictory debatable hypotheses. Modelisation of this process through classical simulation methods cannot be envisaged because they are not adapted to modifications of the model structure, which is the point of interest. For these reasons, we proposed a new approach of automatic search for model. The program consists of four independent connected modules: The generator produces model, based on the rationale of formal grammars. Protocol and experimental data are stored in a set of experiments. The simulator using a protocol and a model provides simulated results. Finally, the supervisor by comparing simulated results and experimental data, adapts the model parameters to increase their fit and either chooses a new experiment to explore, or modifies the model structure. Change of the model structure is performed among still unexplored models according to their "promise" level, which is iteratively evaluated relatively to previously explored models through a proposed model distance. The generator is written in Prolog and the other modules in C++. The architecture of the program allows us to modify or complete a module without changing anything in the other modules. As a consequence, the proposed modeling approach conceived to study T lymphocyte differentiation within the thymus remains independent of this biological phenomenon and can be applied to other biological problems.
authors.affiliation: INSERM U263, Centre de Bioinformatique, Université Paris, France.
authors.forename: L
authors.initials: L
authors.lastname: Buffat
authors.forename: J Y
authors.initials: JY
authors.lastname: Mary
mesh_terms: D002454:Cell Differentiation; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D013601:T-Lymphocytes / Q000166:cytology*; D013950:Thymus Gland / Q000276:immunology*