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Parallel biological in silico simulation

Patrick Amar 1, 2 Muriel Baillieul 3 Dominique Barth 3 Bertrand Lecun 3 Franck Quessette 3 Sandrine Vial 3 
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : It is crucial to understand how biological systems work, in particular the metabolic pathways, if we want to be able to understand diseases. For instance, why and how the apoptosis mechanisms are disturbed in some cancers. One of the author has developed HSIM, a simulator dedicated to the biochemical simulation of the reactions inside the compartments of a virtual cell. Another author is the leader in the development of BOBPP a high level parallelization framework. In this article, we propose an important improvement of BOBPP in order to run HSIM in parallel. This will allow us to simulate more complex models, involving more chemical species and reactions, leading to more realistic results using a smaller amount of computing time.
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Submitted on : Wednesday, November 26, 2014 - 4:43:49 PM
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Patrick Amar, Muriel Baillieul, Dominique Barth, Bertrand Lecun, Franck Quessette, et al.. Parallel biological in silico simulation. 29th Intenational Symposium on Computer and Information Sciences, Oct 2014, Krakow, Poland. pp.387-394, ⟨10.1007/978-3-319-09465-6_40⟩. ⟨hal-01087811⟩



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