Abstract
It is crucial to understand how biological systems work, in particular the metabolic pathways, if we want to be able to understand diseases. 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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Notes
- 1.
This software is freely available at http://www.lri.fr/~pa/Hsim.
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Acknowledgments
This work was partially supported by grant ANR MARMOTE (ANR-12-MONU-0019).
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Amar, P., Baillieul, M., Barth, D., LeCun, B., Quessette, F., Vial, S. (2014). Parallel Biological In Silico Simulation. In: Czachórski, T., Gelenbe, E., Lent, R. (eds) Information Sciences and Systems 2014. Springer, Cham. https://doi.org/10.1007/978-3-319-09465-6_40
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DOI: https://doi.org/10.1007/978-3-319-09465-6_40
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