[en] [en] BACKGROUND: Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In particular, Boolean models are well fit to describe the complexity of signaling networks while being simple enough to scale to a very large number of components. With the advance of Boolean model inference techniques, the field is transforming from an artisanal way of building models of moderate size to a more automatized one, leading to very large models. In this context, adapting the simulation software for such increases in complexity is crucial.
RESULTS: We present two new developments in the continuous time Boolean simulators: MaBoSS.MPI, a parallel implementation of MaBoSS which can exploit the computational power of very large CPU clusters, and MaBoSS.GPU, which can use GPU accelerators to perform these simulations.
CONCLUSION: These implementations enable simulation and exploration of the behavior of very large models, thus becoming a valuable analysis tool for the systems biology community.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Biotechnology Computer science
Author, co-author :
Šmelko, Adam; Department of Distributed and Dependable Systems, Charles University, Prague, Czech Republic
KRATOCHVIL, Miroslav ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Barillot, Emmanuel; Institut Curie, Université PSL, 75005, Paris, France ; INSERM, U900, 75005, Paris, France ; Mines ParisTech, Université PSL, 75005, Paris, France
Noël, Vincent; Institut Curie, Université PSL, 75005, Paris, France. vincent.noel@curie.fr ; INSERM, U900, 75005, Paris, France. vincent.noel@curie.fr ; Mines ParisTech, Université PSL, 75005, Paris, France. vincent.noel@curie.fr
External co-authors :
yes
Language :
English
Title :
Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.
H2020 - 951773 - PerMedCoE - HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE
Funders :
Horizon 2020 Framework Programme Charles University, SSV European Union
Funding text :
The research leading to these results has received funding from the European Union\u2019s Horizon 2020 Programme under the PerMedCoE Project ( http://www.permedcoe.eu ), grant agreement n 951773. The project was partially supported by Charles University, SVV project number 260698.
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