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Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico a...

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Detalles Bibliográficos
Autores principales: Cazzaniga, Paolo, Nobile, Marco S., Besozzi, Daniela, Bellini, Matteo, Mauri, Giancarlo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082904/
https://www.ncbi.nlm.nih.gov/pubmed/25025072
http://dx.doi.org/10.1155/2014/863298
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author Cazzaniga, Paolo
Nobile, Marco S.
Besozzi, Daniela
Bellini, Matteo
Mauri, Giancarlo
author_facet Cazzaniga, Paolo
Nobile, Marco S.
Besozzi, Daniela
Bellini, Matteo
Mauri, Giancarlo
author_sort Cazzaniga, Paolo
collection PubMed
description The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.
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spelling pubmed-40829042014-07-14 Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization Cazzaniga, Paolo Nobile, Marco S. Besozzi, Daniela Bellini, Matteo Mauri, Giancarlo Biomed Res Int Research Article The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations. Hindawi Publishing Corporation 2014 2014-06-16 /pmc/articles/PMC4082904/ /pubmed/25025072 http://dx.doi.org/10.1155/2014/863298 Text en Copyright © 2014 Paolo Cazzaniga et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Cazzaniga, Paolo
Nobile, Marco S.
Besozzi, Daniela
Bellini, Matteo
Mauri, Giancarlo
Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title_full Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title_fullStr Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title_full_unstemmed Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title_short Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
title_sort massive exploration of perturbed conditions of the blood coagulation cascade through gpu parallelization
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082904/
https://www.ncbi.nlm.nih.gov/pubmed/25025072
http://dx.doi.org/10.1155/2014/863298
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