Cargando…
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...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1782324308207468544 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4082904 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT cazzanigapaolo massiveexplorationofperturbedconditionsofthebloodcoagulationcascadethroughgpuparallelization AT nobilemarcos massiveexplorationofperturbedconditionsofthebloodcoagulationcascadethroughgpuparallelization AT besozzidaniela massiveexplorationofperturbedconditionsofthebloodcoagulationcascadethroughgpuparallelization AT bellinimatteo massiveexplorationofperturbedconditionsofthebloodcoagulationcascadethroughgpuparallelization AT maurigiancarlo massiveexplorationofperturbedconditionsofthebloodcoagulationcascadethroughgpuparallelization |