Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
Joint Authors
Nobile, Marco S.
Cazzaniga, Paolo
Bellini, Matteo
Mauri, Giancarlo
Besozzi, Daniela
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-20, 20 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-15
Country of Publication
Egypt
No. of Pages
20
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Cazzaniga, Paolo& Nobile, Marco S.& Besozzi, Daniela& Bellini, Matteo& Mauri, Giancarlo. 2014. Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization. BioMed Research International،Vol. 2014, no. 2014, pp.1-20.
https://search.emarefa.net/detail/BIM-504376
Modern Language Association (MLA)
Cazzaniga, Paolo…[et al.]. Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization. BioMed Research International No. 2014 (2014), pp.1-20.
https://search.emarefa.net/detail/BIM-504376
American Medical Association (AMA)
Cazzaniga, Paolo& Nobile, Marco S.& Besozzi, Daniela& Bellini, Matteo& Mauri, Giancarlo. Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-20.
https://search.emarefa.net/detail/BIM-504376
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-504376