Simulation and Analysis of the Blood Coagulation Cascade Accelerated on GPU

Author

Bellini, M. ; Besozzi, D. ; Cazzaniga, P. ; Mauri, G. ; Nobile, M.S.

Author_Institution

Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy

fYear

2014

fDate

12-14 Feb. 2014

Firstpage

590

Lastpage

593

Abstract

The use of Graphics Processing Units (GPUs) has recently witnessed ever growing applications for different computational analyses in the field of Life Sciences. In this work we present a CUDA-powered computational tool, named coagSODA, that was purposely developed and applied for the analysis of a large model of the blood coagulation cascade defined as a system of ordinary differential equations, based on both mass-action kinetics and Hill functions. We discuss the biological results of the parameter sweep analyses of this model, and show that GPUs can boost the computational performances up to 177x speedup.

Keywords

biology computing; graphics processing units; parallel architectures; CUDA-powered computational tool; GPU; Hill functions; blood coagulation cascade; coagSODA; graphics processing units; mass-action kinetics; Analytical models; Biological system modeling; Coagulation; Computational modeling; Graphics processing units; Mathematical model; Blood Coagulation Cascade; GPGPU computing; LSODA; Parameter Sweep Analysis;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel, Distributed and Network-Based Processing (PDP), 2014 22nd Euromicro International Conference on

Conference_Location

Torino

ISSN

1066-6192

Type

conf

DOI

10.1109/PDP.2014.52

Filename

6787335