Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. (Articolo in rivista)

Type
Label
  • Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. (Articolo in rivista) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1155/2014/863298 (literal)
Alternative label
  • 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.
    in BioMed Research International [electronic resource]
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Cazzaniga, Paolo; Nobile, Marco S; Besozzi, Daniela; Bellini, Matteo; Mauri, Giancarlo (literal)
Pagina inizio
  • 863298 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 2014 (literal)
Rivista
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Dipartimento di Scienze Umane e Sociali, Università degli Studi di Bergamo, Italy; SYSBIO Centre for Systems Biology, Milano, Italy; Istituto di Analisi dei Sistemi ed Informatica \"Antonio Ruberti\", Consiglio Nazionale delle Ricerche, Roma, Italy; Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, Milano, Italy; Università degli Studi di Milano, Dipartimento di Informatica, Milano, Italy (literal)
Titolo
  • Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. (literal)
Abstract
  • 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. (literal)
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