GPU-accelerated simulations of mass-action kinetics models with cupSODA (Articolo in rivista)

Type
Label
  • GPU-accelerated simulations of mass-action kinetics models with cupSODA (Articolo in rivista) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1007/s11227-014-1208-8 (literal)
Alternative label
  • Nobile, Marco S.; Cazzaniga, Paolo; Besozzi, Daniela; Mauri, Giancarlo (2014)
    GPU-accelerated simulations of mass-action kinetics models with cupSODA
    in Journal of supercomputing
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Nobile, Marco S.; Cazzaniga, Paolo; Besozzi, Daniela; Mauri, Giancarlo (literal)
Pagina inizio
  • 17 (literal)
Pagina fine
  • 24 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 69 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali
  • 8 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 1 (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • University of Milano-Bicocca; University of Bergamo; Istituto di Analisi dei Sistemi ed Informatica \"Antonio Ruberti\", Consiglio Nazionale delle Ricerche, Roma; University of Milan; SYSBIO Ctr Syst Biol (literal)
Titolo
  • GPU-accelerated simulations of mass-action kinetics models with cupSODA (literal)
Abstract
  • In the last years, graphics processing units (GPUs) witnessed ever growing applications for a wide range of computational analyses in the field of life sciences. Despite its large potentiality, GPU computing risks remaining a niche for specialists, due to the programming and optimization skills it requires. In this work we present cupSODA, a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA. We show that cupSODA can achieve a speedup on GPUs with respect to equivalent executions of LSODA on the CPU. (literal)
Prodotto di
Insieme di parole chiave

Incoming links:


Prodotto
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#rivistaDi
Autore CNR di
Insieme di parole chiave di
data.CNR.it