Logo del repository
  1. Home
 
Opzioni

Efficient simulation of reaction systems on graphics processing units

Nobile Marco S.
•
Porreca Antonio E.
•
Spolaor Simone
altro
Besozzi Daniela
2017
  • journal article

Periodico
FUNDAMENTA INFORMATICAE
Abstract
Reaction systems represent a theoretical framework based on the regulation mechanisms of facilitation and inhibition of biochemical reactions. The dynamic process defined by a reaction system is typically derived by hand, starting from the set of reactions and a given context sequence. However, this procedure may be error-prone and time-consuming, especially when the size of the reaction system increases. Here we present HERESY, a simulator of reaction systems accelerated on Graphics Processing Units (GPUs). HERESY is based on a fine-grained parallelization strategy, whereby all reactions are simultaneously executed on the GPU, therefore reducing the overall running time of the simulation. HERESY is particularly advantageous for the simulation of large-scale reaction systems, consisting of hundreds or thousands of reactions. By considering as test case some reaction systems with an increasing number of reactions and entities, as well as an increasing number of entities per reaction, we show that HERESY allows up to 29× speed-up with respect to a CPU-based simulator of reaction systems. Finally, we provide some directions for the optimization of HERESY, considering minimal reaction systems in normal form.
DOI
10.3233/FI-2017-1568
WOS
WOS:000411027800022
Archivio
http://hdl.handle.net/11368/2947804
info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85027366731
https://content.iospress.com/articles/fundamenta-informaticae/fi1568
Diritti
closed access
FVG url
https://arts.units.it/request-item?handle=11368/2947804
Soggetti
  • reaction system

  • general-purpose GPU c...

  • high-performance comp...

  • simulation

Scopus© citazioni
10
Data di acquisizione
Jun 14, 2022
Vedi dettagli
Web of Science© citazioni
10
Data di acquisizione
Mar 28, 2024
Visualizzazioni
1
Data di acquisizione
Apr 19, 2024
Vedi dettagli
google-scholar
Get Involved!
  • Source Code
  • Documentation
  • Slack Channel
Make it your own

DSpace-CRIS can be extensively configured to meet your needs. Decide which information need to be collected and available with fine-grained security. Start updating the theme to match your nstitution's web identity.

Need professional help?

The original creators of DSpace-CRIS at 4Science can take your project to the next level, get in touch!

Realizzato con Software DSpace-CRIS - Estensione mantenuta e ottimizzata da 4Science

  • Impostazioni dei cookie
  • Informativa sulla privacy
  • Accordo con l'utente finale
  • Invia il tuo Feedback