The rejection-based stochastic simulation algorithm (RSSA) is an exact simulation for realising temporal behaviour of biochemical reactions. It reduces the number of propensity updates during the simulation by using propensity bounds of reactions to select the next reaction firing. We present in this paper a new efficient formulation of RSSA and extend it for incorporating biochemical reactions with time delays. Our new algorithm explicitly keeps track of the putative firing times of reactions and uses these to select the next reaction firing. By using such a representation, it can efficiently handle biochemical reactions with delays and achieve computational efficiency over existing approaches for exact simulation.

Efficient formulation of the rejection-based algorithm for biochemical reactions with delays / Thanh, V. H.; Zunino, R.; Priami, C.. - In: INTERNATIONAL JOURNAL OF BIOINFORMATICS RESEARCH AND APPLICATIONS. - ISSN 1744-5493. - 15:2(2019), pp. 159-173. [10.1504/IJBRA.2019.099573]

Efficient formulation of the rejection-based algorithm for biochemical reactions with delays

Zunino R.;
2019-01-01

Abstract

The rejection-based stochastic simulation algorithm (RSSA) is an exact simulation for realising temporal behaviour of biochemical reactions. It reduces the number of propensity updates during the simulation by using propensity bounds of reactions to select the next reaction firing. We present in this paper a new efficient formulation of RSSA and extend it for incorporating biochemical reactions with time delays. Our new algorithm explicitly keeps track of the putative firing times of reactions and uses these to select the next reaction firing. By using such a representation, it can efficiently handle biochemical reactions with delays and achieve computational efficiency over existing approaches for exact simulation.
2019
2
Thanh, V. H.; Zunino, R.; Priami, C.
Efficient formulation of the rejection-based algorithm for biochemical reactions with delays / Thanh, V. H.; Zunino, R.; Priami, C.. - In: INTERNATIONAL JOURNAL OF BIOINFORMATICS RESEARCH AND APPLICATIONS. - ISSN 1744-5493. - 15:2(2019), pp. 159-173. [10.1504/IJBRA.2019.099573]
File in questo prodotto:
File Dimensione Formato  
publisher version - IJBRA 15(2) Paper 5.pdf

Solo gestori archivio

Tipologia: Versione editoriale (Publisher’s layout)
Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 251.54 kB
Formato Adobe PDF
251.54 kB Adobe PDF   Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/239372
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 0
  • ???jsp.display-item.citation.isi??? ND
social impact