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

Authors: Vo Hong Thanh; Roberto Zunino; Corrado Priami

Addresses: The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy ' Department of Mathematics, University of Trento, Trento, Italy ' Department of Mathematics, University of Trento, Italy; The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy

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.

Keywords: computational biology; rejection-based stochastic simulation algorithm; stochastic simulation.

DOI: 10.1504/IJBRA.2019.099573

International Journal of Bioinformatics Research and Applications, 2019 Vol.15 No.2, pp.159 - 173

Received: 03 Sep 2016
Accepted: 19 Dec 2016
Published online: 13 May 2019 *

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