In this study we propose an improvement for the stochastic simulation algorithm (SSA), a standard method to properly realize the stochastic nature of biochemical reactions. Our algorithm is named {\em RSSA} after ``rejection-based SSA'', and is tailored for the efficient simulation of large models, which is typically done to understand the complex behavior of regulatory systems. The large models are highly coupled, and full of interconnection and feedback loops. In addition, in these models a compex propensity function is often used to express the stochastic rate of biochemical reactions. Evaluating and updating the reaction propensities is therefore rather computationally expensive. RSSA reduces this computational burden by postponing the full update and only computing the propensity as needed. We experiment with our algorithm on concrete biological models to demonstrate its efficiency.

RSSA: a Rejection-based Stochastic Simulation Algorithm / Vo Hong, Thanh; Zunino, Roberto. - ELETTRONICO. - (2013), pp. 1-22.

RSSA: a Rejection-based Stochastic Simulation Algorithm

Vo, Hong Thanh
Primo
;
Roberto, Zunino
Ultimo
2013-01-01

Abstract

In this study we propose an improvement for the stochastic simulation algorithm (SSA), a standard method to properly realize the stochastic nature of biochemical reactions. Our algorithm is named {\em RSSA} after ``rejection-based SSA'', and is tailored for the efficient simulation of large models, which is typically done to understand the complex behavior of regulatory systems. The large models are highly coupled, and full of interconnection and feedback loops. In addition, in these models a compex propensity function is often used to express the stochastic rate of biochemical reactions. Evaluating and updating the reaction propensities is therefore rather computationally expensive. RSSA reduces this computational burden by postponing the full update and only computing the propensity as needed. We experiment with our algorithm on concrete biological models to demonstrate its efficiency.
2013
Trento
Università degli Studi di Trento, Dipartimento di Ingegneria e Scienza dell'Informazione
RSSA: a Rejection-based Stochastic Simulation Algorithm / Vo Hong, Thanh; Zunino, Roberto. - ELETTRONICO. - (2013), pp. 1-22.
Vo Hong, Thanh; Zunino, Roberto
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/358987
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