RSSA: a Rejection-based Stochastic Simulation Algorithm

Vo, Hong Thanh and Roberto, Zunino (2013) RSSA: a Rejection-based Stochastic Simulation Algorithm. [Other] (Unpublished)

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    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.

    Item Type: Other
    Department or Research center: Information Engineering and Computer Science
    Subjects: Q Science > QA Mathematics > QA075 Electronic computers. Computer science
    Uncontrolled Keywords: Stochastic simulation, Rejection-based SSA, RSSA, Systems biology
    Repository staff approval on: 18 Jun 2013 16:34

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