Exact Stochastic Sşmulation Algorithms and Impulses in Biological Systems

Abstract

The stochastic model is the only sort of expressions which can capture the randomness of biological systems under different reactions. There are mainly three methods;  Gillespie, first reaction and next reaction algorithms; for implementing exact stochastic simulations in these systems. Although these algorithms are successful in explaining the natural behaviors of the systems’ activation, they cannot describe the absurd changes, i.e.,  impulses. Moreover, the source codes in R are not available and open for all users. In this study, we produce these R codes and insert two major scenarios inside. In the application, we use distinct dimensional systems and compare their computational demands.

Keywords

• Stochastic simulations,Impulses,Chemical master equations,Biological systems,Bioinformatics

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