Parallel stochastic simulation using graphics processing units for the Systems Biology Toolbox for MATLAB

This document briefly introduces parallel computations on graphics processing units (GPUs) and the implemented exact stochastic simulation algorithms (i) the stochastic simulation algorithm (SSA) byGillespie [5], (ii) the logarithmic direct method (LDM) by Li and Petzold [10] and (iii) the next reaction method of Gibson and Bruck [3]. The LDM and NRM are more efficient reformulations of the SSA. Section 1 briefly introduces the application of GPUs to general purpose computation. Section 2 motivates the stochastic simulation of well-mixed chemical reaction systems and introduces the implemented simulation algorithms. Section 3 provides details on the threading approach taken and section 4 on the sampling regimes used. Section 5 lists the features and limitations of our stochastic simulation MATLAB plugin. Section 6 lists the hardware and software used.