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

4 May 2010
13:15
Guido Klingbeil
Abstract
Graphics processing units (GPU) are well suited to decrease the computational in- tensity of stochastic simulation of chemical reaction systems. We compare Gillespie’s Direct Method and Gibson-Bruck’s Next Reaction Method on GPUs. The gain of the GPU implementation of these algorithms is approximately 120 times faster than on a CPU. Furthermore our implementation is integrated into the Systems Biology Toolbox for Matlab and acts as a direct replacement of its Matlab based implementation.
  • Junior Applied Mathematics Seminar