Parallel stochastic simulation using graphics processing units for the Systems Biology Toolbox for MATLAB
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Tue, 04/05/2010 13:15 |
Guido Klingbeil (Oxford) |
Junior Applied Mathematics Seminar  |
DH 1st floor SR |
| 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. | |||