BIOINFORMATICS Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit

Motivation: In biological systems formed by living cells, the small populations of some reactant species can result in inherent randomness which cannot be captured by traditional deterministic approaches. In that case, a more accurate simulation can be obtained by using the Stochastic Simulation Algorithm (SSA). Many stochastic realizations are required to capture accurate statistical information of the solution. This carries a very high computational cost. The current generation of graphics processing units (GPU) is well-suited to this task. Results: We describe our implementation, and present some computational experiments illustrating the power of this technology for this important and challenging class of problems. Contact