An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems

Stochastic simulation of biochemical systems has become one of major approaches to study life processes as system, yet is a computational challenge to run the simulation due to its vast calculation cost. This paper shows the implementation and evaluation of a stochastic simulation algorithm (SSA) called "first reaction method" on an FPGA-based biochemical simulator. It achieves high throughput by (1) consecutively throwing data into deeply-pipelined floating point arithmetic units, and (2) by distributing multiple simulators for parallel execution. As the result of evaluation on an FPGA-based simulation platform called ReC-SiP2, the simulator outperforms execution on Xeon 2.80 GHz by approximately 80 times, even with large-scale biochemical systems