Name
Title | ||
|---|---|---|
Practical implementation of a network-based stochastic biochemical simulation system on an FPGA |
Abstract | ||
|---|---|---|
Stochastic simulation of biochemical reaction networks are widely focused by life scientists to represent stochastic behaviors in cellular processes. Stochastic algorithm has loop-and thread-level parallelism, and it is suitable for running on application specific hardware to achieve high performance with low cost. We have implemented and evaluated the FPGA-based stochastic simulator according to theoretical research of the algorithm. This paper introduces an improved architecture for accelerating a stochastic simulation algorithm called the Next Reaction Method. This new architecture has scalability to various size of FPGA. As the result with a middle-range FPGA, 5.38 times higher throughput was obtained compared to software running on a Core 2 Quad Q6600 2.40 GHz. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1109/FPL.2008.4630034 | Heidelberg |
Keywords | Field | DocType |
biochemistry,chemistry computing,field programmable gate arrays,stochastic processes,FPGA,network-based stochastic biochemical simulation system,next reaction method,stochastic algorithm | Stochastic simulation,Application specific,Simulation system,Computer science,Stochastic process,Field-programmable gate array,Real-time computing,Software,Throughput,Scalability | Conference |
ISSN | ISBN | Citations |
1946-1488 | 978-1-4244-1961-6 | 2 |
PageRank | References | Authors |
0.44 | 5 | 9 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Masato Yoshimi | 1 | 106 | 22.49 |
| Yuri Nishikawa | 2 | 20 | 5.16 |
| Yasunori Osana | 3 | 92 | 18.24 |
| Akira Funahashi | 4 | 264 | 20.32 |
| Yuichiro Shibata | 5 | 157 | 37.99 |
| Hideki Yamada | 6 | 20 | 3.81 |
| Noriko Hiroi1 | 7 | 42 | 7.11 |
| Hiroaki Kitano | 8 | 3515 | 539.37 |
| Hideharu Amano | 9 | 1375 | 210.21 |