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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Yoshimi, M. Osana, Y. Iwaoka, Y. Nishikawa, Y. Kojima, T. Funahashi, A. Hiroi, N. Shibata, Y. Iwanaga, N. Kitano, H. Amano, H. |
| Copyright Year | 2006 |
| Description | Author affiliation: Keio Univ., Yokohama (Yoshimi, M.; Osana, Y.; Iwaoka, Y.; Nishikawa, Y.; Kojima, T.) |
| Abstract | 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 |
| Starting Page | 1 |
| Ending Page | 6 |
| File Size | 173704 |
| Page Count | 6 |
| File Format | |
| ISBN | 142440312X |
| DOI | 10.1109/FPL.2006.311218 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2006-08-28 |
| Publisher Place | Spain |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Field programmable gate arrays Throughput Stochastic systems Large-scale systems Computational modeling Circuit simulation Costs Stochastic processes Biology computing Symbiosis |
| Content Type | Text |
| Resource Type | Article |
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