| Presentation | 2006-01-18 A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP Yuri NISHIKAWA, Yasunori OSANA, Masato YOSHIMI, Yow IWAOKA, Toshinori KOJIMA, Akira FUNAHASHI, Noriko HIROI, Yuichiro SHIBATA, Naoki IWANAGA, Hiroaki KITANO, Hideharu AMANO, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | Computational simulation is a highly effective solution for cellular analyses in recent bioinformatics. As the scale of analysis objects are rapidly expanding, however, it is a prime task to develop a simulator with high throughput. ReCSiP, an FPGA-based biochemical simulator, is being exploited for this necessity. Further speed-up of the simulator is enhanced with an improvement of its pipelining efficiency, by a parallel operation of a rate-law solver module and a numerical integration module. This research report discusses the methodology of enhancing the performance of ReCSiP, its implementation and the evaluation result. Speed-up of 1.96x in maximum is achieved with an area increase of 29% compared to the conventional implementation. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | Biochemical simulator / Numerical integration / Euler's Method / Pipelining efficiency / FPGA |
| Paper # | VLD2005-106,CPSY2005-62,RECONF2005-95 |
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| Conference Information | |
| Committee | CPSY |
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| Conference Date | 2006/1/11(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Paper Information | |
| Registration To | Computer Systems (CPSY) |
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| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP |
| Sub Title (in English) | |
| Keyword(1) | Biochemical simulator |
| Keyword(2) | Numerical integration |
| Keyword(3) | Euler's Method |
| Keyword(4) | Pipelining efficiency |
| Keyword(5) | FPGA |
| 1st Author's Name | Yuri NISHIKAWA |
| 1st Author's Affiliation | Faculty of Science and Technology, Keio University() |
| 2nd Author's Name | Yasunori OSANA |
| 2nd Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 3rd Author's Name | Masato YOSHIMI |
| 3rd Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 4th Author's Name | Yow IWAOKA |
| 4th Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 5th Author's Name | Toshinori KOJIMA |
| 5th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 6th Author's Name | Akira FUNAHASHI |
| 6th Author's Affiliation | Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency |
| 7th Author's Name | Noriko HIROI |
| 7th Author's Affiliation | Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency |
| 8th Author's Name | Yuichiro SHIBATA |
| 8th Author's Affiliation | Dept. of Computer and Information Sciences, Nagasaki University |
| 9th Author's Name | Naoki IWANAGA |
| 9th Author's Affiliation | Dept. of Computer and Information Sciences, Nagasaki University |
| 10th Author's Name | Hiroaki KITANO |
| 10th Author's Affiliation | Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency |
| 11th Author's Name | Hideharu AMANO |
| 11th Author's Affiliation | Graduate School of Science and Technology, Keio University |
| Date | 2006-01-18 |
| Paper # | VLD2005-106,CPSY2005-62,RECONF2005-95 |
| Volume (vol) | vol.105 |
| Number (no) | 516 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |