| Presentation | 2007-05-17 Automatic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP Hideki YAMADA, Naoki IWANAGA, Yuichiro SHIBATA, Yasunori OSANA, Masato YOSHIMI, Yow IWAOKA, Yuri NISHIKAWA, Toshinori KOJIMA, Hideharu AMANO, Akira FUNAHASHI, Noriko HIROI, Hiroaki KITANO, Kiyoshi OGURI, |
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| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources is essential. This paper proposes a method which combines a common terms in rate law functions appeared in biochemical models to generate a shared hardware module used for numerical integration in a reconfigurable biochemical simulator. In this approach, two functions are combined in a tree structure level followed by pipeline scheduling and arithmetic module binding. The evaluation results reveals that this combining approach reduces hardware costs by 31.36 % on average at the cost of 14.4 % throughput degradation. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | biochemical simulation / arithmetic scheduling / rate law function / FPGA |
| Paper # | RECONF2007-3 |
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| Conference Information | |
| Committee | RECONF |
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| Conference Date | 2007/5/10(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Paper Information | |
| Registration To | Reconfigurable Systems (RECONF) |
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| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Automatic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP |
| Sub Title (in English) | |
| Keyword(1) | biochemical simulation |
| Keyword(2) | arithmetic scheduling |
| Keyword(3) | rate law function |
| Keyword(4) | FPGA |
| 1st Author's Name | Hideki YAMADA |
| 1st Author's Affiliation | Faculty of Engineering, Nagasaki University() |
| 2nd Author's Name | Naoki IWANAGA |
| 2nd Author's Affiliation | Faculty of Engineering, Nagasaki University |
| 3rd Author's Name | Yuichiro SHIBATA |
| 3rd Author's Affiliation | Faculty of Engineering, Nagasaki University |
| 4th Author's Name | Yasunori OSANA |
| 4th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 5th Author's Name | Masato YOSHIMI |
| 5th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 6th Author's Name | Yow IWAOKA |
| 6th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 7th Author's Name | Yuri NISHIKAWA |
| 7th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 8th Author's Name | Toshinori KOJIMA |
| 8th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 9th Author's Name | Hideharu AMANO |
| 9th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 10th Author's Name | Akira FUNAHASHI |
| 10th Author's Affiliation | Faculty of Science and Technology, Keio University |
| 11th Author's Name | Noriko HIROI |
| 11th Author's Affiliation | EMBL-EBI, Thornton group |
| 12th Author's Name | Hiroaki KITANO |
| 12th Author's Affiliation | Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency |
| 13th Author's Name | Kiyoshi OGURI |
| 13th Author's Affiliation | Faculty of Engineering, Nagasaki University |
| Date | 2007-05-17 |
| Paper # | RECONF2007-3 |
| Volume (vol) | vol.107 |
| Number (no) | 41 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |