| Presentation | 2007-11-22 Evaluation of a Data-Driven Architecture for a Stochastic Biochemical Simulator on an FPGA Masato YOSHIMI, Yuri NISHIKAWA, Toshinori KOJIMA, Yasunori OSANA, Akira FUNAHASHI, Noriko HIROI, Yuichiro SHIBATA, Hideki YAMADA, Hiroaki KITANO, Hideharu AMANO, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method. Whole procedure of the algorithm is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. Area and throughput were measured for each type of network configuration, as well as studying each cause of bottleneck. By performing a multi-threading simulation, maximum of 3.6 times speedup was obtained compared to an execution on Xeon 3.20 GHz. Although current designs did not achieve significant speedup, performance analysis study of each network configuration suggested capability of throughput enhancement. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | Data-transfer network / Data-driven / On-chip network / FPGA / Stochastic biochemical simulation |
| Paper # | RECONF2007-50 |
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| Conference Information | |
| Committee | RECONF |
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| Conference Date | 2007/11/15(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Vice Chair | |
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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) | Evaluation of a Data-Driven Architecture for a Stochastic Biochemical Simulator on an FPGA |
| Sub Title (in English) | |
| Keyword(1) | Data-transfer network |
| Keyword(2) | Data-driven |
| Keyword(3) | On-chip network |
| Keyword(4) | FPGA |
| Keyword(5) | Stochastic biochemical simulation |
| 1st Author's Name | Masato YOSHIMI |
| 1st Author's Affiliation | Graduate School of Science and Technology, Keio University() |
| 2nd Author's Name | Yuri NISHIKAWA |
| 2nd Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 3rd Author's Name | Toshinori KOJIMA |
| 3rd Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 4th Author's Name | Yasunori OSANA |
| 4th Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 5th Author's Name | Akira FUNAHASHI |
| 5th Author's Affiliation | Graduate School of Science and Technology, Keio University |
| 6th Author's Name | Noriko HIROI |
| 6th Author's Affiliation | EMBL-EBI, Thornton group Wellcome Trust Genome Campus |
| 7th Author's Name | Yuichiro SHIBATA |
| 7th Author's Affiliation | Dept. of Computer and Information Sciences, Nagasaki University |
| 8th Author's Name | Hideki YAMADA |
| 8th Author's Affiliation | Dept. of Computer and Information Sciences, Nagasaki University |
| 9th Author's Name | Hiroaki KITANO |
| 9th Author's Affiliation | Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency |
| 10th Author's Name | Hideharu AMANO |
| 10th Author's Affiliation | Graduate School of Science and Technology, Keio University |
| Date | 2007-11-22 |
| Paper # | RECONF2007-50 |
| Volume (vol) | vol.107 |
| Number (no) | 342 |
| Page | pp.pp.- |
| #Pages | 6 |
| Date of Issue | |