FPGA-based Stochastic Biochemical Simulator
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Accession number;07A0176826
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| Title;FPGA-based Stochastic Biochemical Simulator |
| Author;
YOSHIMI MASATO
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
OSANA YASUNORI
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
IWAOKA YO
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
NISHIKAWA YURI
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
KOJIMA TOSHINORI
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
SHIBATA YUICHIRO
(Nagasaki Univ., Fac. of Eng.)
IWANAGA NAOKI
(Nagasaki Univ., Fac. of Eng.)
FUNAHASHI AKIRA
(Jst-erato-sorst)
HIROI NORIKO
(Jst-erato-sorst)
KITANO HIROAKI
(Jst-erato-sorst)
AMANO HIDEHARU
(Keio Univ., Graduate School of Sci. and Tedhnol., JPN)
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Journal Title;IPSJ Transactions on Database
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Journal Code:Z0778A
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ISSN:0387-5806
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VOL.48;NO.SIG3(ACS17);PAGE.45-58(2007)
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| Figure&Table&Reference;FIG.16, TBL.5, REF.24 |
| Pub. Country;Japan |
| Language;Japanese |
| Abstract;This paper discusses an FPGA implementation and evaluation of a Stochastic Simulation Algorithm (SSA) called the First Reaction Method. SSAs are widely known as rigorous methods for simulating the stochastic behaviors of various biochemical systems, but also as CPU-hogging applications due to vast repetition of the algorithm. This work accelerates the execution by achieving high throughput with concurrent simulations of highly utilized pipelined arithmetic units. For upgrading practical utility, the design stores intermediate data in a BlockRAM so that reconfiguration is unnecessary for different target biochemical systems. Benchmark results on an FPGA (Xilinx XC2VP70-5) have shown that the circuit provides throughput of approximately 83 times and 95 times compared to software execution on Xeon 2.80 GHz when it was evaluated with biochemical models called TIS and D4S, respectively. (author abst.) |
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