TY - GEN
T1 - A framework for implementing a network-based stochastic biochemical simulator on an FPGA
AU - Yoshimi, Masato
AU - Nishikawa, Yuri
AU - Kojima, Toshlinori
AU - Osana, Yasunori
AU - Funahashi, Akira
AU - Hiroi, Noriko
AU - Shibata, Yuichiro
AU - Yamada, Hideki
AU - Kitano, Hiroaki
AU - Amano, Hideharu
PY - 2007/12/1
Y1 - 2007/12/1
N2 - This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method, known for its large number of calculattion involved. The procedure 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. By performing a multi-threading simulation, 3.6 times speedup was obtained compared with an execution on general purpose processors.
AB - This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method, known for its large number of calculattion involved. The procedure 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. By performing a multi-threading simulation, 3.6 times speedup was obtained compared with an execution on general purpose processors.
UR - http://www.scopus.com/inward/record.url?scp=50149090656&partnerID=8YFLogxK
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U2 - 10.1109/FPT.2007.4439249
DO - 10.1109/FPT.2007.4439249
M3 - Conference contribution
AN - SCOPUS:50149090656
SN - 1424414725
SN - 9781424414727
T3 - ICFPT 2007 - International Conference on Field Programmable Technology
SP - 193
EP - 200
BT - ICFPT 2007 - International Conference on Field Programmable Technology
T2 - International Conference on Field Programmable Technology, ICFPT 2007
Y2 - 12 December 2007 through 14 December 2007
ER -