TY - GEN
T1 - The design of scalable stochastic biochemical simulator on FPGA
AU - Yoshimi, Masato
AU - Osana, Yasunori
AU - Iwaoka, Yow
AU - Funahashi, Akira
AU - Hiroi, Noriko
AU - Shibata, Yuichiro
AU - Iwanaga, Naoki
AU - Kitano, Hiroaki
AU - Amano, Hideharu
PY - 2005
Y1 - 2005
N2 - Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO, As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40GHz by 17.1 times.
AB - Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO, As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40GHz by 17.1 times.
UR - http://www.scopus.com/inward/record.url?scp=33846618770&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33846618770&partnerID=8YFLogxK
U2 - 10.1109/FPT.2005.1568590
DO - 10.1109/FPT.2005.1568590
M3 - Conference contribution
AN - SCOPUS:33846618770
SN - 0780394070
SN - 9780780394070
T3 - Proceedings - 2005 IEEE International Conference on Field Programmable Technology
SP - 339
EP - 340
BT - Proceedings - 2005 IEEE International Conference on Field Programmable Technology
T2 - 2005 IEEE International Conference on Field Programmable Technology
Y2 - 11 December 2005 through 14 December 2005
ER -