TY - GEN
T1 - Performance evaluation of an FPGA-based biochemical simulator ReCSiP
AU - Osana, Yasunori
AU - Yoshimi, Masato
AU - Iwaoka, Yow
AU - Kojima, Toshinori
AU - Nishikawa, Yuri
AU - Funahashi, Akira
AU - Hiroi, Noriko
AU - Kitano, Hiroaki
AU - Amano, Hideharu
AU - Shibata, Yuichiro
AU - Iwanaga, Naoki
PY - 2006/12/1
Y1 - 2006/12/1
N2 - ReCSiP is an FPGA-based biochemical simulator to accelerate kinetic simulations of biochemical pathways. Biochemical models are described as a set of ordinary differential equations (ODEs). Each equation in the model is called "rate law function", which represents the velocity of corresponding biochemical reaction mechanism. ReCSiP achieves high-throughput simulation with statically pipelined rate law function modules and numerical integration modules on an FPGA. This paper shows the basic structure of ReCSiP, and results of evaluation in 2 aspects: area and throughput. As the summary of evaluation, 1) about 64% of the total circuit area is occupied by floating-point arithmetic units, and 2) with an XC2VP70, ReCSiP at 90MHz can achieve 20x or more speedup compared to Intel's Pentium4 microprocessor at 3.2GHz.
AB - ReCSiP is an FPGA-based biochemical simulator to accelerate kinetic simulations of biochemical pathways. Biochemical models are described as a set of ordinary differential equations (ODEs). Each equation in the model is called "rate law function", which represents the velocity of corresponding biochemical reaction mechanism. ReCSiP achieves high-throughput simulation with statically pipelined rate law function modules and numerical integration modules on an FPGA. This paper shows the basic structure of ReCSiP, and results of evaluation in 2 aspects: area and throughput. As the summary of evaluation, 1) about 64% of the total circuit area is occupied by floating-point arithmetic units, and 2) with an XC2VP70, ReCSiP at 90MHz can achieve 20x or more speedup compared to Intel's Pentium4 microprocessor at 3.2GHz.
UR - http://www.scopus.com/inward/record.url?scp=46249114938&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=46249114938&partnerID=8YFLogxK
U2 - 10.1109/FPL.2006.311327
DO - 10.1109/FPL.2006.311327
M3 - Conference contribution
AN - SCOPUS:46249114938
SN - 142440312X
SN - 9781424403127
T3 - Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
SP - 845
EP - 850
BT - Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
T2 - 2006 International Conference on Field Programmable Logic and Applications, FPL
Y2 - 28 August 2006 through 30 August 2006
ER -