TY - GEN
T1 - A combining technique of rate law functions for a cost-effective reconfigurable biological simulator
AU - Yamada, Hideki
AU - Iwanaga, Naoki
AU - Shibata, Yuichiro
AU - Osana, Yasunori
AU - Yoshimi, Masato
AU - Iwaoka, Yow
AU - Nishikawa, Yuri
AU - Kojima, Toshinori
AU - Amano, Hideharu
AU - Funahashi, Akira
AU - Hiroi, Noriko
AU - Hiroaki Kitano, Kitano
AU - Kiyoshi Oguri, Oguri
PY - 2007
Y1 - 2007
N2 - In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources are essential. This paper proposes a method which combines common terms in rate law functions appeared in biochemical models and generates a shared hardware module used for numerical integration. In this approach, two functions are combined in a tree structure level, followed by pipeline scheduling and arithmetic module binding. The evaluation result reveals that this approach reduces hardware resources by 31.4 % on average at the cost of 14.4 % throughput degradation.
AB - In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources are essential. This paper proposes a method which combines common terms in rate law functions appeared in biochemical models and generates a shared hardware module used for numerical integration. In this approach, two functions are combined in a tree structure level, followed by pipeline scheduling and arithmetic module binding. The evaluation result reveals that this approach reduces hardware resources by 31.4 % on average at the cost of 14.4 % throughput degradation.
UR - http://www.scopus.com/inward/record.url?scp=48149097027&partnerID=8YFLogxK
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U2 - 10.1109/FPL.2007.4380774
DO - 10.1109/FPL.2007.4380774
M3 - Conference contribution
AN - SCOPUS:48149097027
SN - 1424410606
SN - 9781424410606
T3 - Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
SP - 808
EP - 811
BT - Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
T2 - 2007 International Conference on Field Programmable Logic and Applications, FPL
Y2 - 27 August 2007 through 29 August 2007
ER -