Abstract
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.
| Original language | English |
|---|---|
| Title of host publication | Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL |
| Pages | 808-811 |
| Number of pages | 4 |
| DOIs | |
| Publication status | Published - 2007 |
| Event | 2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands Duration: 2007 Aug 27 → 2007 Aug 29 |
Other
| Other | 2007 International Conference on Field Programmable Logic and Applications, FPL |
|---|---|
| Country | Netherlands |
| City | Amsterdam |
| Period | 07/8/27 → 07/8/29 |
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ASJC Scopus subject areas
- Computer Science Applications
- Electrical and Electronic Engineering
Cite this
A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. / Yamada, Hideki; Iwanaga, Naoki; Shibata, Yuichiro; Osana, Yasunori; Yoshimi, Masato; Iwaoka, Yow; Nishikawa, Yuri; Kojima, Toshinori; Amano, Hideharu; Funahashi, Akira; Hiroi, Noriko; Hiroaki Kitano, Kitano; Kiyoshi Oguri, Oguri.
Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 808-811 4380774.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
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
UR - http://www.scopus.com/inward/citedby.url?scp=48149097027&partnerID=8YFLogxK
U2 - 10.1109/FPL.2007.4380774
DO - 10.1109/FPL.2007.4380774
M3 - Conference contribution
SN - 1424410606
SN - 9781424410606
SP - 808
EP - 811
BT - Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
ER -