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Paper Abstract and Keywords
Presentation 2007-05-17 14:00
Autometic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP
Hideki Yamada, Naoki Iwanaga, Yuichiro Shibata (Nagasaki Univ.), Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Hideharu Amano, Akira Funahashi (Keio Univ.), Noriko Hiroi (EMBL-EBI), Hiroaki Kitano (JST), Kiyoshi Oguri (Nagasaki Univ.) RECONF2007-3
Abstract (in Japanese) (See Japanese page) 
(in English) In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources is essential. This paper proposes a method which combines a common terms in rate law functions appeared in biochemical models to generate a shared hardware module used for numerical integration in a reconfigurable biochemical simulator. In this approach, two functions are combined in a tree structure level followed by pipeline scheduling and arithmetic module binding. The evaluation results reveals that this combining approach reduces hardware costs by 31.36 \% on average at the cost of 14.4 \% throughput degradation.
Keyword (in Japanese) (See Japanese page) 
(in English) biochemical simulation / arithmetic scheduling / rate law function / FPGA / / / /  
Reference Info. IEICE Tech. Rep., vol. 107, no. 41, RECONF2007-3, pp. 13-18, May 2007.
Paper # RECONF2007-3 
Date of Issue 2007-05-10 (RECONF) 
ISSN Print edition: ISSN 0913-5685    Online edition: ISSN 2432-6380
Copyright
and
reproduction		 All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034)
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Conference Information
Committee RECONF  
Conference Date 2007-05-17 - 2007-05-18 
Place (in Japanese) (See Japanese page) 
Place (in English) Kanazawa Bunka Hall 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Reconfigurable Systems, etc. 
Paper Information
Registration To RECONF 
Conference Code 2007-05-RECONF 
Language Japanese 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) Autometic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP 
Sub Title (in English)  
Keyword(1) biochemical simulation  
Keyword(2) arithmetic scheduling  
Keyword(3) rate law function  
Keyword(4) FPGA  
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1st Author's Name Hideki Yamada  
1st Author's Affiliation Nagasaki University (Nagasaki Univ.)
2nd Author's Name Naoki Iwanaga  
2nd Author's Affiliation Nagasaki University (Nagasaki Univ.)
3rd Author's Name Yuichiro Shibata  
3rd Author's Affiliation Nagasaki University (Nagasaki Univ.)
4th Author's Name Yasunori Osana  
4th Author's Affiliation Keio University (Keio Univ.)
5th Author's Name Masato Yoshimi  
5th Author's Affiliation Keio University (Keio Univ.)
6th Author's Name Yow Iwaoka  
6th Author's Affiliation Keio University (Keio Univ.)
7th Author's Name Yuri Nishikawa  
7th Author's Affiliation Keio University (Keio Univ.)
8th Author's Name Toshinori Kojima  
8th Author's Affiliation Keio University (Keio Univ.)
9th Author's Name Hideharu Amano  
9th Author's Affiliation Keio University (Keio Univ.)
10th Author's Name Akira Funahashi  
10th Author's Affiliation Keio University (Keio Univ.)
11th Author's Name Noriko Hiroi  
11th Author's Affiliation EMBL-EBI, Thornton Group (EMBL-EBI)
12th Author's Name Hiroaki Kitano  
12th Author's Affiliation Japan Science and Technology Agency (JST)
13th Author's Name Kiyoshi Oguri  
13th Author's Affiliation Nagasaki University (Nagasaki Univ.)
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Speaker Author-1 
Date Time 2007-05-17 14:00:00 
Presentation Time 30 minutes 
Registration for RECONF 
Paper # RECONF2007-3 
Volume (vol) vol.107 
Number (no) no.41 
Page pp.13-18 
#Pages 6 
Date of Issue 2007-05-10 (RECONF) 

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