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Paper Abstract and Keywords
Presentation 2007-11-22 13:25
Evaluation of a Data-Driven Architecture for a Stochastic Biochemical Simulator on an FPGA
Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi (Keio Univ.), Noriko Hiroi (EMBL-EBI), Yuichiro Shibata, Hideki Yamada (Nagasaki Univ.), Hiroaki Kitano (JST), Hideharu Amano (Keio Univ.) RECONF2007-50
Abstract (in Japanese) (See Japanese page) 
(in English) This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method. Whole procedure of the algorithm is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. Area and throughput were measured for each type of network configuration, as well as studying each cause of bottleneck. By performing a multi-threading simulation, maximum of 3.6 times speedup was obtained compared to an execution on Xeon 3.20 GHz. Although current designs did not achieve significant speedup, performance analysis study of each network configuration suggested capability of throughput enhancement.
Keyword (in Japanese) (See Japanese page) 
(in English) Data-transfer network / Data-driven / FPGA / stochastic biochemical simulation / On-chip network / / /  
Reference Info. IEICE Tech. Rep., vol. 107, no. 342, RECONF2007-50, pp. 43-48, Nov. 2007.
Paper # RECONF2007-50 
Date of Issue 2007-11-15 (RECONF) 
ISSN Print edition: ISSN 0913-5685    Online edition: ISSN 2432-6380
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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 VLD CPSY RECONF DC IPSJ-SLDM IPSJ-ARC  
Conference Date 2007-11-20 - 2007-11-22 
Place (in Japanese) (See Japanese page) 
Place (in English) Kitakyushu International Conference Center 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Design Gaia 2007 ---A New Frontier in VLSI Design--- 
Paper Information
Registration To RECONF 
Conference Code 2007-11-VLD-CPSY-RECONF-DC-IPSJ-SLDM-IPSJ-ARC 
Language Japanese 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) Evaluation of a Data-Driven Architecture for a Stochastic Biochemical Simulator on an FPGA 
Sub Title (in English)  
Keyword(1) Data-transfer network  
Keyword(2) Data-driven  
Keyword(3) FPGA  
Keyword(4) stochastic biochemical simulation  
Keyword(5) On-chip network  
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Keyword(7)  
Keyword(8)  
1st Author's Name Masato Yoshimi  
1st Author's Affiliation Keio University (Keio Univ.)
2nd Author's Name Yuri Nishikawa  
2nd Author's Affiliation Keio University (Keio Univ.)
3rd Author's Name Toshinori Kojima  
3rd Author's Affiliation Keio University (Keio Univ.)
4th Author's Name Yasunori Osana  
4th Author's Affiliation Keio University (Keio Univ.)
5th Author's Name Akira Funahashi  
5th Author's Affiliation Keio University (Keio Univ.)
6th Author's Name Noriko Hiroi  
6th Author's Affiliation EMBL-EBI, Thornton group Wellcome Trust Genome Campus (EMBL-EBI)
7th Author's Name Yuichiro Shibata  
7th Author's Affiliation Nagasaki University (Nagasaki Univ.)
8th Author's Name Hideki Yamada  
8th Author's Affiliation Nagasaki University (Nagasaki Univ.)
9th Author's Name Hiroaki Kitano  
9th Author's Affiliation Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency (JST)
10th Author's Name Hideharu Amano  
10th Author's Affiliation Keio University (Keio Univ.)
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Speaker Author-1 
Date Time 2007-11-22 13:25:00 
Presentation Time 25 minutes 
Registration for RECONF 
Paper # RECONF2007-50 
Volume (vol) vol.107 
Number (no) no.342 
Page pp.43-48 
#Pages
Date of Issue 2007-11-15 (RECONF) 


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