ReCSiP: An FPGA-based general-purpose biochemical simulator

被引：7

作者：

Osana, Yasunori ^{[1
]}

Yoshimi, Masato

Iwaoka, Yow

Kojima, Toshinori

Nishikawa, Yuri

Funahashi, Akira

Hiroi, Noriko

Shibata, Yuichiro

Iwanaga, Naoki

Kitano, Hiroaki

Amano, Hideharu

机构：

[1] Keio Univ, Fac Sci & Technol, Dept Biosci & Informat, Yokohama, Kanagawa 223, Japan

[2] Keio Univ, Grad Sch Sci & Technol, Yokohama, Kanagawa 223, Japan

[3] ERATO, SORST, Japan Sci & Technol, Kitano Symbiot Syst Project, Tokyo 150, Japan

[4] Nagasaki Univ, Dept Comp & Informat Sci, Nagasaki 852, Japan

[5] Keio Univ, Fac Sci & Technol, Dept Informat & Comp Sci, Yokohama, Kanagawa 223, Japan

来源：

ELECTRONICS AND COMMUNICATIONS IN JAPAN PART II-ELECTRONICS | 2007年 / 90卷 / 07期

关键词：

FPGA; biochemical simulations; ordinary differential equations; rate-law functions; Runge-Kutta method;

D O I：

10.1002/ecjb.20370

中图分类号：

TM [电工技术]; TN [电子技术、通信技术];

学科分类号：

0808 ; 0809 ;

摘要：

Mathematical modeling and simula tion of cellular systems are essential to modern biological researches. However, simulating with software-based simulators on general-purpose microprocessors cannot provide enough throughput. ReCSiP is an FPGA-based solution for biochemical simulation and parameter scanning. This paper describes its design and hardware implementation. With Xilinx's XC2VP70-5, this method achieved 50- to 80-fold speed-up compared to Intel's Pentium4 processor. (c) 2007 Wiley Periodicals, Inc.

引用

页码：1 / 10

页数：10

共 50 条

[41] A general-purpose framework for FPGA-accelerated genetic algorithms
Guo, Liucheng
Funie, Andreea Ingrid
Xie, Zhongliu
Thomas, David
Luk, Wayne
INTERNATIONAL JOURNAL OF BIO-INSPIRED COMPUTATION, 2015, 7 (06) : 361 - 375
[42] A GENERAL-PURPOSE DIGITAL SIMULATOR AND EXAMPLES OF ITS APPLICATION .1. DESCRIPTION OF THE SIMULATOR
EFRON, R
GORDON, G
IBM SYSTEMS JOURNAL, 1964, 3 (01) : 22 - 34
[43] DEVELOPMENT OF GENERAL-PURPOSE ENERGY SYSTEM ANALYSIS SIMULATOR "ENERGY FLOW
Nakano, Takahiro
Saito, Kiyoshi
INTERNATIONAL JOURNAL OF TECHNOLOGY, 2011, 2 (03) : 257 - 265
[44] MEMBRANE SEPARATIONS IN BIOCHEMICAL RECOVERY - PHYSICAL AND BIOCHEMICAL CONSIDERATIONS FOR GENERAL-PURPOSE APPLICATION
HUDDLESTON, JG
SANSOMESMITH, A
WU, DX
LYDDIATT, A
MEMBRANE SEPARATION PROCESSES, 1989, : 253 - 265
[45] Development and Implementation of Parameterized FPGA-Based General Purpose Neural Networks for Online Applications
Gomperts, Alexander
Ukil, Abhisek
Zurfluh, Franz
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS, 2011, 7 (01) : 78 - 89
[46] Design of general-purpose electric simulator for satellite attitude and orbit control system based on SOC
Hu, Di
Dong, Yunfeng
Zhongguo Kongjian Kexue Jishu/Chinese Space Science and Technology, 2010, 30 (02): : 24 - 30
[47] Framework design of a general-purpose power market simulator based on multi-agent technology
Liu, HJ
Yuan, B
Dai, HW
Lin, JK
2001 POWER ENGINEERING SOCIETY SUMMER MEETING, VOLS 1-3, CONFERENCE PROCEEDINGS, 2001, : 1478 - 1482
[48] Automatic pipeline construction focused on similarity of rate law functions for an FPGA-based biochemical simulator
Nagasaki University, Japan
不详
不详
不详
IPSJ Trans. Syst. LSI Des. Methodol., (244-256):
[49] General-purpose definition
Emerson, DM
DATAMATION, 1995, 41 (23): : 14 - 14
[50] General-purpose cells?
Solter, D
Gearhart, J
RECHERCHE, 1999, (320): : 32 - 34

← 1 2 3 4 5 →