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
收藏
页码：1 / 10
页数：10
相关论文
共 50 条
  • [31] Using general-purpose programming languages for FPGA design
    Hutchings, BL
    Nelson, BE
    37TH DESIGN AUTOMATION CONFERENCE, PROCEEDINGS 2000, 2000, : 561 - 566
  • [32] SCAMP - A GENERAL-PURPOSE SIMULATOR AND METABOLIC CONTROL ANALYSIS PROGRAM
    SAURO, HM
    COMPUTER APPLICATIONS IN THE BIOSCIENCES, 1993, 9 (04): : 441 - 450
  • [33] Fast simulation of power system dynamics in a general-purpose simulator
    Baratella, P
    Cova, B
    Damonte, M
    Gaglioti, E
    Marconato, R
    Scarpellini, P
    CONTROL ENGINEERING PRACTICE, 1997, 5 (01) : 123 - 129
  • [34] ESACAP - A PC-IMPLEMENTED GENERAL-PURPOSE CIRCUIT SIMULATOR
    STANGERUP, P
    IEEE CIRCUITS AND DEVICES MAGAZINE, 1988, 4 (04): : 20 - 25
  • [35] GENERAL-PURPOSE INTERFACE BUS DATA TRANSFER SIMULATOR.
    Anon
    IBM technical disclosure bulletin, 1985, 28 (04): : 1546 - 1549
  • [36] MODELING 8-BIT MICROPROCESSORS FOR A GENERAL-PURPOSE SIMULATOR
    WINDER, R
    MICROPROCESSORS AND MICROSYSTEMS, 1988, 12 (08) : 443 - 453
  • [37] STRUCTURE AND APPLICATION OF NNSIM - A GENERAL-PURPOSE NEURAL NETWORK SIMULATOR
    NIJHUIS, J
    SPAANENBURG, L
    WARKOWSKI, F
    MICROPROCESSING AND MICROPROGRAMMING, 1989, 27 (1-5): : 189 - 194
  • [38] A General-Purpose Simulator for Metamaterials with Three-Dimensional Elements
    Mittra, R.
    Pelletti, C.
    Arya, R. K.
    Dong, T.
    Bianconi, G.
    PROCEEDINGS OF 2013 URSI INTERNATIONAL SYMPOSIUM ON ELECTROMAGNETIC THEORY (EMTS), 2013, : 78 - 80
  • [39] QUANTITATIVE MEASUREMENTS OF FPGA UTILITY IN SPECIAL AND GENERAL-PURPOSE PROCESSORS
    FAGIN, BS
    JOURNAL OF VLSI SIGNAL PROCESSING, 1993, 6 (02): : 129 - 137
  • [40] EDEN: A High-Performance, General-Purpose, NeuroML-Based Neural Simulator
    Panagiotou, Sotirios
    Sidiropoulos, Harry
    Soudris, Dimitrios
    Negrello, Mario
    Strydis, Christos
    FRONTIERS IN NEUROINFORMATICS, 2022, 16
12345