FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL

Volumn , Issue , 2007, Pages 254-259

  Yoshimi, Masato ^a   Iwaoka, Yow ^a   Nishikawa, Yuri ^a   Kojima, Toshinori ^a   Osana, Yasunori ^a   Funahashi, Akira ^b   Hiroi, Noriko ^b   Shibata, Yuichiro ^a   Iwanaga, Naoki ^a   Yamada, Hideki ^b   Kitano, Hiroaki ^a   Amano, Hideharu ^c  

^a KEIO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NAGASAKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NETWORKS (CIRCUITS);

ARITHMETIC CIRCUITS; BIO-CHEMICALS; BIOCHEMICAL MODELS; FPGA IMPLEMENTATIONS; REACTION METHODS; RECONFIGURABLE DEVICES; SIMULATION CIRCUITS; SPEED-UP; STOCHASTIC SIMULATION ALGORITHMS;

FIELD PROGRAMMABLE GATE ARRAYS (FPGA);

EID: 48149095060     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FPL.2007.4380656     Document Type: Conference Paper

References (8)

1. D. T. Gillespie, "A general method for numerically simulating the stochastic time evolution of coupled chemical reactions," Journal of Computational Physics, vol. 22, pp. 403-434, 1976.
2. J. F. Keane, C. Bradley, and C. Ebeling, "A compiled accelerator for biological cell signaling simulations," in The 12th International Symposium on Field-Programmable Gate Ar-rays(FPGA), Feb. 2004, pp. 233-241.
3. M. Yoshimi, Y. Osana, Y. Iwaoka, Y. Nishikawa, T. Kojima, A. Funahashi, N. Hiroi, Y. Shibata, N. Iwanaga, H. Kitano, and H. Amano, "An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems," in The 16th International Conference on Field Programmable Logic and Applications, Aug. 2006, pp. 227-232.
4. M. A. Gibson and J. Bruck, "Efficient exact stochastic simulation of chemical systems with many species and many channels," Journal of Physical Chemistry A, vol. 104, no. 9, pp. 1876-1889, 2000.
5. Y. Cao, H. Li, and L. Petzold, "Efficient formulation of the stochastic simulation algorithm for chemically recting systems," Journal of Chemical Physics, vol. 121, no. 9, pp. 4059-4067, 2004.
6. K. Takahashi, K. Yugi, K. Hashimoto, Y. Yamada, C. J. F. Pickett, and M. Tomita, "A multi-algorithm, multi-timescale method for cell simulation," Bioinformatics, vol. 20, no. 4, pp. 538-546, Mar. 2004.
7. L. Salwinski and D. Eisenberg, "In silico simulation of biological network dynamics," Nature Biotechnology, vol. 22, no. 8, pp. 1017-1019, Aug. 2004.
8. M. Yoshimi, Y. Osana, T. Fukushima, and H. Amano, "Stochastic simulation for biochemical reactions on FPGA," in The 14th International Conference on Field Programmable Logic and Applications, ser. Lecture Notes in Computer Science, vol. 3203. Springer, Aug. 2004, pp. 105-114.