TY - GEN
T1 - A framework for ODE-based multimodel biochemical simulations on an FPGA
AU - Osana, Yasunori
AU - Fukushima, Tomonori
AU - Yoshimi, Masato
AU - Iwaoka, Yow
AU - Funahashi, Akira
AU - Hiroi, Noriko
AU - Shibata, Yuichiro
AU - Iwanaga, Naoki
AU - Kitano, Hiroaki
AU - Amano, Hideharu
PY - 2005/12/1
Y1 - 2005/12/1
N2 - Today, mathematical modeling and simulation of biochemical pathways take a major role in biological researches. However, modern microprocessors cannot provide enough throughput to explore the large parameter space of target pathways. To address this problem, ReCSiP (a ReConfigurable Cell Simulation Platform), an FPGA-based biochemical simulator is proposed. It's an ODE-based simulator, which solves the rate-law functions. The framework proposed in this paper, enables to simulate pathways consisting many different types of chemical reactions by connecting the rate-law modules (solvers) on an FPGA. It provides the solver-to-solver communication mechanism on an FPGA and automatic configuration software to generate the circuit.
AB - Today, mathematical modeling and simulation of biochemical pathways take a major role in biological researches. However, modern microprocessors cannot provide enough throughput to explore the large parameter space of target pathways. To address this problem, ReCSiP (a ReConfigurable Cell Simulation Platform), an FPGA-based biochemical simulator is proposed. It's an ODE-based simulator, which solves the rate-law functions. The framework proposed in this paper, enables to simulate pathways consisting many different types of chemical reactions by connecting the rate-law modules (solvers) on an FPGA. It provides the solver-to-solver communication mechanism on an FPGA and automatic configuration software to generate the circuit.
UR - http://www.scopus.com/inward/record.url?scp=33746865589&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33746865589&partnerID=8YFLogxK
U2 - 10.1109/FPL.2005.1515788
DO - 10.1109/FPL.2005.1515788
M3 - Conference contribution
AN - SCOPUS:33746865589
SN - 0780393627
SN - 9780780393622
T3 - Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
SP - 574
EP - 577
BT - Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
T2 - 2005 International Conference on Field Programmable Logic and Applications, FPL
Y2 - 24 August 2005 through 26 August 2005
ER -