Run time reconfiguration of FPGA for scanning genomic databases
作者： E. Lemoine , D. Merceron
关键词: Orders of magnitude (time) 、 Control reconfiguration 、 Netlist 、 Sequence 、 Routing (electronic design automation) 、 Field-programmable gate array 、 Embedded system 、 Genomic databases 、 Reduced instruction set computing 、 Computer science
摘要: This paper evaluates the feasibility of reconfiguring an FPGA at run time, and tests its performance using a "Grand Challenge Problem", high speed scanning genomic sequence databases. Algorithm implementation into XC3090 is described, methods proposed for generating placed Xilinx Netlist File that can be efficiently routed time by Automated Placing Routing tools, in order to increase density design. The same algorithm carefully optimised on RISC processor has been compared with reconfigurated FPGA, shows latter have improvement two three orders magnitude.
ieeecomputersociety.org参考文章(15)
D. Roncin, J. Vuillemin, P. Bertin, Introduction to programmable active memories Systolic array processors. pp. 301- 309 ,(1990)
M. Robert, P. Gorria, J. Miteran, S. Turgis, Architectures for a real time classification processor custom integrated circuits conference. pp. 197- 200 ,(1994) , 10.1109/CICC.1994.379737
M. Gokhale, W. Holmes, A. Kopser, S. Lucas, R. Minnich, D. Sweely, D. Lopresti, Building and using a highly parallel programmable logic array IEEE Computer. ,vol. 24, pp. 81- 89 ,(1991) , 10.1109/2.67197
J.G. Eldredge, B.L. Hutchings, RRANN: the run-time reconfiguration artificial neural network custom integrated circuits conference. pp. 77- 80 ,(1994) , 10.1109/CICC.1994.379763
Joël Quinqueton, Eric Lemoine, Jean Sallantin, High speed pattern matching in genetic data base with reconfigurable hardware. intelligent systems in molecular biology. ,vol. 2, pp. 269- 275 ,(1994)
Engelbert Mephu Nguifo, Jean Sallantin, Prediction of Primate Splice Junction Gene Sequences with a Cooperative Knowledge Acquisition System intelligent systems in molecular biology. ,vol. 1, pp. 292- 300 ,(1993)
D.T. Hoang, Searching genetic databases on Splash 2 [1993] Proceedings IEEE Workshop on FPGAs for Custom Computing Machines. pp. 185- 191 ,(1993) , 10.1109/FPGA.1993.279464
E. Lemoine, Reconfigurable hardware for molecular biology computing systems international conference on application specific array processors. pp. 184- 187 ,(1993) , 10.1109/ASAP.1993.397141
J.E. Vuillemin, P. Bertin, D. Roncin, M. Shand, H.H. Touati, P. Boucard, Programmable active memories: reconfigurable systems come of age IEEE Transactions on Very Large Scale Integration Systems. ,vol. 4, pp. 611- 624 ,(1996) , 10.1109/92.486081
C.E. Cox, W.E. Blanz, GANGLION-a fast field-programmable gate array implementation of a connectionist classifier IEEE Journal of Solid-state Circuits. ,vol. 27, pp. 288- 299 ,(1992) , 10.1109/4.121550