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FPL
2010
Springer
188views Hardware» more  FPL 2010»
13 years 4 months ago
SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing
We demonstrate how Field Programmable Gate Arrays (FPGAs) may be used to address the computing challenges associated with assembling genome sequences from recent ultra-high-through...
Kristian Stevens, Henry Chen, Terry Filiba, Peter ...
BMCBI
2006
129views more  BMCBI 2006»
13 years 6 months ago
Fast index based algorithms and software for matching position specific scoring matrices
Background: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences....
Michael Beckstette, Robert Homann, Robert Giegeric...
ASAP
2005
IEEE
133views Hardware» more  ASAP 2005»
13 years 11 months ago
Speedups from Partitioning Critical Software Parts to Coarse-Grain Reconfigurable Hardware
In this paper, we propose a hardware/software partitioning method for improving applications’ performance in embedded systems. Critical software parts are accelerated on hardwar...
Michalis D. Galanis, Grigoris Dimitroulakos, Costa...
SIGSOFT
2003
ACM
14 years 6 months ago
ARCHER: using symbolic, path-sensitive analysis to detect memory access errors
Memory corruption errors lead to non-deterministic, elusive crashes. This paper describes ARCHER (ARray CHeckER) a static, effective memory access checker. ARCHER uses path-sensit...
Yichen Xie, Andy Chou, Dawson R. Engler
PLDI
2005
ACM
13 years 11 months ago
Formal loop merging for signal transforms
A critical optimization in the domain of linear signal transforms, such as the discrete Fourier transform (DFT), is loop merging, which increases data locality and reuse and thus ...
Franz Franchetti, Yevgen Voronenko, Markus Pü...