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BMCBI
2007
233views more  BMCBI 2007»
13 years 7 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
Isaac T. S. Li, Warren Shum, Kevin Truong
ISPDC
2010
IEEE
13 years 6 months ago
Resource-Aware Compiler Prefetching for Many-Cores
—Super-scalar, out-of-order processors that can have tens of read and write requests in the execution window place significant demands on Memory Level Parallelism (MLP). Multi- ...
George C. Caragea, Alexandros Tzannes, Fuat Keceli...
FPL
2010
Springer
124views Hardware» more  FPL 2010»
13 years 5 months ago
Finding System-Level Information and Analyzing Its Correlation to FPGA Placement
One of the more popular placement algorithms for Field Programmable Gate Arrays (FPGAs) is called Simulated Annealing (SA). This algorithm tries to create a good quality placement ...
Farnaz Gharibian, Lesley Shannon, Peter Jamieson
BMCBI
2011
12 years 11 months ago
The Proteogenomic Mapping Tool
Background: High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the...
William S. Sanders, Nan Wang, Susan M. Bridges, Br...
IWMM
2011
Springer
254views Hardware» more  IWMM 2011»
12 years 10 months ago
Short-term memory for self-collecting mutators
We propose a new memory model called short-term memory for managing objects on the heap. In contrast to the traditional persistent memory model for heap management, objects in sho...
Martin Aigner, Andreas Haas, Christoph M. Kirsch, ...