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BCB
2010
156views Bioinformatics» more  BCB 2010»
15 years 2 months ago
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
Many biologically motivated problems are expressed as dynamic programming recurrences and are difficult to parallelize due to the intrinsic data dependencies in their algorithms. ...
Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhl...
JOCN
2011
66views more  JOCN 2011»
15 years 2 months ago
The Packet Switching Brain
■ The computer metaphor has served brain science well as a tool for comprehending neural systems. Nevertheless, we propose here that this metaphor be replaced or supplemented by...
Daniel J. Graham, Daniel N. Rockmore
220
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JPDC
2010
133views more  JPDC 2010»
15 years 2 months ago
Lock-free parallel dynamic programming
We show a method for parallelizing top down dynamic programs in a straightforward way by a careful choice of a lock-free shared hash table implementation and randomization of the ...
Alex Stivala, Peter J. Stuckey, Maria Garcia de la...
213
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PRESENCE
2010
76views more  PRESENCE 2010»
15 years 2 months ago
Modularity for Large Virtual Reality Applications
This paper focuses on the design of high performance VR applications. These applications usually involve various I/O devices and complex simulations. A parallel architecture or gri...
Jérémie Allard, Jean-Denis Lesage, B...
179
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VLSISP
2010
119views more  VLSISP 2010»
15 years 2 months ago
Hardware Acceleration of HMMER on FPGAs
We propose a new parallelization scheme for the hmmsearch function of the HMMER software, in order to target FPGA technology. hmmsearch is a very compute intensive software for bio...
Steven Derrien, Patrice Quinton
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