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» Production of Large Computer Programs
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BMCBI
2010
175views more  BMCBI 2010»
15 years 2 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...
PPOPP
2010
ACM
15 years 3 months ago
Helper locks for fork-join parallel programming
Helper locks allow programs with large parallel critical sections, called parallel regions, to execute more efficiently by enlisting processors that might otherwise be waiting on ...
Kunal Agrawal, Charles E. Leiserson, Jim Sukha
CF
2010
ACM
15 years 5 months ago
Hybrid parallel programming with MPI and unified parallel C
The Message Passing Interface (MPI) is one of the most widely used programming models for parallel computing. However, the amount of memory available to an MPI process is limited ...
James Dinan, Pavan Balaji, Ewing L. Lusk, P. Saday...
BMCBI
2010
141views more  BMCBI 2010»
15 years 2 months ago
Computing and visually analyzing mutual information in molecular co-evolution
Background: Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due t...
Sebastian Bremm, Tobias Schreck, Patrick Boba, Ste...
FPL
2010
Springer
188views Hardware» more  FPL 2010»
14 years 12 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 ...