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BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
14 years 2 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
IISWC
2008
IEEE
14 years 1 months ago
STAMP: Stanford Transactional Applications for Multi-Processing
Abstract—Transactional Memory (TM) is emerging as a promising technology to simplify parallel programming. While several TM systems have been proposed in the research literature,...
Chi Cao Minh, JaeWoong Chung, Christos Kozyrakis, ...
IPPS
2008
IEEE
14 years 1 months ago
Overcoming scaling challenges in biomolecular simulations across multiple platforms
NAMD† is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique now used by most scalable pr...
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. ...
ANSS
2007
IEEE
14 years 1 months ago
JANE - The Java Ad Hoc Network Development Environment
This work describes a Java based development platform which is intended to support ad hoc network researchers in application and protocol design. Software development within this ...
Daniel Görgen, Hannes Frey, Christian Hiedels
IEEEPACT
2007
IEEE
14 years 1 months ago
JudoSTM: A Dynamic Binary-Rewriting Approach to Software Transactional Memory
With the advent of chip-multiprocessors, we are faced with the challenge of parallelizing performance-critical software. Transactional memory (TM) has emerged as a promising progr...
Marek Olszewski, Jeremy Cutler, J. Gregory Steffan