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  1. Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences (ECMLS '12)
  2. Accelerating tandem MS protein database searches using OpenCL
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Image-based biomedical modeling, simulation and visualization
Workflow as a service: an approach to workflow farming
Understanding mapreduce-based next-generation sequencing alignment on distributed cyberinfrastructure
Accelerating virtual high-throughput ligand docking: screening one million compounds using a petascale supercomputer
Visualizing the protein sequence universe
HyMR: a hybrid MapReduce workflow system
Information-theoretic analysis of molecular (co)evolution using graphics processing units
Accelerating tandem MS protein database searches using OpenCL
An iterative parameter estimation method for biological systems
A lightweight platform for managing biomedical simulation

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Accelerating tandem MS protein database searches using OpenCL

Content Provider ACM Digital Library
Author Peterson, Gregory D. Weber, Rick Lineback, Nicholas Jenkins, David D.
Abstract GPUs and multicore processors are now pervasive in com- putational sciences and high-performance computing. Their high arithmetic throughput and memory bandwidth com- bined with their ever increasing programmability make them suitable for a widening variety of applications. We give a high level overview of Specmaster, a peptide search al- gorithm running on multi-core processors and GPUs via OpenCL. We give details and benchmarks highlighting per- formance tradeoffs on three devices: Intel's Sandy Bridge, Nvidia's GTX 480, and AMD's Radeon 7970. We demon- strate a single codebase running on all three architectures and give a description on how to improve performance for specific architectures while still maintaining one code base in future work.
Starting Page 59
Ending Page 63
Page Count 5
File Format PDF
ISBN 9781450313391
DOI 10.1145/2483954.2483964
Language English
Publisher Association for Computing Machinery (ACM)
Publisher Date 2012-06-18
Publisher Place New York
Access Restriction Subscribed
Subject Keyword Multi-core Proteomics Opencl Gpu Mass spectrometry
Content Type Text
Resource Type Article
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