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permGPU: Using graphics processing units in RNA microarray association studies.

Publication ,  Journal Article
Shterev, ID; Jung, S-H; George, SL; Owzar, K
Published in: BMC Bioinformatics
June 16, 2010

BACKGROUND: Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS: We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. CONCLUSIONS: permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

Duke Scholars

Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

June 16, 2010

Volume

11

Start / End Page

329

Location

England

Related Subject Headings

  • Software
  • RNA
  • Neoplasms
  • Microarray Analysis
  • Humans
  • Genetic Association Studies
  • Gene Expression Profiling
  • Bioinformatics
  • 49 Mathematical sciences
  • 46 Information and computing sciences
 

Citation

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Shterev, I. D., Jung, S.-H., George, S. L., & Owzar, K. (2010). permGPU: Using graphics processing units in RNA microarray association studies. BMC Bioinformatics, 11, 329. https://doi.org/10.1186/1471-2105-11-329
Shterev, Ivo D., Sin-Ho Jung, Stephen L. George, and Kouros Owzar. “permGPU: Using graphics processing units in RNA microarray association studies.BMC Bioinformatics 11 (June 16, 2010): 329. https://doi.org/10.1186/1471-2105-11-329.
Shterev ID, Jung S-H, George SL, Owzar K. permGPU: Using graphics processing units in RNA microarray association studies. BMC Bioinformatics. 2010 Jun 16;11:329.
Shterev, Ivo D., et al. “permGPU: Using graphics processing units in RNA microarray association studies.BMC Bioinformatics, vol. 11, June 2010, p. 329. Pubmed, doi:10.1186/1471-2105-11-329.
Shterev ID, Jung S-H, George SL, Owzar K. permGPU: Using graphics processing units in RNA microarray association studies. BMC Bioinformatics. 2010 Jun 16;11:329.
Journal cover image

Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

June 16, 2010

Volume

11

Start / End Page

329

Location

England

Related Subject Headings

  • Software
  • RNA
  • Neoplasms
  • Microarray Analysis
  • Humans
  • Genetic Association Studies
  • Gene Expression Profiling
  • Bioinformatics
  • 49 Mathematical sciences
  • 46 Information and computing sciences