Comparing the performance of clusters, hadoop, and active disks on microarray correlation computations

16th International Conference on High Performance Computing, HiPC 2009 - Proceedings

Volumn , Issue , 2009, Pages 378-387

  Delmerico, Jeffrey A ^a   Byrnes, Nathanial A ^b   Bruno, Andrew E ^c   Jones, Matthew D ^c   Gallo, Steven M ^c   Chaudhary, Vipin ^a  

^a the State University of New York   (United States)

^b Netezza Corporation   (United States)

^c UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTER ARCHITECTURE; COMPARATIVE GENOMIC HYBRIDIZATIONS; COPY NUMBER; CORRELATION COMPUTATIONS; DATA INTENSIVE; DATA-INTENSIVE APPLICATION; DISTRIBUTED COMPUTING; DISTRIBUTED FILE SYSTEMS; HIGH RESOLUTION; HIGH-THROUGHPUT; MICROARRAY EXPERIMENTS; MICROARRAY TECHNOLOGIES; PAIRWISE CORRELATION; PARALLEL FILE SYSTEM; PARALLELIZATIONS; PERFORMANCE ANALYSIS; SOFTWARE FRAMEWORKS; STORAGE HARDWARE; STORAGE RESOURCES;

BENCHMARKING; DATA WAREHOUSES; DISKS (STRUCTURAL COMPONENTS); GENE EXPRESSION; SCALABILITY;

CLUSTER COMPUTING;

EID: 77952112991     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HIPC.2009.5433190     Document Type: Conference Paper

References (24)

1. A. Acharya, M. Uysal, and J. Saltz, "Active Disks: Programming Model, Algorithms and Evaluation", Proc.Conf. Architectural Support for Programming Languages and Operating Systems, IEEE Press, Piscataway, N.J., Oct. 1998, pp. 81-91. (Pubitemid 128453129)
2. E. Riedel, C. Faloutsos, G. A. Gibson, and D. Nagle, "Active Disks for Large-Scale Data Processing", IEEE Computer, June 2001, pp. 68-74.
3. M. Gokhale, "Disruptive Technologies: Field Programmable Gate Arrays", Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, June 14, 2007. http://www.csm.ornl.gov/workshops/SOS11/ presentations/m gokale.pdf
4. G. S. Davidson, K. W. Boyack, R. A. Zacharski, S. C. Helmreich, and J. R. Cowie, "Data-Centric Computing with the Netezza Architecture", SANDIA REPORT, SAND2006-1853, Unlimited Release, Printed April 2006.
5. D. Andersen, J. Franklin, A. Phanishayee, L. Tan, and V. Vasudevan, "FAWN: A Fast Array of Wimpy Nodes", Carnegie Mellon University PDL Tech. Report CMU-PDL-08-108, May 2008.
6. A. S. Szalay, G. Bell, J. Vandenberg, A. Wonders, R. Burns, D. Fay, J. Heasley, T. Hey, M. Nieto-SantiSteban, A. Thakar, C. van Ingen, R. Wilton, "GrayWulf: Scalable Clustered Architecture for Data Intensive Computing", Microsoft Technical Report MSR-TR-2008-2187, Sep. 2008.
7. M. Bredel, C. Bredel, D. Juric, G. R. Harsh, H. Vogel, L. D. Recht, B. I. Sikic, "High-Resolution Genome-Wide Mapping of Genetic Alterations in Human Glial Brain Tumors", Cancer Research 65, 4088-4096, May 15, 2005.
8. H. Lee, S. W. Kong, and P. J. Park, "Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes", Bioinformatics 2008 24(7):889-896.
9. S. Bilke, Q. R. Chen, C. C. Whiteford, J. Khan, "Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays", Bioinformatics 2005 21(7):1138-1145.
10. J. M. Nigro, A. Misra, L. Zhang, I. Smirnov, H. Colman, C. Grifn, N. Ozburn, M. Chen, E. Pan, D. Koul, W. K. Yung, B. G. Feuerstein, K. D. Aldape, "Integrated array-comparative genomic hybridization and expression array proles identify clinically relevant molecular subtypes of glioblastoma", Cancer Research 65: 16781686, March 1, 2005.
11. J. A. Veltman, J. Fridlyand, S. Pejavar, A. B. Olshen, J. E. Korkola, S. DeVries, P. Carroll, W. L. Kuo, D. Pinkel, D. Albertson, C. Cordon-Cardo, A. N. Jain, F. M. Waldman, "Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors", Cancer Research (2003) 63: 287280.
12. E. Riedel, G. Gibson, C. Faloutsos, "Active Storage For Large-Scale Data Mining and Multimedia", Proceedings of the 24th Conference on Very Large Databases, August 1998.
13. A. Acharya, M. Uysal, R. Bennett, A. Mendelson, M. Beynon, J. Hollingsworth, J. Saltz, A. Sussman, "Tuning the Performance of I/OIntensive Parallel Applications", Proceedings of the Fourth ACM Workshop on I/O in Parallel and Distributed Systems, May 1996.
14. (04/09/2009). Map/Reduce Tutorial. Retrieved May 21, 2009 from http://hadoop.apache.org/core/docs/current/mapred tutorial.html
15. J. Dean, S. Ghemawat, "MapReduce: Simplied Data Processing on Large Clusters", Google, Inc., December, 2004. http://labs.google.com/papers/ mapreduce.html
16. (04/09/2009). Cluster Setup. Retrieved May 21, 2009 from http://hadoop.apache.org/core/docs/current/cluster setup.html
17. Class JobTracker. Retrieved May 21, 2009 from http://hadoop.apache.org/ core/docs/current/api/org/apache/hadoop/mapred/JobTracker.html
18. (05/20/2009). HadoopMapReduce. Retrieved May 21, 2009 from http://wiki.apache.org/hadoop/HadoopMapReduce
19. (09/20/2008). SequenceFile. Retrieved May 21, 2009 from http://wiki.apache.org/hadoop/SequenceFile
20. (05/20/2009). MapReduce. Retrieved May 21, 2009 from http://wiki.apache. org/hadoop/MapReduce
21. J. Chilson, "Parallel Computation of High Dimensional Robust Correlation and Covariance Matrices." Master's thesis, Western Oregon University, 2001.
22. Interactive Supercomputing. Genomic Correlation at National Cancer Institute. Retrieved August 28, 2009 from http://www.interactivesupercomputing. com/success/genomic correlation.php
23. SPRINT: A new parallel framework for R. Retrieved August 28, 2009 from http://www.r-sprint.org/
24. S. Guha. RHIPE - R and Hadoop Integrated Processing Environment. Retrieved August 28, 2009 from http://ml.stat.purdue.edu/rhipe/index. html