BioPerf: A benchmark suite to evaluate high-performance computer architecture on bioinformatics applications

Proceedings of the 2005 IEEE International Symposium on Workload Characterization, IISWC-2005

Volumn 2005, Issue , 2005, Pages 163-173

  Bader, David A ^a   Li, Yue ^b   Li, Tao ^b   Sachdeva, Vipin ^c  

^a Georgia Institute of Technology   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL BIOLOGY; COMPUTER WORKLOADS; SOURCE CODES;

BENCHMARKING; COMPUTER SIMULATION; GENETIC ENGINEERING; LARGE SCALE SYSTEMS; LIVING SYSTEMS STUDIES; PROGRAM COMPILERS;

COMPUTER ARCHITECTURE;

EID: 33749079198     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IISWC.2005.1526013     Document Type: Conference Paper

References (38)

1. J. L. Weber and E. W. Myers, Human Whole Genome Shotgun Sequencing, Genome Research, 7(5): 401-409, 1997.
2. E. Anson and E. W. Myers, Algorithms for Whole Genome Shotgun Sequencing, In Proceedings of 3rd Annual International Conference on Computational Molecular Biology, 1999.
3. J. C. Venter et al., The Sequence of the Human Genome, Science, 291(5507):1304-1351, 2001.
4. M. Schena, D. Shalon, R.W. Davis, and P.O. Brown. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray, Science, 270(5235):467-470, 1995.
5. http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html
6. Bioinformation Market Study for Washington Technology Center, Alta Biomedical Group LLC, www.altabiomedical.com, June 2003.
7. T. Sherwood, E. Perelman, G. Hamerly and B. Calder, Automatically Characterizing Large Scale Program Behavior, In Proceedings of the International Conference on Architectural Support for Programming Languages and Operating Systems, 2002.
8. S. C. Woo, M. Ohara, E. Torrie, J. P. Singh, and A. Gupta, The SPLASH-2 Programs: Characterization and Methodological Considerations, In Proceedings of the International Symposium on Computer Architecture, 1995.
9. K. Albayraktaroglu, A. Jaleel, X. Wu, M. Franklin, B. Jacob, C.-W. Tseng, and D. Yeung, BioBench: A Benchmark Suite of Bioinformatics Applications, In Proceedings of the International Symposium on Performance Analysis of Software and Systems, 2005.
10. Y. Li, T. Li, T. Kahveci and J. Fortes, Workload Characterization of Bioinformatics Applications on Pentium 4 Architecture, In Proceedings of the International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems, 2005.
11. D. A. Bader, V. Sachdeva, V. Agarwal, G. Goel, A. N. Singh, BioSPLASH: A Sample Workload for Bioinformatics and Computational Biology for Optimizing Next-Generation Performance Computer Systems, Technical Report, University of New Mexico, April 2005.
12. The RCSB Protein Data Bank, http://www.rcsb.org/pdb/
13. D. A. Bader, Computational Biology and High-Performance Computing, Special Issue on Bioinformatics, Communications of the ACM, 47(11):34-41, 2004.
14. European Molecular Biology Laboratory, http://www.embl-heidelberg.de
15. DNA Data Bank of Japan, http://www.ddbj.nig.ac.jp/
16. The UniProt/Swiss-Prot Database, http://www.ebi.ac.uk/swissprot/
17. S. Altschul, W. Gish, W. Miller, E. W. Meyers and D. J. Lipman, Basic Local Alignment Search Tool, Journal of Molecular Biology, vol. 215, no. 3, pages 403-410, 1990.
18. W. R. Pearson and D. J. Lipman, Improved Tools for Biological Sequence Comparison, Proc. Natl. Acad. Sci., 85 (1988), 3244-3248.
19. J. D. Thompson, D. G. Higgins, and T. J. Gibson, Clustal W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Positions-specific Gap Penalties and Weight Matrix Choice, Nucleic Acids Research, vol. 22, no. 22, pages 4673-4680, 1994.
20. S. R. Eddy, Profile Hidden Markov Models, Bioinformatics Review, vol. 14, no. 9, page 755-763, 1998.
21. C. Notredame, D. Higgins, and J. Heringa. T-Coffee: A Novel Method for Multiple Sequence Alignments, J. Molecular Biology, 302:205-217, 2000.
22. S. Salzberg, A. Deicher, S. Kasif, and O. White, Microbial Gene Identification using Interpolated Markov Models, Nucleic Acids Research, vol. 26, no. 2, page 544-548, 1998.
23. J. Felsenstein, PHYLIP - Phylogeny Inference Package (version 3.2), Cladistics, 5: 164-166, 1989.
24. B. M. E. Moret, D. A. Bader, T. Warnow, S. K. Wyman, and M. Yan, GRAPPA: A High Performance Computational Tool for Phylogeny Reconstruction from Gene-Order Data, In Proc. Botany, Albuquerque, NM, August 2001.
25. M. Blanchette, G. Bourque, and D. Sankoff, Breakpoint Phylogenies, In S. Miyano and T. Takagi, editors, Genome Informatics, pages 25-34. University Academy Press, Tokyo, Japan, 1997.
26. D. A. Bader, B. M. E. Moret, and M. Yan, A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study, Journal of Computational Biology, 8(5):483-491, 2001.
27. I. N. Shindyalov, and P. E. Bourne, Protein Structure Alignment by Incremental Combinatorial Extension (CE) of the Optimal Path, Protein Engineering, vol. 11, no. 99, page 739-747, 1998.
28. D. Frishman, and P. Argos, 75% Accuracy in Protein Secondary Structure Prediction, Proteins, vol. 27, page 329-335, 1997.
29. Y. Li and T. Li, BioInfoMark: A Bioinformatics Benchmark Suite for Computer Architecture Research, Technical Report, IDEAL Research, ECE Dept., University of Florida, January 2005.
30. T. Kahveci, V. Ramaswamy, H. Tao and T. Li, Approximate Global Alignment of Sequences, IEEE Symposium on Bioinformatics and Bioengineering, 2005.
31. Simplescalar, http://www.simplescalar.com/
32. R. Desikan, D. Burger, and S. W. Keckler. Measuring Experimental Error in Microprocessor Simulation, In Proceedings of the International Symposium on Computer Architecture, 2001.
33. The M5 Simulator System, http://m5.eecs.umich.edu/
34. G. Hamerly, E. Perelman and B. Calder, How to Use SimPoint to Pick Simulation Points, ACM SIGMETRICS Performance Evaluation Review, 2004.
35. D. A. Bader, V. Sachdeva, A. Trehan, V. Agarwal, G. Gupta, and A.N. Singh, BioSPLASH: A Sample Workload from Bioinformatics and Computational Biology for Optimizing Next-Generation High-Performance Computer Systems, (Poster Session), 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005).
36. D. A. Bader, V. Sachdeva, BioSPLASH: Incorporating Life Sciences Applications in the Architectural Optimizations of Next-Generation Petaflop-System, (Poster Session), The 4th IEEE Computational Systems 4th IEEE Computational Systems Bioinformatics Conference (CSB 2005).
37. P. Bohrer, M. Elnozahy, A. Gheith, C. Lefurgy, T. Nakra, J. Peterson, R. Rajamony, R. Rockhold, H. Shafi, R. Simpson, E. Speight, K. Sudeep, E. Van Hensbergen, and L. Zhang. Mambo - A Full System Simulator for the PowerPC Architecture, ACM SIGMETRICS Performance Evaluation Review, 31(4):8-12, 2004.
38. Apple Computer, Inc. PowerPC G5: White Paper, images.apple.com/powermac/ pdf/PowerPCG5WP06092004.pdf.