Hybrid cloud and cluster computing paradigms for life science applications

BMC Bioinformatics

Volumn 11, Issue SUPPL. 12, 2010, Pages

  Qiu, Judy ^a,b   Ekanayake, Jaliya ^a,b   Gunarathne, Thilina ^a,b   Choi, Jong Y ^a,b   Bae, Seung Hee ^a,b   Li, Hui ^a,b   Zhang, Bingjing ^a,b   Wu, Tak Lon ^a,b   Ruan, Yang ^a,b   Ekanayake, Saliya ^a,b   Hughes, Adam ^a,b   Fox, Geoffrey ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTER ENVIRONMENTS; DATA-INTENSIVE COMPUTING; DESIGN AND IMPLEMENTATIONS; ITERATIVE MAPREDUCE; ITERATIVE STRUCTURES; PRODUCTION ENVIRONMENTS; PROGRAMMING ENVIRONMENT; WINDOWS ENVIRONMENT;

CLUSTER COMPUTING; LINEAR ALGEBRA; WINDOWS OPERATING SYSTEM;

OPEN SYSTEMS;

ARTICLE; BIOLOGY; BIOMEDICINE; CLUSTER ANALYSIS; COMPUTER PROGRAM; DATA MINING; METAGENOMICS; METHODOLOGY;

BIOLOGICAL SCIENCE DISCIPLINES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATA MINING; METAGENOMICS; SOFTWARE;

EID: 78650818855     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S12-S3     Document Type: Article

References (33)

1. Armbrust M, Fox, Griffith R, Joseph AD, Katz R, Konwinski A, Lee G, Patterson D, Rabkin A, Stoica I, Zaharia M. Above the Clouds: A Berkeley View of Cloud Computing. Technical report , http://www.eecs.berkeley.edu/Pubs/TechRpts/2009/EECS-2009-28.pdf
2. Press Release Gartner's 2009 Hype Cycle Special Report Evaluates Maturity of 1,650 Technologies. Press Release., http://www.gartner.com/it/page.jsp?id=1124212
3. Cloud Computing Forum & Workshop. 2010, NIST Information Technology Laboratory, Washington DC., http://www.nist.gov/itl/cloud.cfm
4. Nimbus Cloud Computing for Science. , http://www.nimbusproject.org/
5. OpenNebula Open Source Toolkit for Cloud Computing. , http://www.opennebula.org/
6. Sector and Sphere Data Intensive Cloud Computing Platform. , http://sector.sourceforge.net/doc.html
7. Eucalyptus Open Source Cloud Software. , http://open.eucalyptus.com/
8. FutureGrid Grid Testbed. , http://www.futuregrid.org
9. Magellan Cloud for Science. , http://magellan.alcf.anl.gov/, http://www.nersc.gov/nusers/systems/magellan/
10. European Framework 7 project starting June 1 2010 VENUS-C Virtual multidisciplinary EnviroNments USing Cloud infrastructure.
11. Recordings of Presentations Cloud Futures 2010. 2010, Redmond WA., http://research.microsoft.com/en-us/events/cloudfutures2010/videos.aspx
12. Lockheed Martin Cyber Security Alliance: Cloud Computing Whitepaper. 2010, http://www.lockheedmartin.com/data/assets/isgs/documents/CloudComputingWhitePaper.pdf
13. Walker E. Benchmarking Amazon EC2 for High Performance Scientific Computing. USENIX 2008, 33(5)., http://www.usenix.org/publications/login/2008-10/openpdfs/walker.pdf
14. Ekanayake J, Qiu XH, Gunarathne T, Beason S, Fox G. High Performance Parallel Computing with Clouds and Cloud Technologies. Book chapter to Cloud Computing and Software Services: Theory and Techniques 2010, CRC Press (Taylor and Francis), 1439803153., http://grids.ucs.indiana.edu/ptliupages/publications/cloud_handbook_final-with-diagrams.pdf
15. Evangelinos C, Hill CN. Cloud Computing for parallel Scientific HPC Applications: Feasibility of running Coupled Atmosphere-Ocean Climate Models on Amazon's EC2. CCAO8: Cloud Computing and its Applications 2008, Chicago ILL USA.
16. Lange J, Pedretti K, Hudson T, Dinda P, Cui Z, Xia L, Bridges P, Gocke A, laconette S, Levenhagen M, Brightwell R. Palacios and Kitten: New High Performance Operating Systems For Scalable Virtualized and Native Supercomputing. 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010) 2010, Atlanta, GA, USA.
17. Fox G. White Paper: FutureGrid Platform FGPlatform: Rationale and Possible Directions). 2010, http://grids.ucs.indiana.edu/ptliupages/publications/FGPlatform.docx
18. Dean J, Ghemawat S. MapReduce: simplified data processing on large clusters. Commun 2008, 51(1):107-113. ACM.
19. Open source MapReduce Apache Hadoop. , http://hadoop.apache.org/core/
20. Ekanayake J, Gunarathne T, Qiu J, Fox G, Beason S, Choi JY, Ruan Y, Bae SH, Li H. Technical Report: Applicability of DryadLINQ to Scientific Applications. 2010, http://grids.ucs.indiana.edu/ptliupages/publications/DryadReport.pdf
21. Ekanayake J, Balkir A, Gunarathne T, Fox G, Poulain C, Araujo N, Barga R. DryadLINQ for Scientific Analyses. 5th IEEE International Conference on e-Science 2009, Oxford UK.
22. Fox GC, Qiu XH, Beason S, Choi JY, Rho M, Tang H, Devadasan N, Liu G. Biomedical Case Studies in Data Intensive Computing. Keynote talk at The 1st International Conference on Cloud Computing (CloudCom 2009) at Beijing Jiaotong University, China December 1-4, 2009 2009, 2-18. Springer Verlag LNC 5931 "Cloud Computing", Jaatun M., Zhao, G., Rong, C.
23. Bae SH, Choi JH, Qiu J, Fox J. Dimension Reduction and Visualization of Large High-dimensional Data via Interpolation. Proceedings of ACM HPDC 2010 conference 2010, Chicago, Illinois.
24. Sammon JW. A nonlinear mapping for data structure analysis. IEEE Trans. Computers 1969, C-18:401-409.
25. Ekanayake J, . Computer Science PhD ARCHITECTURE AND PERFORMANCE OF RUNTIME ENVIRONMENTS FOR DATA INTENSIVE SCALABLE COMPUTING. 2010, Bloomington: Indiana, Computer Science PhD.
26. Fox GC. Algorithms and Application for Grids and Clouds. 22nd ACM Symposium on Parallelism in Algorithms and Architectures 2010, http://grids.ucs.indiana.edu/ptliupages/presentations/SPAAJune14-10.pptx
27. Fox GC, Williams RD, Messina PC. Parallel computing works!. 1994, Morgan Kaufmann Publishers., http://www.old-npac.org/copywrite/pcw/node278.html#SECTION001440000000000000000
28. Chu, Cheng T, Sang KK, Yi LA, Yu Y, Bradski R, Ng A, Olukotun K. Map-Reduce for Machine Learning on Multicore. NIPS 2006, MIT Press.
29. Twister Home page. , http://www.iterativemapreduce.org/
30. Qiu X, Ekanayake J, Beason S, Gunarathne T, Fox G, Barga R, Gannon D. Cloud Technologies for Bioinformatics Applications. Proceedings of the 2nd ACM Workshop on Many-Task Computing on Grids and Supercomputers (SC09) 2009, Portland, Oregon., http://grids.ucs.indiana.edu/ptliupages/publications/MTAGSOct22-09A.pdf
31. The ClueWeb09 Dataset. , http://boston.lti.cs.cmu.edu/Data/clueweb09/
32. Ekanayake J, Li H, Bingjing B, Gunarathne T, Bae SH, Qiu J, Fox G. Twister: A Runtime for Iterative MapReduce. Proceedings of the First International Workshop on MapReduce and its Applications of ACM HPDC 2010 conference 2010, Chicago, Illinois.
33. Gunarathne T, Wu TL, Qiu J, Fox G. Cloud Computing Paradigms for Pleasingly Parallel Biomedical Applications. Proceedings of Emerging Computational Methods for the Life Sciences Workshop of ACM HPDC 2010 conference 2010, 20-25. Chicago, Illinois.