Streaming support for data intensive cloud-based sequence analysis

BioMed Research International

Volumn 2013, Issue , 2013, Pages

  Issa, Shadi A ^a   Kienzler, Romeo ^b   El Kalioby, Mohamed ^a   Tonellato, Peter J ^c   Wall, Dennis ^c   Bruggmann, Rémy ^d   Abouelhoda, Mohamed ^a,e  

^a NILE UNIVERSITY   (Egypt)

^b IBM   (Switzerland)

^c Harvard Medical School Center for Biomedical Informatics   (United States)

^d UNIVERSITY OF BERN   (Switzerland)

^e CAIRO UNIVERSITY   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CLIENT SERVER APPLICATION; CLOUD COMPUTING SERVICE; COMPUTER PROGRAM; COST EFFECTIVENESS ANALYSIS; DATA PROCESSING; ELASTICITY; HUMAN; NEXT GENERATION SEQUENCING; ONLINE ANALYSIS; WORKFLOW; BIOLOGY; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; INTERNET; PROCEDURES; METHODOLOGY;

COMPUTATIONAL BIOLOGY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; SEQUENCE ANALYSIS, DNA; SOFTWARE; WORKFLOW;

EID: 84878124088     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2013/791051     Document Type: Article

References (46)

1. AWS (Amazon Web Services),. http://aws.amazon.com/
2. Azure W.,. http://www.microsoft.com/windowsazure/
3. IBM Smart Cloud Enterprise,. http://www.ibm.com/cloud-computing/
4. Rackspace,. http://www.rackspace.com/
5. Magellan-a cloud for Science. http://magellan.alcf.anl.gov/
6. DIAG-Data Intensive Academic Grid,. http://diagcomputing.org/
7. Pennisi E., Will computers crash genomics? Science 2011 331 6018 666 668 2-s2.0-79951480044 10.1126/science.331.6018.666
8. Schatz M. C., Langmead B., Salzberg S. L., Cloud computing and the DNA data race. Nature Biotechnology 2010 28 7 691 693 2-s2.0-77954492012 10.1038/nbt0710-691
9. Bateman A., Wood M., Cloud computing. Bioinformatics 2009 25 12 1475 2-s2.0-66349097904 10.1093/bioinformatics/btp274
10. Dudley J. T., Butte A. J., In silico research in the era of cloud computing. Nature Biotechnology 2010 28 11 1181 1185 2-s2.0-78149299776 10.1038/nbt1110-1181
11. Stein L. D., The case for cloud computing in genome informatics. Genome Biology 2010 11 5, article 207 2-s2.0-77954526823 10.1186/gb-2010-11-5-207
12. Fusaro V., Patil P., Gafni E., Wall D., Tonellato P., Biomedical cloud computing with Amazon web services. PLOS Computational Biology 2011 7 8 e1002147
13. Langmead B., Schatz M. C., Lin J., Pop M., Salzberg S. L., Searching for SNPs with cloud computing. Genome Biology 2009 10 11, article R134 2-s2.0-72849149423 10.1186/gb-2009-10-11-r134
14. Wall D., Kudtarkar P., Fusaro V., Pivovarov R., Patil P., Tonellato P., Cloud computing for comparative genomics. BMC Bioinformatics 2010 11 article 259 10.1186/1471-2105-11-259
15. Langmead B., Hansen K. D., Leek J. T., Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 2010 11 8, article R83 2-s2.0-77955343193 10.1186/gb-2010-11-8-r83
16. Schatz M. C., CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009 25 11 1363 1369 2-s2.0-65649120715 10.1093/bioinformatics/ btp236
17. Langmead B., Trapnell C., Pop M., Salzberg S. L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009 10 3, article R25 2-s2.0-62349130698 10.1186/gb-2009-10-3-r25
18. Rapier C., Bennett B., High speed bulk data transfer using the SSH protocol. 11 Proceedings of the 15th ACM Mardi Gras Conference: From Lightweight Mash-Ups to Lambda grids: Understanding the Spectrum of Distributed Computing Requirements, Applications, Tools, Infrastructures, Interoperability, and the Incremental Adoption of Key Capabilities (MG '08) ACM 1 11
19. Oinn T., Addis M., Ferris J., Marvin D., Senger M., Greenwood M., Carver T., Glover K., Pocock M. R., Wipat A., Li P., Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004 20 17 3045 3054 2-s2.0-10244255212 10.1093/bioinformatics/bth361 (Pubitemid 39619196)
20. Hull D., Wolstencroft K., Stevens R., Goble C., Pocock M. R., Li P., Oinn T., Taverna: a tool for building and running workflows of services. Nucleic Acids Research 2006 34 W729 W732 2-s2.0-33747833111 10.1093/nar/gkl320 (Pubitemid 44529867)
21. Giardine B., Riemer C., Hardison R. C., Burhans R., Elnitski L., Shah P., Zhang Y., Blankenberg D., Albert I., Taylor J., Miller W., Kent W. J., Nekrutenko A., Galaxy: a platform for interactive large-scale genome analysis. Genome Research 2005 15 10 1451 1455 2-s2.0-25844449770 10.1101/gr.4086505 (Pubitemid 41400913)
22. StarCluster,. http://web.mit.edu/stardev/cluster/
23. Vappio,. http://vappio.sf.net/
24. Afgan E., Baker D., Coraor N., Chapman B., Nekrutenko A., Taylor J., Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 2010 11 supplement 12, article S4 2-s2.0-78650841579 10.1186/1471-2105-11-S12-S4
25. Goecks J., Nekrutenko A., Taylor J., Team T. G., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 2010 8, article R86 2-s2.0-77955801615 10.1186/gb-2010-11-8-r86
26. Graefe G., Query evaluation techniques for large databases. ACM Computing Surveys 1993 25 2 73 170 2-s2.0-0027608375 10.1145/152610.152611 (Pubitemid 23712749)
27. Logothetis D., Trezzo C., Webb K., Yocum K., In-situ MapReduce for log processing. Proceedings of the USENIX Conference on USENIX Annual Technical Conference (USENIXATC'11) 2011 USENIX Association 9 9
28. Backman N., Pattabiraman K., Cetintemel U., C-MR: a continuous MapReduce processing model for low-latency stream processing on multi-core architectures. 2010
29. Kienzler R., Bruggmann R., Ranganathan A., Tatbul N., Large-scale DNA sequence analysis in the cloud: a stream-based approach. Proceedings of the Euro-Par VHPC Workshop 2011
30. Kienzler R., Bruggmann R., Ranganathan A., Tatbul N., Stream as you go: the case for incremental data access and processing in the cloud. Proceedings of the ICDE DMC Workshop 2012
31. Rumble S. M., Lacroute P., Dalca A. V., Fiume M., Sidow A., Brudno M., SHRiMP: accurate mapping of short color-space reads. PLoS Computational Biology 2009 5 5 2-s2.0-67049159825 10.1371/journal.pcbi.1000386 e1000386
32. s3fs, FUSE-based le system backed by Amazon S3. http://code.google.com/p/ s3fs/
33. Dean J., Ghemawat S., MapReduce: simplied data processing on large clusters. 6 Proceedings of the 6th Conference on Symposium on Opearting Systems Design and Implementation (OSDI '04) 2004 USENIX Association 10 10
34. Linke B., Giegerich R., Goesmann A., Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics 2011 27 7 903 911 2-s2.0-79953305104 10.1093/bioinformatics/btr040 btr040
35. Ludäscher B., Altintas I., Berkley C., Higgins D., Jaeger E., Jones M., Lee E. A., Tao J., Zhao Y., Scientific workflow management and the Kepler system. Concurrency Computation Practice and Experience 2006 18 10 1039 1065 2-s2.0-33646040949 10.1002/cpe.994 (Pubitemid 44258497)
36. Taylor I., Shields M., Wang I., Harrison A., Visual grid workflow in Triana. Journal of Grid Computing 2005 3 3-4 153 169 2-s2.0-33244488521 10.1007/s10723-005-9007-3 (Pubitemid 43280300)
37. Taylor I., Shields M., Wang I., Harrison A., The Triana work ow environment: architecture and applications. Workflows for e-Science 2007 New York, NY, USA Springer 320 339
38. Deelman E., Singh G., Su M. H., Blythe J., Gil Y., Kesselman C., Mehta G., Vahi K., Berriman G. B., Good J., Laity A., Jacob J. C., Katz D. S., Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Scientific Programming 2005 13 3 219 237 2-s2.0-29644434815 (Pubitemid 43022937)
39. Shah S. P., He D. Y. M., Sawkins J. N., Druce J. C., Quon G., Lett D., Zheng G. X. Y., Xu T., Ouellette B. F. F., Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004 5 article 40 2-s2.0-2942544409 10.1186/1471-2105-5-40 (Pubitemid 38751296)
40. Rice P., Longden L., Bleasby A., EMBOSS: the european molecular biology open software suite. Trends in Genetics 2000 16 6 276 277 2-s2.0-0034201441
41. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009 25 16 2078 2079 2-s2.0-68549104404 10.1093/bioinformatics/ btp352
42. FASTX-Toolkit,. http://hannonlab.cshl.edu/fastx-toolkit/
43. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J., Basic local alignment search tool. Journal of Molecular Biology 1990 215 3 403 410 2-s2.0-0025183708 10.1006/jmbi.1990.9999 (Pubitemid 20364473)
44. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997 25 17 3389 3402 2-s2.0-0030801002 10.1093/nar/25.17.3389 (Pubitemid 27359211)
45. Zhang Z., Schwartz S., Wagner L., Miller W., A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 2000 7 1-2 203 214 2-s2.0-0034053725 10.1089/10665270050081478 (Pubitemid 30412170)
46. Eriksen M., Trickle: a userland bandwidth shaper for Unix-like systems. Proceedings of the Annual Conference on USENIX Annual Technical Conference (ATEC '05) 2005 43 43