Bioinformatics clouds for big data manipulation

Biology Direct

Volumn 7, Issue , 2012, Pages

  Dai, Lin ^a,b   Gao, Xin ^c   Guo, Yan ^d   Xiao, Jingfa ^a   Zhang, Zhang ^a  

^a Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^b BEIJING INSTITUTE OF TECHNOLOGY   (China)

^c KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^d IBM Research   (China)

Author keywords

Big data; Bioinformatics; Cloud computing; Data analysis; Data storage

Indexed keywords

ACCESS TO INFORMATION; BIOLOGY; CLASSIFICATION; COMPUTER INTERFACE; COMPUTER PROGRAM; EVALUATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; REVIEW;

ACCESS TO INFORMATION; COMPUTATIONAL BIOLOGY; DATA COLLECTION; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84870057823     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-7-43     Document Type: Review

References (44)

1. Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race. Nat Biotechnol 2010, 28(7):691-693. 10.1038/nbt0710-691, 2904649, 20622843.
2. Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012, 30(4):295-296. 10.1038/nbt0412-295, 22491260.
3. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology. Nat Rev Genet 2011, 12(3):224.
4. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet 2010, 11(9):647-657. 10.1038/nrg2857, 3124937, 20717155.
5. Grossman RL, White KP. A vision for a biomedical cloud. J Intern Med 2012, 271(2):122-130. 10.1111/j.1365-2796.2011.02491.x, 22142244.
6. Armbrust M, Fox A, Griffith R, Joseph AD, Katz RH, Konwinski A, Lee G, Patterson DA, Rabkin A, Stoica I, et al. Above the Clouds: A Berkeley View of Cloud Computing 2009, Berkeley: EECS Department, University of California.
7. Garfinkel SL. Architects of the Information Society: Thirty-Five Years of the Laboratory for Computer Science at MIT 1999, Cambridge, MA: The MIT Press.
8. Buyya R, Yeo CS, Venugopal S, Broberg J, Brandic I. Cloud computing and emerging IT platforms: vision, hype, and reality for delivering computing as the 5th utility. Future Gener Comp Sy 2009, 25(6):599-616.
9. Dudley JT, Butte AJ. In silico research in the era of cloud computing. Nat Biotechnol 2010, 28(11):1181-1185. 10.1038/nbt1110-1181, 21057489.
10. Stein LD. The case for cloud computing in genome informatics. Genome Biol 2010, 11(5):207. 10.1186/gb-2010-11-5-207, 2898083, 20441614.
11. Taylor RC. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics 2010, 11(Suppl 12):S1. 10.1186/1471-2105-11-S12-S1, 21351385.
12. Stanoevska-Slabeva K, Wozniak T. Cloud Basics - An Introduction to Cloud Computing. Grid and Cloud Computing: Business Perspective on Technology and Applications 2010, 47-61. Berlin: Springer, Stanoevska K, Wozniak T, Ristol S.
13. Truong HL, Dustdar S. On Analyzing and Specifying Concerns for Data as a Service. 2009 Ieee Asia-Pacific Services Computing Conference (Apscc 2009) 2009, 83-90.
14. DaaS: The New Information Goldmine http://online.wsj.com/article/SB125071202052143965.html.
15. Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol 2011, 7(8):e1002147. 10.1371/journal.pcbi.1002147, 3161908, 21901085.
16. Nguyen T, Shi W, Ruden D. CloudAligner: a fast and full-featured MapReduce based tool for sequence mapping. BMC Res Notes 2011, 4:171. 10.1186/1756-0500-4-171, 3127959, 21645377.
17. Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009, 25(11):1363-1369. 10.1093/bioinformatics/btp236, 2682523, 19357099.
18. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol 2009, 10(11):R134. 10.1186/gb-2009-10-11-r134, 3091327, 19930550.
19. Matsunaga A, Tsugawa M, Fortes J. Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications. Fourth IEEE International Conference on eScience 2008, 222-229.
20. Hong D, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, et al. FX: an RNA-Seq analysis tool on the cloud. Bioinformatics 2012, 28(5):721-723. 10.1093/bioinformatics/bts023, 22257667.
21. Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 2010, 11(8):R83. 10.1186/gb-2010-11-8-r83, 2945785, 20701754.
22. Zhang L, Gu S, Liu Y, Wang B, Azuaje F. Gene set analysis in the cloud. Bioinformatics 2012, 28(2):294-295. 10.1093/bioinformatics/btr630, 22084254.
23. Wall DP, Kudtarkar P, Fusaro VA, Pivovarov R, Patil P, Tonellato PJ. Cloud computing for comparative genomics. BMC Bioinformatics 2010, 11:259. 10.1186/1471-2105-11-259, 3098063, 20482786.
24. Feng X, Grossman R, Stein L. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics 2011, 12:139. 10.1186/1471-2105-12-139, 3103446, 21554709.
25. Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012, Epub ahead of print.
26. Wang Z, Wang Y, Tan KL, Wong L, Agrawal D. eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study. Bioinformatics 2011, 27(8):1045-1051. 10.1093/bioinformatics/btr091, 21367868.
27. Jourdren L, Bernard M, Dillies M-A, Le Crom S. Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses. Bioinformatics 2012, published online April 5, 2012.
28. Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. Harnessing cloud computing with Galaxy Cloud. Nat Biotechnol 2011, 29(11):972-974. 10.1038/nbt.2028, 22068528.
29. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 2010, 11(Suppl 12):S4. 10.1186/1471-2105-11-S12-S4, 3040530, 21210983.
30. Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson K. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 2012, 13(1):42. 10.1186/1471-2105-13-42, 3372431, 22429538.
31. Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 2011, 12:356. 10.1186/1471-2105-12-356, 3228541, 21878105.
32. Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Genome Med 2010, 2(8):51. 10.1186/gm172, 2945008, 20691073.
33. Zhang Z, Bajic VB, Yu J, Cheung K-H, Townsend JP. Data Integration in Bioinformatics: Current Efforts and Challenges. Bioinformatics - Trends and Methodologies 2011, Rijeka, Croatia: InTech - Open Access Publisher, Mahdavi MA.
34. Fox A. Cloud computing-what's in it for me as a scientist?. Science 2011, 331(6016):406-407. 10.1126/science.1198981, 21273473.
35. Deorowicz S, Grabowski S. Compression of DNA sequence reads in FASTQ format. Bioinformatics 2011, 27(6):860-862. 10.1093/bioinformatics/btr014, 21252073.
36. Cox AJ, Bauer MJ, Jakobi T, Rosone G. Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics 2012, 28(11):1415-1419. 10.1093/bioinformatics/bts173, 22556365.
37. Langille MGI, Eisen JA. BioTorrents: a file sharing service for scientific data. PLoS One 2010, 5(4):e10071. 10.1371/journal.pone.0010071, 2854681, 20418944.
38. Sangket U, Phongdara A, Chotigeat W, Nathan D, Kim WY, Bhak J, Ngamphiw C, Tongsima S, Khan AM, Lin H, et al. Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Bioinformatics 2008, 24(2):299-301. 10.1093/bioinformatics/btm570, 18037613.
39. Bishop M. e-Science. Brief Bioinform 2003, 4(3):208-209. 10.1093/bib/4.3.208, 14582515.
40. Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Brief Bioinform 2009, 10(1):1-10. 2638627, 18842678.
41. Marx V. My data are your data. Nat Biotechnol 2012, 30(6):509-511. 10.1038/nbt.2243, 22678394.
42. Rosenthal A, Mork P, Li MH, Stanford J, Koester D, Reynolds P. Cloud computing: a new business paradigm for biomedical information sharing. J Biomed Inform 2010, 43(2):342-353. 10.1016/j.jbi.2009.08.014, 19715773.
43. Dillon T, Wu C, Chang E. Cloud Computing: Issues and Challenges. Int Con Adv Info Net 2011, 27-33.
44. Parameswaran AV, Chaddha A. Cloud interoperability and standardization. SETLabs Briefings 2009, 7(7):19-26.