Biomedical cloud computing with amazon web services

PLoS Computational Biology

Volumn 7, Issue 8, 2011, Pages

  Fusaro, Vincent A ^a   Patil, Prasad ^a   Gafni, Erik ^a   Wall, Dennis P ^a,b   Tonellato, Peter J ^a,b  

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

^b BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMAZON WEB SERVICES; CLOUD-COMPUTING;

CLOUD COMPUTING;

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; BIOMEDICAL TECHNOLOGY ASSESSMENT; COMPUTER SECURITY; COST BENEFIT ANALYSIS; DATA EXTRACTION; GENE MAPPING; INTERNET; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEDICAL INFORMATICS; MEDICAL RESEARCH; ONLINE SYSTEM; PROCESS DEVELOPMENT; WEB BROWSER; BIOLOGY; COMPUTER PROGRAM; ECONOMICS; INFORMATION RETRIEVAL; METHODOLOGY;

COMPUTATIONAL BIOLOGY; COMPUTER SECURITY; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SOFTWARE;

EID: 80052308152     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002147     Document Type: Article

References (14)

1. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL, (2009) Searching for SNPs with cloud computing. Genome Biol 10: R134.
2. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
3. Schatz MC, (2009) CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 25: 1363-1369.
4. Wall DP, Kudtarkar P, Fusaro VA, Pivovarov R, Patil P, et al. (2010) Cloud computing for comparative genomics. BMC Bioinformatics 11: 259.
5. Halligan BD, Geiger JF, Vallejos AK, Greene AS, Twigger SN, (2009) Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms. J Proteome Res 8: 3148-3153.
6. Vaquero L, Merino L, Caceres J, Lindner M, (2009) A break in the clouds: towards a cloud definition. ACM SIGCOMM Computer Communication Review 39: 50-55.
7. Kudtarkar P, Deluca TF, Fusaro VA, Tonellato PJ, Wall DP, (2010) Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Evol Bioinform Online 6: 197-203.
8. Dean JG, Ghemawat S, (2004) MapReduce: simplified data processing on large clusters. OSDI'04 Proceedings of the 6th conference on Symposium on Opearting Systems Design & Implementation; 6-8 December 2004; San Francisco, California, USA. Volume 6. New York: ACM pp. 137-150.
9. Taylor RC, (2010) An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics 11 (Suppl 12): S1.
10. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
11. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
12. Armbrust M, Fox A, Griffith R, Joseph AD, Katz RH, et al. (2009) Above the clouds: a berkeley view of cloud computing. Berkeley EECS Department, University of California, Berkeley.
13. Rosenthal A, Mork P, Li MH, Stanford J, Koester D, et al. (2009) Cloud computing: a new business paradigm for biomedical information sharing. J Biomed Inform 43: 342-353.
14. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP, (2010) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11: 647-657.