CloudMan as a platform for tool, data, and analysis distribution

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Afgan, Enis ^a,c   Chapman, Brad ^b   Taylor, James ^c  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c EMORY UNIVERSITY   (United States)

Author keywords

Accessibility; Cloud computing; Galaxy; Reproducibility; Service customization

Indexed keywords

ACCESSIBILITY; CLOUD ANALYSIS; COMPUTATIONAL ANALYSIS; REPRODUCIBILITIES; SERVICE CUSTOMIZATION;

CLOUD COMPUTING; GALAXIES;

RESEARCH;

ARTICLE; COMPUTER PROGRAM; INFORMATION RETRIEVAL;

INFORMATION STORAGE AND RETRIEVAL; SOFTWARE;

MLCS; MLOWN;

EID: 84869862536     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-315     Document Type: Article

References (16)

1. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 2010, 11(12):S4. 10.1186/1471-2105-11-S12-S4, 3040530, 21210983.
2. Afgan E, Baker D, Coraor N, Goto H, Makova K, Nekrutenko A, Taylor J. Harnessing cloud-computing for biomedical research with Galaxy Cloud. Nat Biotechnol 2011, 29(11):972-974. 10.1038/nbt.2028, 22068528.
3. Cloud Biolinux http://www.cloudbiolinux.com/.
4. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
5. Afgan E, Goecks J, Baker D, Coraor N, Nekrutenko A, Taylor J. Galaxy - a gateway to tools in e-science. Guide to e-science: next generation scientific research and discovery 2011, 145-177. London: Springer, Yang K.
6. Big data rains down on seattle http://www.hpcwire.com/hpcwire/2011-10-20/big_data_rains_down_on_seattle.html.
7. 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.
8. 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.
9. Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009, 25(11):1363-1369. 10.1093/bioinformatics/btp236, 2682523, 19357099.
10. Afgan E, Baker D, Nekrutenko A, Taylor J. A reference model for deploying applications in virtualized environments. Concurrency and Computation: Practice and Experience 2012, 24(12):1349-1361. in press.
11. Picard http://picard.sourceforge.net/.
12. FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
13. DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5)):491-498. 3083463, 21478889.
14. SnpEff: variant effect prediction http://snpeff.sourceforge.net/.
15. bcbio_nextgen https://github.com/chapmanb/bcbb/tree/master/nextgen.
16. CloudMan wiki https://bitbucket.org/galaxy/cloudman/wiki/SharedInstances.