-
1
-
-
84893335124
-
-
AWE project
-
AWE project. https://github.com/MG-RAST/AWE
-
-
-
-
2
-
-
84893307247
-
-
Earth Microbiome Project. http://www.earthmicrobiome.org
-
-
-
-
3
-
-
84893267109
-
-
FASTA format. http://en.wikipedia.org/wiki/FASTA format
-
-
-
-
4
-
-
84893218700
-
-
MG-RAST website
-
MG-RAST website. http://metagenomics.anl.gov
-
-
-
-
5
-
-
84893249433
-
-
MongoDB. http://www.mongodb.org
-
-
-
-
6
-
-
84893273053
-
-
NIH Human Microbiome Project
-
NIH Human Microbiome Project. http://www.hmpdacc.org
-
-
-
-
7
-
-
84893309896
-
-
Shock project
-
Shock project. https://github.com/MG-RAST/Shock
-
-
-
-
8
-
-
84893319436
-
-
Oracle Grid Engine
-
Oracle Grid Engine. http://www.oracle.com/us/products/tools/oracle- gridengine-075549.html
-
-
-
-
10
-
-
44449119442
-
Metagenomics: Exploring unseen communities
-
N. Blow, "Metagenomics: Exploring unseen communities," Nature, 453:687-690, 2008.
-
(2008)
Nature
, vol.453
, pp. 687-690
-
-
Blow, N.1
-
11
-
-
77951226627
-
The sanger fastq file format for sequences with quality scores, and the solexa/illumina fastq variants
-
P. Cock, C. Fields, N. Goto, M. Heuer, and P. Rice,"The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants," Nucl. Acids Res., 38(6):1767-1771, 2010.
-
(2010)
Nucl. Acids Res.
, vol.38
, Issue.6
, pp. 1767-1771
-
-
Cock, P.1
Fields, C.2
Goto, N.3
Heuer, M.4
Rice, P.5
-
13
-
-
29644434815
-
Pegasus: A framework for mapping complex scientific workflows onto distributed systems
-
E. Deelman, G. Singh, M. Su, J. Blythe, Y. Gil, C. Kesselman, G. Mehta, K. Vahi, G. Berriman, J. Good, A. Laity, J. Jacob, and D. Katz, "Pegasus: A framework for mapping complex scientific workflows onto distributed systems," Scientific Programming, 13:219-237, 2005.
-
(2005)
Scientific Programming
, vol.13
, pp. 219-237
-
-
Deelman, E.1
Singh, G.2
Su, M.3
Blythe, J.4
Gil, Y.5
Kesselman, C.6
Mehta, G.7
Vahi, K.8
Berriman, G.9
Good, J.10
Laity, A.11
Jacob, J.12
Katz, D.13
-
14
-
-
84856456747
-
From genomics to metagenomics
-
N. Desai, D. Antonopoulos, J. Gilbert, E. Glass, and F. Meyer, "From genomics to metagenomics," Current Opinion in Biotechnology, 23:72-76, 2012.
-
(2012)
Current Opinion in Biotechnology
, vol.23
, pp. 72-76
-
-
Desai, N.1
Antonopoulos, D.2
Gilbert, J.3
Glass, E.4
Meyer, F.5
-
16
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life science
-
J. Goecks, A. Nekrutenko, J. Taylor, et al., "Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life science," Genome Biology, 11:R86, 2010.
-
(2010)
Genome Biology
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
17
-
-
0036226603
-
Blat-The blast-like alignment tool
-
W. J. Kent, "BLAT-The BLAST-like alignment tool," Genome Research, 12(4):656-664, 2002.
-
(2002)
Genome Research
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
18
-
-
33646040949
-
Scientific workflow management and the kepler system
-
B. Ludascher, C. Berkley, M. Jones, and E. A. Lee, "Scientific workflow management and the Kepler system," Concurrency and Computation: Practice and Experience, 18(10):1039-1065, 2006.
-
(2006)
Concurrency and Computation: Practice and Experience
, vol.18
, Issue.10
, pp. 1039-1065
-
-
Ludascher, B.1
Berkley, C.2
Jones, M.3
Lee, E.A.4
-
19
-
-
77956295988
-
The genome analysis toolkit: A mapreduce framework for analyzing next-generation dna sequencing data
-
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M. DePristo, "The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data," Genome Research, 20(9):1297-1303, 2010.
-
(2010)
Genome Research
, vol.20
, Issue.9
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
Depristo, M.11
-
20
-
-
53549118607
-
The metagenomics rast server-A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
F. Meyer, D. Paarmann, M. D'Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, and R. Edwards, " The metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes," BMC Bioinformatics, 9(386):1-8, 2008.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.386
, pp. 1-8
-
-
Meyer, F.1
Paarmann, D.2
D'souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
Wilkening, J.11
Wards, R.12
-
21
-
-
77955037242
-
Taverna, reloaded
-
P. Missier, S. Soiland-Reyes, S. Owen, W. Tan, A. Nenadic, I. Dunlop, A. Williams, T. Oinn, and C. Goble, "Taverna, reloaded," In Proc. of International Conference on Scientific and Statistical Database Management (SSDBM), 2010.
-
(2010)
Proc. of International Conference on Scientific and Statistical Database Management (SSDBM)
-
-
Missier, P.1
Soiland-Reyes, S.2
Owen, S.3
Tan, W.4
Nenadic, A.5
Dunlop, I.6
Williams, A.7
Oinn, T.8
Goble, C.9
-
23
-
-
70249089090
-
Single-molecule sequencing of an individual human genome
-
D. Pushkarev, N. Neff, and S. Quake, "Single-molecule sequencing of an individual human genome," Nature Biotechnoly, 27:847-850, 2009.
-
(2009)
Nature Biotechnoly
, vol.27
, pp. 847-850
-
-
Pushkarev, D.1
Neff, N.2
Quake, S.3
-
24
-
-
78650818855
-
Hybrid cloud and cluster computing paradigms for life science applications
-
J. Qiu, J. Ekanayake, T. Gunarathne, J. Y. Choi, S.-H. Bae, H. Li, B. Zhang, T.-L.Wu, Y. Ruan, S. Ekanayake, A. Hughes, and G. Fox, "Hybrid cloud and cluster computing paradigms for life science applications," BMC Bioinformatics, 11(12):53, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.12
, pp. 53
-
-
Qiu, J.1
Ekanayake, J.2
Gunarathne, T.3
Choi, J.Y.4
Bae, S.-H.5
Li, H.6
Zhang, B.7
Wu, T.-L.8
Ruan, Y.9
Ekanayake, S.10
Hughes, A.11
Fox, G.12
-
25
-
-
77956001224
-
Grid portals for bioinformatics
-
L. Ramakrishnan, M. S. Reed, J. L. Tilson, and D. A. Reed, "Grid portals for bioinformatics," in International Workshop on Grid Computing Environments, 2006.
-
(2006)
International Workshop on Grid Computing Environments
-
-
Ramakrishnan, L.1
Reed, M.S.2
Tilson, J.L.3
Reed, D.A.4
-
26
-
-
78651266825
-
Community cyberinfrastructure for advanced microbial ecology research and analysis: The camera resource
-
doi: 10.1093/nar/gkq1102
-
S. Sun, J. Chen, W. Li, I. Altinatas, A. Lin, S. Peltier, K. Stocks, E. Allen, M. Ellisman, J. Grethe, and J. Wooley, "Community cyberinfrastructure for advanced microbial ecology research and analysis: The CAMERA resource," Nucleic Acids Research, 2010. doi: 10.1093/nar/gkq1102
-
(2010)
Nucleic Acids Research
-
-
Sun, S.1
Chen, J.2
Li, W.3
Altinatas, I.4
Lin, A.5
Peltier, S.6
Stocks, K.7
Allen, E.8
Ellisman, M.9
Grethe, J.10
Wooley, J.11
-
27
-
-
84886729585
-
Multi-domain job coscheduling on leadership computing systems
-
W. Tang, N. Desai, V. Vishwanath, and Z. Lan, "Multi-domain job coscheduling on leadership computing systems," The Journal of Supercomputing, 63(2):367-384, 2013.
-
(2013)
The Journal of Supercomputing
, vol.63
, Issue.2
, pp. 367-384
-
-
Tang, W.1
Desai, N.2
Vishwanath, V.3
Lan, Z.4
-
28
-
-
14244258507
-
Distributed computing in practice: The condor experience
-
D. Thain, T. Tannenbaum, and M. Livny, "Distributed computing in practice: the Condor experience,"Concurrency and Computation: Practice and Experience, 17(2-4): 323-356, 2005.
-
(2005)
Concurrency and Computation: Practice and Experience
, vol.17
, Issue.2-4
, pp. 323-356
-
-
Thain, D.1
Tannenbaum, T.2
Livny, M.3
-
29
-
-
84893278529
-
-
U.S. Department of Energy. The Magellan report on cloud computing at
-
U.S. Department of Energy. The Magellan report on cloud computing. Available at: http://science.energy.gov//media/ascr/pdf/programdocuments/ docs/Magellan Final Report.pdf
-
-
-
-
30
-
-
80052036917
-
Swift: A language for distributed parallel scripting
-
M. Wilde, M. Hategan, J. M. Wozniak, B. Clifford, D. S. Katz, and I. Foster, "Swift: A language for distributed parallel scripting," Parallel Computing, 37(9):633-652, 2011.
-
(2011)
Parallel Computing
, vol.37
, Issue.9
, pp. 633-652
-
-
Wilde, M.1
Hategan, M.2
Wozniak, J.M.3
Clifford, B.4
Katz, D.S.5
Foster, I.6
-
31
-
-
80054941833
-
An experience report: Porting the mg-rast rapid metagenomics analysis pipeline to the cloud
-
A.Wilke, J.Wilkening, E. Glass, N. Desai, and F. Meyer, "An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud," Concurrency and Computation: Practice and Experience, 23:2250-2257, 2011.
-
(2011)
Concurrency and Computation: Practice and Experience
, vol.23
, pp. 2250-2257
-
-
Wilke, A.1
Wilkening, J.2
Glass, E.3
Desai, N.4
Meyer, F.5
-
33
-
-
72049101204
-
Using clouds for metagenomics: A case study
-
J. Wilkening, A. Wilke, N. Desai, and F. Meyer, "Using clouds for metagenomics: A case study," in Proc. of IEEE International Conference on Cluster Computing, 2009.
-
(2009)
Proc. of IEEE International Conference on Cluster Computing
-
-
Wilkening, J.1
Wilke, A.2
Desai, N.3
Meyer, F.4
|