-
1
-
-
77954526823
-
The case for cloud computing in genome informatics
-
Jan.
-
L. D. Stein, "The case for cloud computing in genome informatics." Genome biology, vol. 11, no. 5, p. 207, Jan. 2010.
-
(2010)
Genome Biology
, vol.11
, Issue.5
, pp. 207
-
-
Stein, L.D.1
-
2
-
-
70249111091
-
Targeted capture and massively parallel sequencing of 12 human exomes
-
Sep.
-
S. B. Ng, E. H. Turner, P. D. Robertson, S. D. Flygare, A. W. Bigham, C. Lee, T. Shaffer, M. Wong, A. Bhattacharjee, E. E. Eichler, M. Bamshad, D. A. Nickerson, and J. Shendure, "Targeted capture and massively parallel sequencing of 12 human exomes." Nature, vol. 461, no. 7261, pp. 272-6, Sep. 2009.
-
(2009)
Nature
, vol.461
, Issue.7261
, pp. 272-276
-
-
Ng, S.B.1
Turner, E.H.2
Robertson, P.D.3
Flygare, S.D.4
Bigham, A.W.5
Lee, C.6
Shaffer, T.7
Wong, M.8
Bhattacharjee, A.9
Eichler, E.E.10
Bamshad, M.11
Nickerson, D.A.12
Shendure, J.13
-
3
-
-
84866551236
-
Annotate-it: A swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
-
Sep.
-
A. Sifrim, J. K. Van Houdt, L.-C. Tranchevent, B. Nowakowska, R. Sakai, G. A. Pavlopoulos, K. Devriendt, J. R. Vermeesch, Y. Moreau, and J. Aerts, "Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease." Genome medicine, vol. 4, no. 9, p. 73, Sep. 2012.
-
(2012)
Genome Medicine
, vol.4
, Issue.9
, pp. 73
-
-
Sifrim, A.1
Van Houdt, J.K.2
Tranchevent, L.-C.3
Nowakowska, B.4
Sakai, R.5
Pavlopoulos, G.A.6
Devriendt, K.7
Vermeesch, J.R.8
Moreau, Y.9
Aerts, J.10
-
4
-
-
84887041034
-
EXtasy: Variant prioritization by genomic data fusion
-
Nov.
-
A. Sifrim, D. Popovic, L.-C. Tranchevent, A. Ardeshirdavani, R. Sakai, P. Konings, J. R. Vermeesch, J. Aerts, B. De Moor, and Y. Moreau, "eXtasy: variant prioritization by genomic data fusion." Nature methods, vol. 10, no. 11, pp. 1083-4, Nov. 2013.
-
(2013)
Nature Methods
, vol.10
, Issue.11
, pp. 1083-1084
-
-
Sifrim, A.1
Popovic, D.2
Tranchevent, L.-C.3
Ardeshirdavani, A.4
Sakai, R.5
Konings, P.6
Vermeesch, J.R.7
Aerts, J.8
De Moor, B.9
Moreau, Y.10
-
5
-
-
84896448861
-
A survey of tools for variant analysis of next-generation genome sequencing data
-
Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, and Z. Trajanoski Jan.
-
S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, and Z. Trajanoski, "A survey of tools for variant analysis of next-generation genome sequencing data." Briefings in bioinformatics, pp. bbs086-, Jan. 2013.
-
(2013)
Briefings in Bioinformatics
-
-
Pabinger, S.1
Dander M, A.2
-
6
-
-
84904542288
-
Supporting NGS pipelines in the cloud
-
I. B. Blanquer, G. Brasche, J. Cała, F. Gagliardi, D. Gannon, H. Hiden, H. Soncu, K. Takeda, A. Tomás, and S. Woodman, "Supporting NGS Pipelines in the cloud," EMBnet.journal, vol. 19, pp. 14-16, 2013.
-
(2013)
EMBnet.journal
, vol.19
, pp. 14-16
-
-
Blanquer, I.B.1
Brasche, G.2
Cała, J.3
Gagliardi, F.4
Gannon, D.5
Hiden, H.6
Soncu, H.7
Takeda, K.8
Tomás, A.9
Woodman, S.10
-
7
-
-
84857934962
-
Achieving re-producibility by combining provenance with service and workflow versioning
-
Seattle, WA, USA
-
S. Woodman, H. Hiden, P. Watson, and P. Missier, "Achieving Re-producibility by Combining Provenance with Service and Workflow Versioning," in Procs. WORKS 2011, Seattle, WA, USA, 2011.
-
(2011)
Procs. WORKS 2011
-
-
Woodman, S.1
Hiden, H.2
Watson, P.3
Missier, P.4
-
8
-
-
79953210348
-
The open provenance model - Core specification (v1.1)
-
L. Moreau, B. Clifford, J. Freire, J. Futrelle, Y. Gil, P. Groth, N. Kwas-nikowska, S. Miles, P. Missier, J. Myers, B. Plale, Y. Simmhan, E. Stephan, and J. Van Den Bussche, "The Open Provenance Model - Core Specification (v1.1)," Future Generation Computer Systems, vol. 7, no. 21, pp. 743-756, 2011.
-
(2011)
Future Generation Computer Systems
, vol.7
, Issue.21
, pp. 743-756
-
-
Moreau, L.1
Clifford, B.2
Freire, J.3
Futrelle, J.4
Gil, Y.5
Groth, P.6
Kwas-Nikowska, N.7
Miles, S.8
Missier, P.9
Myers, J.10
Plale, B.11
Simmhan, Y.12
Stephan, E.13
Bussche Den J.Van14
-
9
-
-
84958869126
-
Provenance and data differencing for workflow reproducibility analysis
-
P. Missier, S. Woodman, H. Hiden, and P. Watson, "Provenance and data differencing for workflow reproducibility analysis," Concurrency and Computation: Practice and Experience, vol. in Press, pp. n/a-n/a, 2013.
-
(2013)
Concurrency and Computation: Practice and Experience, Vol. in Press
-
-
Missier, P.1
Woodman, S.2
Hiden, H.3
Watson, P.4
-
10
-
-
84888876464
-
Enabling large-scale biomedical analysis in the cloud
-
Jan.
-
Y.-C. Lin, C.-S. Yu, and Y.-J. Lin, "Enabling large-scale biomedical analysis in the cloud." BioMed research international, vol. 2013, p. 185679, Jan. 2013.
-
(2013)
BioMed Research International
, vol.2013
, pp. 185679
-
-
Lin, Y.-C.1
Yu, C.-S.2
Lin, Y.-J.3
-
11
-
-
84871772514
-
ASAP: An environment for automated preprocessing of sequencing data
-
Jan.
-
E. S. Torstenson, B. Li, and C. Li, "ASAP: an environment for automated preprocessing of sequencing data." BMC research notes, vol. 6, no. 1, p. 5, Jan. 2013.
-
(2013)
BMC Research Notes
, vol.6
, Issue.1
, pp. 5
-
-
Torstenson, E.S.1
Li, B.2
Li, C.3
-
12
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Jan.
-
J. Goecks, A. Nekrutenko, and J. Taylor, "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome biology, vol. 11, no. 8, p. R86, Jan. 2010.
-
(2010)
Genome Biology
, vol.11
, Issue.8
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
13
-
-
80755125553
-
Harnessing cloud computing with galaxy cloud
-
Nov.
-
E. Afgan, D. Baker, N. Coraor, H. Goto, I. M. Paul, K. D. Makova, A. Nekrutenko, and J. Taylor, "Harnessing cloud computing with Galaxy Cloud." Nature biotechnology, vol. 29, no. 11, pp. 972-4, Nov. 2011.
-
(2011)
Nature Biotechnology
, vol.29
, Issue.11
, pp. 972-974
-
-
Afgan, E.1
Baker, D.2
Coraor, N.3
Goto, H.4
Paul, I.M.5
Makova, K.D.6
Nekrutenko, A.7
Taylor, J.8
-
14
-
-
84869862536
-
CloudMan as a platform for tool, data, and analysis distribution
-
Jan.
-
E. Afgan, B. Chapman, and J. Taylor, "CloudMan as a platform for tool, data, and analysis distribution." BMC bioinformatics, vol. 13, no. 1, p. 315, Jan. 2012.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.1
, pp. 315
-
-
Afgan, E.1
Chapman, B.2
Taylor, J.3
-
15
-
-
80053490996
-
Taverna, reloaded
-
M. Gertz, T. Hey, and B. Ludaescher, Eds., Heidelberg, Germany
-
P. Missier, S. Soiland-Reyes, S. Owen, W. Tan, A. Nenadic, I. Dunlop, A. Williams, T. Oinn, and C. Goble, "Taverna, reloaded," in Procs. SSDBM 2010, M. Gertz, T. Hey, and B. Ludaescher, Eds., Heidelberg, Germany, 2010. [Online]. Available: http://www.ssdbm2010.org/
-
(2010)
Procs. SSDBM 2010
-
-
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
-
16
-
-
84860503874
-
Tavaxy: Integrating taverna and galaxy workflows with cloud computing support
-
Jan.
-
M. Abouelhoda, S. A. Issa, and M. Ghanem, "Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support." BMC bioinformatics, vol. 13, p. 77, Jan. 2012.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 77
-
-
Abouelhoda, M.1
Issa, S.A.2
Ghanem, M.3
-
17
-
-
84882314832
-
Experiences in building a next-generation sequencing analysis service using galaxy, globus online and amazon web service
-
R. K. Madduri, P. Dave, D. Sulakhe, L. Lacinski, B. Liu, and I. T. Foster, "Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web service," Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery-XSEDE '13, p. 1, 2013.
-
(2013)
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery-XSEDE '13
, pp. 1
-
-
Madduri, R.K.1
Dave, P.2
Sulakhe, D.3
Lacinski, L.4
Liu, B.5
Foster, I.T.6
-
18
-
-
85006201950
-
Lessons learned from implementing a national infrastructure in sweden for storage and analysis of next-generation sequencing data
-
Jan.
-
S. Lampa, M. Dahlö, P. I. Olason, J. Hagberg, and O. Spjuth, "Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data." GigaScience, vol. 2, no. 1, p. 9, Jan. 2013.
-
(2013)
GigaScience
, vol.2
, Issue.1
, pp. 9
-
-
Lampa, S.1
Dahlö, M.2
Olason, P.I.3
Hagberg, J.4
Spjuth, O.5
-
19
-
-
84877929637
-
Personalized cloud-based bioinformatics services for research and education: Use cases and the elasticHPC package
-
Jan.
-
M. El-Kalioby, M. Abouelhoda, J. Krüger, R. Giegerich, A. Sczyrba, D. P. Wall, and P. Tonellato, "Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package." BMC bioinformatics, vol. 13 Suppl 1, no. Suppl 17, p. S22, Jan. 2012.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL 1
-
-
El-Kalioby, M.1
Abouelhoda, M.2
Krüger, J.3
Giegerich, R.4
Sczyrba, A.5
Wall, D.P.6
Tonellato, P.7
-
20
-
-
84864800625
-
Cloudgene: A graphical execution platform for mapreduce programs on private and public clouds
-
Jan.
-
S. Schönherr, L. Forer, H. Weiß ensteiner, F. Kronenberg, G. Specht, and A. Kloss-Brandstätter, "Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds." BMC bioin-formatics, vol. 13, no. 1, p. 200, Jan. 2012.
-
(2012)
BMC Bioin-formatics
, vol.13
, Issue.1
, pp. 200
-
-
Schönherr, S.1
Forer, L.2
Weißensteiner, H.3
Kronenberg, F.4
Specht, G.5
Kloss-Brandstätter, A.6
-
21
-
-
84883788980
-
Big data, hadoop and cloud computing in genomics
-
A. ODriscoll, J. Daugelaite, and R. D. Sleator, "Big data, Hadoop and cloud computing in genomics," Journal of Biomedical Informatics, vol. 46, no. 5, pp. 774-781, 2013.
-
(2013)
Journal of Biomedical Informatics
, vol.46
, Issue.5
, pp. 774-781
-
-
Odriscoll, A.1
Daugelaite, J.2
Sleator, R.D.3
-
22
-
-
77956295988
-
The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
Sep.
-
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M. a. DePristo, "The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data." Genome research, vol. 20, no. 9, pp. 1297-303, Sep. 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.A.11
-
23
-
-
84874404461
-
Developing cloud applications using the e-science central platform
-
jan
-
H. Hiden, S. Woodman, P. Watson, and J. Cała, "Developing cloud applications using the e-Science Central platform," Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, vol. 371, no. 1983, jan 2013.
-
(2013)
Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
, vol.371
, Issue.1983
-
-
Hiden, H.1
Woodman, S.2
Watson, P.3
Cała, J.4
-
24
-
-
84893786296
-
Cloud computing for fast prediction of chemical activity
-
Feb.
-
J. Cała, H. Hiden, S. Woodman, and P. Watson, "Cloud computing for fast prediction of chemical activity," Future Generation Computer Systems, Feb. 2013.
-
(2013)
Future Generation Computer Systems
-
-
Cała, J.1
Hiden, H.2
Woodman, S.3
Watson, P.4
-
25
-
-
59849095285
-
Workflows and e-science: An overview of workflow system features and capabilities
-
may
-
E. Deelman, D. Gannon, M. Shields, and I. Taylor, "Workflows and e-science: An overview of workflow system features and capabilities," Future Generation Computer Systems, vol. 25, no. 5, pp. 528-540, may 2009.
-
(2009)
Future Generation Computer Systems
, vol.25
, Issue.5
, pp. 528-540
-
-
Deelman, E.1
Gannon, D.2
Shields, M.3
Taylor, I.4
-
26
-
-
84885883700
-
A performance analysis of EC2 cloud computing services for scientific computing
-
S. Ostermann, A. Iosup, N. Yigitbasi, R. Prodan, T. Fahringer, and D. Epema, "A Performance Analysis of EC2 Cloud Computing Services for Scientific Computing," in Cloud Computing, 2010, pp. 115-131.
-
(2010)
Cloud Computing
, pp. 115-131
-
-
Ostermann, S.1
Iosup, A.2
Yigitbasi, N.3
Prodan, R.4
Fahringer, T.5
Epema, D.6
-
27
-
-
70349753672
-
Benchmarking Amazon EC2 for high-performance scientific computing
-
E. Walker, "benchmarking Amazon EC2 for high-performance scientific computing," ;login:, vol. 33, no. 5, pp. 18-23, 2008.
-
(2008)
Login
, vol.33
, Issue.5
, pp. 18-23
-
-
Walker, E.1
-
28
-
-
84880064788
-
A comparative study of high-performance computing on the cloud
-
A. Marathe, R. Harris, D. K. Lowenthal, B. R. de Supinski, B. Rountree, M. Schulz, and X. Yuan, "A comparative study of high-performance computing on the cloud," Proceedings of the 22nd international sympo-sium on High-performance parallel and distributed computing-HPDC '13, p. 239, 2013.
-
(2013)
Proceedings of the 22nd International Sympo-sium on High-performance Parallel and Distributed Computing-HPDC '13
, pp. 239
-
-
Marathe, A.1
Harris, R.2
Lowenthal, D.K.3
De Supinski, B.R.4
Rountree, B.5
Schulz, M.6
Yuan, X.7
|