Computational biology in the cloud: Methods and new insights from computing at scale

Pacific Symposium on Biocomputing

Volumn , Issue , 2013, Pages 451-453

  Kasson, Peter M ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLOUD COMPUTING; MOLECULAR BIOLOGY;

AMOUNT OF INFORMATION; COMPUTATIONAL BIOLOGY; COMPUTING PARADIGM; NON TRIVIAL PROBLEMS; ON-DEMAND COMPUTING; PERFORMANCE LIMITING FACTOR; REPRODUCIBILITIES; STRUCTURE AND DYNAMICS;

DIGITAL STORAGE;

BIOLOGY; COMPUTER INTERFACE; FACTUAL DATABASE; HUMAN; INFORMATION DISSEMINATION; INFORMATION RETRIEVAL; PROCEDURES; STATISTICS AND NUMERICAL DATA; CONFERENCE PAPER; METHODOLOGY; STATISTICS;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; INFORMATION DISSEMINATION; INFORMATION STORAGE AND RETRIEVAL; USER-COMPUTER INTERFACE;

EID: 84891389270     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (11)

1. Konig, R., Y. Zhou, D. Elleder, T.L. Diamond, G.M. Bonamy, J.T. Irelan, C.Y. Chiang, B.P. Tu, P.D. De Jesus, C.E. Lilley, S. Seidel, A.M. Opaluch, J.S. Caldwell, M.D. Weitzman, K.L. Kuhen, S. Bandyopadhyay, T. Ideker, A.P. Orth, L.J. Miraglia, F.D. Bushman, J.A. Young, and S.K. Chanda, Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell, 2008. 135(1): p. 49-60.
2. Karlas, A., N. Machuy, Y. Shin, K.P. Pleissner, A. Artarini, D. Heuer, D. Becker, H. Khalil, L.A. Ogilvie, S. Hess, A.P. Maurer, E. Muller, T. Wolff, T. Rudel, and T.F. Meyer, Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature, 2010. 463(7282): p. 818-22.
3. Hao, L., A. Sakurai, T. Watanabe, E. Sorensen, C.A. Nidom, M.A. Newton, P. Ahlquist, and Y. Kawaoka, Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature, 2008. 454(7206): p. 890-3.
4. Jager, S., P. Cimermancic, N. Gulbahce, J.R. Johnson, K.E. McGovern, S.C. Clarke, M. Shales, G. Mercenne, L. Pache, K. Li, H. Hernandez, G.M. Jang, S.L. Roth, E. Akiva, J. Marlett, M. Stephens, I. D'Orso, J. Fernandes, M. Fahey, C. Mahon, A.J. O'Donoghue, A. Todorovic, J.H. Morris, D.A. Maltby, T. Alber, G. Cagney, F.D. Bushman, J.A. Young, S.K. Chanda, W.I. Sundquist, T. Kortemme, R.D. Hernandez, C.S. Craik, A. Burlingame, A. Sali, A.D. Frankel, and N.J. Krogan, Global landscape of HIV-human protein complexes. Nature, 2012. 481(7381): p. 365-70.
5. Hawrylycz, M.J., E.S. Lein, A.L. Guillozet-Bongaarts, E.H. Shen, L. Ng, J.A. Miller, L.N. van de Lagemaat, K.A. Smith, A. Ebbert, Z.L. Riley, C. Abajian, C.F. Beckmann, A. Bernard, D. Bertagnolli, A.F. Boe, P.M. Cartagena, M.M. Chakravarty, M. Chapin, J. Chong, R.A. Dalley, B.D. Daly, C. Dang, S. Datta, N. Dee, T.A. Dolbeare, V. Faber, D. Feng, D.R. Fowler, J. Goldy, B.W. Gregor, Z. Haradon, D.R. Haynor, J.G. Hohmann, S. Horvath, R.E. Howard, A. Jeromin, J.M. Jochim, M. Kinnunen, C. Lau, E.T. Lazarz, C. Lee, T.A. Lemon, L. Li, Y. Li, J.A. Morris, C.C. Overly, P.D. Parker, S.E. Parry, M. Reding, J.J. Royall, J. Schulkin, P.A. Sequeira, C.R. Slaughterbeck, S.C. Smith, A.J. Sodt, S.M. Sunkin, B.E. Swanson, M.P. Vawter, D. Williams, P. Wohnoutka, H.R. Zielke, D.H. Geschwind, P.R. Hof, S.M. Smith, C. Koch, S.G. Grant, and A.R. Jones, An anatomically comprehensive atlas of the adult human brain transcriptome. Nature, 2012. 489(7416): p. 391-9.
6. Schatz, M.C., B. Langmead, and S.L. Salzberg, Cloud computing and the DNA data race. Nat Biotechnol, 2010. 28(7): p. 691-3.
7. Dudley, J.T. and A.J. Butte, In silico research in the era of cloud computing. Nat Biotechnol, 2010. 28(11): p. 1181-5.
8. Schadt, E.E., M.D. Linderman, J. Sorenson, L. Lee, and G.P. Nolan, Computational solutions to large-scale data management and analysis. Nat Rev Genet, 2010. 11(9): p. 647-57.
9. Dean, J. and S. Ghemawat, MapReduce: A Flexible Data Processing Tool. Communications of the Acm, 2010. 53(1): p. 72-77.
10. Dean, J. and S. Ghemawat, Mapreduce: Simplified data processing on large clusters. Communications of the Acm, 2008. 51(1): p. 107-113.
11. Melnik, S., A. Gubarev, J.J. Long, G. Romer, S. Shivakumar, M. Tolton, and T. Vassilakis, Dremel: Interactive Analysis of Web-Scale Datasets. Communications of the Acm, 2011. 54(6): p. 114-123.