Cloud computing approaches to accelerate drug discovery value chain

Combinatorial Chemistry and High Throughput Screening

Volumn 14, Issue 10, 2011, Pages 861-871

  Garg, Vibhav ^a   Arora, Suchir ^a   Gupta, Chitra ^a  

^a Mascon Global Limited   (India)

Author keywords

Cloud architecture; Cloud computing; Discovery cloud; Docking; Grid computing; High content screening; High throughput screening; Microarrays; Next generation sequencing; On demand computing

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COST EFFECTIVENESS ANALYSIS; HIGH THROUGHPUT SCREENING; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; PRIORITY JOURNAL; TECHNOLOGY; VALIDATION PROCESS;

ANIMALS; DRUG DISCOVERY; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICROARRAY ANALYSIS; SOFTWARE;

EID: 80054957203     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/138620711797537085     Document Type: Article

References (43)

1. Venter, J.C.; Adams, M.D.; Myers, E.W.; Li, P.W.; Mural, R.J.; Sutton, G.G.; Smith, H.O.; Yandell, M.; Evans, C.A.; Holt, R.A.; Gocayne, J.D.; Amanatides, P.; Ballew, R.M.; Huson, D.H.; Wortman, J.R.; Zhang, Q.; Kodira, C.D.; Zheng, X.H.; Chen, L.; Skupski, M.; Subramanian, G.; Thomas, P.D.; Zhang, J.; Gabor Miklos, G.L;; Nelson, C.; Broder, S.; Clark, A.G.; Nadeau, J.; McKusick, V.A.; Zinder, N.; Levine, A.J.; Roberts, R.J.; Simon, M.; Slayman, C.; Hunkapiller, M.; Bolanos, R.; Delcher, A.; Dew, I.; Fasulo, D.; Flanigan, M.; Florea, L.; Halpern, A.; Hannenhalli, S.; Kravitz, S.; Levy, S.; Mobarry, C.; Reinert, K.; Remington, K.; Abu-Threideh, J.; Beasley, E.; Biddick, K.; Bonazzi, V.; Brandon, R.; Cargill, M.; Chandramouliswaran, I.; Charlab, R.; Chaturvedi, K.; Deng, Z.; Di Francesco, V.; Dunn, P.; Eilbeck, K.; Evangelista, C.; Gabrielian, A.E.; Gan, W.; Ge, W.; Gong, F.; Gu, Z.; Guan, P.; Heiman, T.J.; Higgins, M.E.; Ji, R.R.; Ke, Z.; Ketchum, K.A.; Lai, Z.; Lei, Y.; Li, Z.; Li, J.; Liang, Y.; Lin, X.; Lu, F.; Merkulov, G.V.; Milshina, N.; Moore, H.M.; Naik, A.;, Narayan, V.A.; Neelam, B.; Nusskern, D.; Rusch, D.B.; Salzberg, S.; Shao, W.; Shue, B.; Sun, J.; Wang, Z.; Wang, A.; Wang, X.; Wang, J.; Wei, M.; Wides, R.; Xiao, C.; Yan, C.; Yao, A.; Ye, J.; Zhan, M.; Zhang, W.; Zhang, H.; Zhao, Q.; Zheng, L.; Zhong, F.; Zhong, W.; Zhu, S.; Zhao, S.; Gilbert, D.; Baumhueter, S.; Spier, G.; Carter, C.; Cravchik, A.; Woodage, T.; Ali, F.; An, H.; Awe, A.; Baldwin, D.; Baden, H.; Barnstead, M.; Barrow, I.; Beeson, K.; Busam, D.; Carver, A.; Center, A.; Cheng, M.L.; Curry, L.; Danaher, S.; Davenport, L.; Desilets, R.; Dietz, S.; Dodson, K.; Doup, L.; Ferriera, S.; Garg, N.; Gluecksmann, A.; Hart, B.; Haynes, J.; Haynes, C.; Heiner, C.; Hladun, S.; Hostin, D.; Houck, J.; Howland, T.; Ibegwam, C.; Johnson, J.; Kalush, F.; Kline, L.; Koduru, S.; Love, A.; Mann, F.; May, D.; McCawley, S.; McIntosh, T.; McMullen, I.; Moy, M.; Moy, L.; Murphy, B.; Nelson, K.; Pfannkoch, C.; Pratts, E.; Puri, V.; Qureshi, H.; Reardon, M.; Rodriguez, R.; Rogers, Y.H.; Romblad, D.; Ruhfel, B.; Scott, R.; Sitter, C.; Smallwood, M.; Stewart, E.; Strong, R.; Suh, E.; Thomas, R.; Tint, N.N.; Tse, S.; Vech, C.; Wang, G.; Wetter, J.; Williams, S.; Williams, M.; Windsor, S.; Winn-Deen, E.; Wolfe, K.; Zaveri, J.; Zaveri, K.; Abril, J.F.; Guigó, R.; Campbell, M.J.; Sjolander, K.V.;, Karlak, B.; Kejariwal, A.; Mi, H.; Lazareva, B.; Hatton, T.; Narechania, A.; Diemer, K.; Muruganujan. A.; Guo, N.; Sato, S.; Bafna, V.; Istrail, S.; Lippert, R.; Schwartz, R.; Walenz, B.; Yooseph, S.; Allen, D.; Basu, A.; Baxendale, J.; Blick, L.; Caminha, M.; Carnes-Stine, J.; Caulk, P.; Chiang. Y.H.; Coyne, M.; Dahlke, C.; Mays, A.; Dombroski, M.; Donnelly, M.; Ely, D.; Esparham, S.; Fosler, C.; Gire, H.; Glanowski, S.; Glasser. K.; Glodek, A.; Gorokhov, M.; Graham, K.; Gropman, B.; Harris, M.; Heil, J.; Henderson, S.; Hoover, J.; Jennings, D.; Jordan, C.; Jordan. J.; Kasha, J.; Kagan, L.; Kraft, C.; Levitsky, A.; Lewis, M.; Liu, X.; Lopez, J.; Ma, D.; Majoros, W.; McDaniel, J.; Murphy, S.; Newman, M.; Nguyen, T.; Nguyen, N.; Nodell, M.; Pan, S.; Peck, J.; Peterson, M.; Rowe, W.; Sanders. R.; Scott, J.; Simpson, M.; Smith, T.; Sprague, A.; Stockwell, T.; Turner, R.; Venter, E.; Wang, M.; Wen, M.; Wu, D.; Wu, M.; Xia, A.; Zandieh, A.; Zhu X. The sequence of the human genome. Science, 2001, 291(5507), 1304-1351. (Pubitemid 32173090)
2. Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA, 1977, 74 (12), 5463-5467.
3. Sanger, F.; Air, G.M.; Barrell, B.G.; Brown, N.L.; Coulson, A.R.; Fiddes, C.A.; Hutchinson, C.A.; Slocombe, P.M.; Smith M. Nucleotide sequence of bacteriophage πX174 DNA. Nature, 1977, 265 (5596), 687-695. (Pubitemid 8039446)
4. Ritcher, B.G.; Sexton D.P. Managing and analyzing next-generation sequencing data. PLoS Computational Biology, 2009, Vol 5(6), e1000369.
5. Wikipedia: en.wiktionary.org/wiki/cloud-computing
6. ServePath: www.servepath.com/support/definitions.php
7. NIST Special Publication 800-125, Guide to Security for Full Virtualization Technologies. http://www.nist.gov/itl/csd/cloud-072 110.cfm
8. Stein, L.D. The case for cloud computing in genome informatics. Genome Biol., 2010, 11, 207.
9. DNANexus: https://dnanexus.com/
10. Genomequest: http://www.genomequest.com/enomequest-60betabrings- sequence-data-management-new-category-of-product-promi ses-to-fundamentally-. xhtml
11. Crossbow: Whole Genome Resequencing using Cloud Computing. http://bowtie-bio.sourceforge.net/crossbow/
12. Langmead, B.; Michael, C. S.; Jimmy, L.; Mihai, P.; Steven, L. S. Searching for SNPs with cloud computing. Genome Biol., 2009, 10: R134.
13. Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 2009, 10, R25.
14. Li, R.; Li, Y.; Kristiansen, K.; Wang, J. SOAP: Short oligonucleotide alignment program. Bioinformatics, 2008, 24, 713-714. (Pubitemid 351321217)
15. Wang, J.; Wang, W.; Li. R.; Li, Y.; Tian, G.; Goodman, L.; Fan, W.; Zhang, J.; Li, J.; Guo, Y.; Feng, B.; Li, H.; Lu, Y.; Fang, X.; Liang, H.; Du, Z.; Li, D.; Zhao, Y.; Hu, Y.; Yang, Z.; Zheng, H.; Hellmann, I.; Inouye, M.; Pool, J.; Yi, X.; Zhao, J.; Duan, J.; Zhou, Y.; Qin, J.; Ma, L.; et al. The diploid genome sequence of an Asian individual. Nature, 2008, 456, 60-65.
16. Bleicher, K. H.; Boehm, H. J.; Mueller, K.; Alanine, A.I. Hit and lead generation: Beyond high-throughput screening. Nat. Rev. Drug. Discovery, 2003, 2, 369-378. (Pubitemid 37361707)
17. Boehm H. J., Schneider, G. Virtual Screening For Bioactive Molecules. High Throughput Screening and Virtual Screening Entry Points To Drug Discovery. Methods and Principles in Medicinal Chemistry, Volume 10.
18. Breman, J.G., Alilio, M.S., Mills, A. Conquering the intolerable burden of malaria: what's new, what's needed: a summary. Am. J. Trop. Med. Hyg., 2004, 71S, 1-15. (Pubitemid 39127486)
19. Irwin, J.J. Shoichet, B.K. ZINC - A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model, 2005, 45, 177-182. (Pubitemid 40736970)
20. A Free database for virtual screening. ZINC is not commercial. http://blaster.docking.org/zinc/ UCSF, University of California, San Francisco.
21. Gagliardi, F.; Jones, B.; Grey, F.; Begin, M.E.; Heikkurinenn M. Building an infrastructure for scientific Grid computing: status and goals of the EGEE project. Philosophical Transactions: Mathematical, Physical and Engineering Sciences, 2005, 363, 1729-1742 (http://www.eu-egee.org/) (Pubitemid 41343799)
22. Auvergrid, available at www.auvergrid.fr
23. EELA, available at www.eu-eela.org
24. EuChinaGrid, available at www.euchinagrid.org
25. EuMedGrid, available at www.eumedgrid.org
26. Salzemann, J.; Kasam, V.; Jacq, N.; Maass, A.; Schwichtenberg, H.; Berton, V. Grid Enabled High Throughput Virtual Screening Against Four Different Targets Implicated in Malaria. In: Healthgrid Conference: Genève, Switzerland, 2007.
27. http://www.bio-itworld.com/news/2009/05/22/ec2.html
28. http://cloudcomputing.sys-con.com/node/1447223
29. Bickel, M. Live cell high content screening in drug development. Eur. Pharm.l Rev., 2008, 13, 4.
30. http://www.ddwonline.com/screening/302933/high-throughput-scr eening-high-content-screening-primary-and-stem-cells.html
31. Eglen, R.M. High throughput screening, high content screening, primary and stem cells new techniques now converging. Spring 09 edition of DDW.
32. Bickel, M. The Beautiful Cell: High Content Screening in Drug Discovery. Analytical & Bioanalytical Chemistry, 2010, 398(1), 219-226.
33. Prudencio, M.; Rodrigues, C.D.; Hannus, M.; Martin, C.; Real, E.; Goncalves, L.A.; Carret, C.; Dorkin, R.; Rohl, I.; Jahn-Hoffmann, K.; Luty, A.J.F.; Sauerwein, R.; Echeverri, C.J.; Mota, M.M. Kinome-Wide RNAi Screen Implicates at Least 5 Host Hepatocyte Kinases in Plasmodium Sporozoite Infection. PloS Pathogens, 2008, 4 (11), e1000201.
34. Ovcharenko D.; Kelnar, K.; Johnson, C.; Leng, N.; Brown, D. Genome-Scale MicroRNA and Small Interfering RNA Screens Identify Small RNA Modulators of TRAIL-Induced Apoptosis Pathway. Cancer Res., 2007, 67, 10782-10788. (Pubitemid 350145906)
35. Bickel, M. Live cell high content screening in drug development. Eur. Pharm. Rev., 2008, 13(4), 2008.
36. High Content Screening: http://www.saworldview.com/article/highcontent- is-king
37. Bajo, J.; Zato, C.; Prieta, F.D.L.; Luis, A.D.; Tapia, D. Distributed computing and artificial intellegence. Advances in Soft Computing, 2010, 79, 147-155.
38. Shirasuna, S.; Gannon, D. "XBaya: A graphical workflow composer for the web services architecture", Indiana University 2006.
39. GenomeQuest: http://www.genomequest.com/enomequest-60betabrings- sequence-data-management-new-category-of-product-promi ses-to-fundamentally-. xhtml
40. R: http://www.r-project.org/
41. Cloud Computing: http://cloudcomputing.sys-con.com/node/1478253
42. Balabit: http://www.balabit.com/support/documentation
43. http://www.hpcinthecloud.com/blogs/cloud-infrastructure-and- FDACompliance- 92894189.html