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Items: 1 to 20 of 185

1.

Galaxy CloudMan: delivering cloud compute clusters.

Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S4. doi: 10.1186/1471-2105-11-S12-S4.

2.

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

Afgan E, Chapman B, Jadan M, Franke V, Taylor J.

Curr Protoc Bioinformatics. 2012 Jun;Chapter 11:Unit11.9. doi: 10.1002/0471250953.bi1109s38.

3.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A.

PLoS One. 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829. eCollection 2015.

4.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF.

BMC Bioinformatics. 2011 Aug 30;12:356. doi: 10.1186/1471-2105-12-356.

5.

Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing.

Trudgian DC, Mirzaei H.

J Proteome Res. 2012 Dec 7;11(12):6282-90. doi: 10.1021/pr300694b. Epub 2012 Oct 29.

PMID:
23088505
6.

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

Angiuoli SV, White JR, Matalka M, White O, Fricke WF.

PLoS One. 2011;6(10):e26624. doi: 10.1371/journal.pone.0026624. Epub 2011 Oct 19.

7.

Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

Abouelhoda M, Issa SA, Ghanem M.

BMC Bioinformatics. 2012 May 4;13:77. doi: 10.1186/1471-2105-13-77.

8.

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O.

Genetics. 2012 Dec;192(4):1249-69. doi: 10.1534/genetics.112.144204. Epub 2012 Oct 10.

9.

Cloud computing for comparative genomics.

Wall DP, Kudtarkar P, Fusaro VA, Pivovarov R, Patil P, Tonellato PJ.

BMC Bioinformatics. 2010 May 18;11:259. doi: 10.1186/1471-2105-11-259.

10.

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

Halligan BD, Geiger JF, Vallejos AK, Greene AS, Twigger SN.

J Proteome Res. 2009 Jun;8(6):3148-53. doi: 10.1021/pr800970z.

11.

Community-driven computational biology with Debian Linux.

Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. doi: 10.1186/1471-2105-11-S12-S5.

12.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE.

BMC Bioinformatics. 2012 Mar 19;13:42. doi: 10.1186/1471-2105-13-42.

13.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S.

BMC Genomics. 2013 Jun 27;14:425. doi: 10.1186/1471-2164-14-425.

14.

Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

Kudtarkar P, Deluca TF, Fusaro VA, Tonellato PJ, Wall DP.

Evol Bioinform Online. 2010 Dec 22;6:197-203. doi: 10.4137/EBO.S6259.

15.

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

Afgan E, Chapman B, Taylor J.

BMC Bioinformatics. 2012 Nov 27;13:315. doi: 10.1186/1471-2105-13-315.

16.

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P.

BMC Bioinformatics. 2012;13 Suppl 17:S22. doi: 10.1186/1471-2105-13-S17-S22. Epub 2012 Dec 13.

17.

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.

Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23.

18.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.

PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146. eCollection 2014.

19.

Exploiting parallel R in the cloud with SPRINT.

Piotrowski M, McGilvary GA, Sloan TM, Mewissen M, Lloyd AD, Forster T, Mitchell L, Ghazal P, Hill J.

Methods Inf Med. 2013;52(1):80-90. doi: 10.3414/ME11-02-0039. Epub 2012 Dec 7.

20.

Gene set analysis in the cloud.

Zhang L, Gu S, Liu Y, Wang B, Azuaje F.

Bioinformatics. 2012 Jan 15;28(2):294-5. doi: 10.1093/bioinformatics/btr630. Epub 2011 Nov 13.

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