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Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds.

Schönherr S, Forer L, Weißensteiner H, Kronenberg F, Specht G, Kloss-Brandstätter A.

BMC Bioinformatics. 2012 Aug 13;13:200. doi: 10.1186/1471-2105-13-200.


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.


Pegasys: software for executing and integrating analyses of biological sequences.

Shah SP, He DY, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GX, Xu T, Ouellette BF.

BMC Bioinformatics. 2004 Apr 19;5:40.


Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment.

Meng B, Pratx G, Xing L.

Med Phys. 2011 Dec;38(12):6603-9. doi: 10.1118/1.3660200.


Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends.

Mohammed EA, Far BH, Naugler C.

BioData Min. 2014 Oct 29;7:22. doi: 10.1186/1756-0381-7-22. eCollection 2014. Review.


CloudBurst: highly sensitive read mapping with MapReduce.

Schatz MC.

Bioinformatics. 2009 Jun 1;25(11):1363-9. doi: 10.1093/bioinformatics/btp236. Epub 2009 Apr 8.


A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.

Gigascience. 2015 Jun 4;4:26. doi: 10.1186/s13742-015-0058-5. eCollection 2015.


An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

Taylor RC.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S1. doi: 10.1186/1471-2105-11-S12-S1.


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.


Initial steps towards a production platform for DNA sequence analysis on the grid.

Luyf AC, van Schaik BD, de Vries M, Baas F, van Kampen AH, Olabarriaga SD.

BMC Bioinformatics. 2010 Dec 14;11:598. doi: 10.1186/1471-2105-11-598.


Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A.

Bioinformatics. 2012 Jun 15;28(12):1647-9. doi: 10.1093/bioinformatics/bts199. Epub 2012 Apr 27.


Wildfire: distributed, Grid-enabled workflow construction and execution.

Tang F, Chua CL, Ho LY, Lim YP, Issac P, Krishnan A.

BMC Bioinformatics. 2005 Mar 24;6:69.


Ergatis: a web interface and scalable software system for bioinformatics workflows.

Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV.

Bioinformatics. 2010 Jun 15;26(12):1488-92. doi: 10.1093/bioinformatics/btq167. Epub 2010 Apr 22.


Hybrid cloud and cluster computing paradigms for life science applications.

Qiu J, Ekanayake J, Gunarathne T, Choi JY, Bae SH, Li H, Zhang B, Wu TL, Ruan Y, Ekanayake S, Hughes A, Fox G.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S3. doi: 10.1186/1471-2105-11-S12-S3.


DMET-analyzer: automatic analysis of Affymetrix DMET data.

Guzzi PH, Agapito G, Di Martino MT, Arbitrio M, Tassone P, Tagliaferri P, Cannataro M.

BMC Bioinformatics. 2012 Oct 5;13:258. doi: 10.1186/1471-2105-13-258.


An integrated web interface for large-scale characterization of sequence data.

Cheung KH, Kumar A, Snyder M, Miller P.

Funct Integr Genomics. 2000 May;1(1):70-5.


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.


BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.

Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA.

BMC Genomics. 2011 Aug 8;12:402. doi: 10.1186/1471-2164-12-402.


ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

Stocker G, Rieder D, Trajanoski Z.

Bioinformatics. 2004 Mar 22;20(5):805-7. Epub 2004 Jan 29.

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