{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:24:13Z","timestamp":1764689053990},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":377,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern.<\/jats:p>\n               <jats:p>Availability and implementation: Source code is available at https:\/\/bitbucket.org\/booz-allen-sci-comp-team\/cl-dash.git.<\/jats:p>\n               <jats:p>Contact: \u00a0hodor_paul@bah.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv553","type":"journal-article","created":{"date-parts":[[2015,10,2]],"date-time":"2015-10-02T01:44:04Z","timestamp":1443750244000},"page":"301-303","source":"Crossref","is-referenced-by-count":11,"title":["cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud"],"prefix":"10.1093","volume":"32","author":[{"given":"Paul","family":"Hodor","sequence":"first","affiliation":[{"name":"Booz Allen Hamilton, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amandeep","family":"Chawla","sequence":"additional","affiliation":[{"name":"Booz Allen Hamilton, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Clark","sequence":"additional","affiliation":[{"name":"Booz Allen Hamilton, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren","family":"Neal","sequence":"additional","affiliation":[{"name":"Booz Allen Hamilton, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,1]]},"reference":[{"key":"2023020110283022200_btv553-B1","doi-asserted-by":"crossref","first-page":"e98146","DOI":"10.1371\/journal.pone.0098146","article-title":"CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce","volume":"9","author":"Chung","year":"2014","journal-title":"PLoS One"},{"key":"2023020110283022200_btv553-B2","doi-asserted-by":"crossref","first-page":"e1002147","DOI":"10.1371\/journal.pcbi.1002147","article-title":"Biomedical cloud computing with Amazon Web Services","volume":"7","author":"Fusaro","year":"2011","journal-title":"PLoS Comput. 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Biol."},{"key":"2023020110283022200_btv553-B6","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bib\/bbs088","article-title":"Survey of MapReduce frame operation in bioinformatics","volume":"15","author":"Zou","year":"2013","journal-title":"Brief. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/2\/301\/49016620\/bioinformatics_32_2_301.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/2\/301\/49016620\/bioinformatics_32_2_301.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:53:58Z","timestamp":1675281238000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/2\/301\/1743933"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,1]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2016,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv553","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,1,15]]},"published":{"date-parts":[[2015,10,1]]}}}