{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:57:47Z","timestamp":1761541067557},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows.<\/jats:p>\n               <jats:p>Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http:\/\/sashimi.svn.sourceforge.net\/viewvc\/sashimi\/trunk\/trans_proteomic_pipeline\/extern\/xtandem\/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http:\/\/ica.svn.sourceforge.net\/viewvc\/ica\/trunk\/mr-tandem\/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL.<\/jats:p>\n               <jats:p>Contact: \u00a0brian.pratt@insilicos.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr615","type":"journal-article","created":{"date-parts":[[2011,11,10]],"date-time":"2011-11-10T06:32:04Z","timestamp":1320906724000},"page":"136-137","source":"Crossref","is-referenced-by-count":42,"title":["MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services"],"prefix":"10.1093","volume":"28","author":[{"given":"Brian","family":"Pratt","sequence":"first","affiliation":[{"name":"Insilicos LLC, Seattle WA, USA"}]},{"given":"J. Jeffry","family":"Howbert","sequence":"additional","affiliation":[{"name":"Insilicos LLC, Seattle WA, USA"}]},{"given":"Natalie I.","family":"Tasman","sequence":"additional","affiliation":[{"name":"Insilicos LLC, Seattle WA, USA"}]},{"given":"Erik J.","family":"Nilsson","sequence":"additional","affiliation":[{"name":"Insilicos LLC, Seattle WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,11,8]]},"reference":[{"key":"2023061011451061300_B1","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023061011451061300_B2","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1021\/pr0701198","article-title":"X!!Tandem, an improved method for running X!Tandem on Collections of Commodity Computers","volume":"7","author":"Bjornson","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023061011451061300_B3","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1021\/pr050058i","article-title":"Parallel Tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem","volume":"4","author":"Duncan","year":"2005","journal-title":"J. Proteome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/136\/50568407\/bioinformatics_28_1_136.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/136\/50568407\/bioinformatics_28_1_136.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:46:26Z","timestamp":1686397586000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/1\/136\/220835"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,8]]},"references-count":3,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr615","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,1]]},"published":{"date-parts":[[2011,11,8]]}}}