{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T17:20:39Z","timestamp":1776187239628,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,29]],"date-time":"2017-11-29T00:00:00Z","timestamp":1511913600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54DE023798"],"award-info":[{"award-number":["U54DE023798"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["JDRF 3-SRA-2016-141-Q-R"],"award-info":[{"award-number":["JDRF 3-SRA-2016-141-Q-R"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG005220"],"award-info":[{"award-number":["R01HG005220"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DBI-1053486"],"award-info":[{"award-number":["DBI-1053486"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG005969"],"award-info":[{"award-number":["R01HG005969"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["ARO W911NF-11-1-0473"],"award-info":[{"award-number":["ARO W911NF-11-1-0473"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>bioBakery is a meta\u2019omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>bioBakery (http:\/\/huttenhower.sph.harvard.edu\/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx754","type":"journal-article","created":{"date-parts":[[2017,11,28]],"date-time":"2017-11-28T20:15:11Z","timestamp":1511900111000},"page":"1235-1237","source":"Crossref","is-referenced-by-count":313,"title":["bioBakery: a meta\u2019omic analysis environment"],"prefix":"10.1093","volume":"34","author":[{"given":"Lauren J","family":"McIver","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"},{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA, USA"}]},{"given":"Galeb","family":"Abu-Ali","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"},{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA, USA"}]},{"given":"Eric A","family":"Franzosa","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"},{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA, USA"}]},{"given":"Randall","family":"Schwager","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"},{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA, USA"}]},{"given":"Xochitl C","family":"Morgan","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T. H. 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