{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T17:20:55Z","timestamp":1774027255872,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,13]],"date-time":"2017-02-13T00:00:00Z","timestamp":1486944000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>PMAnalyzer v2.0 can be found at https:\/\/edwards.sdsu.edu\/pmanalyzer\/. Source code for the pipeline can be found on GitHub at https:\/\/github.com\/dacuevas\/PMAnalyzer. Source code for the online implementation can be found on GitHub at https:\/\/github.com\/dacuevas\/PMAnalyzerWeb.<\/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\/btx084","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T08:58:08Z","timestamp":1487149088000},"page":"1905-1906","source":"Crossref","is-referenced-by-count":20,"title":["PMAnalyzer: a new web interface for bacterial growth curve analysis"],"prefix":"10.1093","volume":"33","author":[{"given":"Daniel A","family":"Cuevas","sequence":"first","affiliation":[{"name":"Computational Science Research Center, San Diego State University, San Diego, CA, USA"}]},{"given":"Robert A","family":"Edwards","sequence":"additional","affiliation":[{"name":"Computational Science Research Center, San Diego State University, San Diego, CA, USA"},{"name":"Department of Computer Science, San Diego State University, San Diego, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,2,13]]},"reference":[{"key":"2023020205484684100_btx084-B1","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1007\/s12155-015-9584-3","article-title":"Modeling microbial growth curves with GCAT","volume":"8","author":"Bukhman","year":"2015","journal-title":"BioEnergy Res"},{"key":"2023020205484684100_btx084-B2","doi-asserted-by":"crossref","first-page":"210","DOI":"10.12688\/f1000research.5140.2","article-title":"Elucidating genomic gaps using phenotypic profiles","volume":"3","author":"Cuevas","year":"2016","journal-title":"F1000Research"},{"key":"2023020205484684100_btx084-B3","doi-asserted-by":"crossref","first-page":"907.","DOI":"10.3389\/fmicb.2016.00907","article-title":"From DNA to FBA: how to build your own genome-scale metabolic model","volume":"7","author":"Cuevas","year":"2016","journal-title":"Front. 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Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/12\/1905\/49040021\/bioinformatics_33_12_1905.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/12\/1905\/49040021\/bioinformatics_33_12_1905.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:51:51Z","timestamp":1675317111000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/12\/1905\/2991429"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,2,13]]},"references-count":8,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2017,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx084","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,6,15]]},"published":{"date-parts":[[2017,2,13]]}}}