{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:27:35Z","timestamp":1767918455502,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,4,6]],"date-time":"2017-04-06T00:00:00Z","timestamp":1491436800000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA179243"],"award-info":[{"award-number":["R01CA179243"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED\u2019s ability to automatically reconstruct metabolic models with COBRApy\u2019s advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>This package works with Python 2.7, 3.4, and 3.5 on MacOS, Linux and Windows. The source code is available from https:\/\/github.com\/mmundy42\/mackinac.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx185","type":"journal-article","created":{"date-parts":[[2017,3,29]],"date-time":"2017-03-29T03:10:35Z","timestamp":1490757035000},"page":"2416-2418","source":"Crossref","is-referenced-by-count":17,"title":["Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models"],"prefix":"10.1093","volume":"33","author":[{"given":"Michael","family":"Mundy","sequence":"first","affiliation":[{"name":"Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helena","family":"Mendes-Soares","sequence":"additional","affiliation":[{"name":"Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA"},{"name":"Department of Information Technology, Mayo Clinic, Rochester, MN, USA"},{"name":"Department of Surgery, Mayo Clinic, Rochester, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Chia","sequence":"additional","affiliation":[{"name":"Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA"},{"name":"Department of Surgery, Mayo Clinic, Rochester, MN, USA"},{"name":"Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,3,30]]},"reference":[{"key":"2023063012504968500_btx185-B1","doi-asserted-by":"crossref","first-page":"e1003882.","DOI":"10.1371\/journal.pcbi.1003882","article-title":"Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models","volume":"10","author":"Benedict","year":"2014","journal-title":"PLoS Comput. 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Protoc"},{"key":"2023063012504968500_btx185-B8","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1093\/bioinformatics\/btu321","article-title":"FastGapFill: efficient gap filling in metabolic networks","volume":"30","author":"Thiele","year":"2014","journal-title":"Bioinformatics"},{"key":"2023063012504968500_btx185-B9","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis resource","volume":"42","author":"Wattam","year":"2014","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2416\/50756593\/bioinformatics_33_15_2416.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2416\/50756593\/bioinformatics_33_15_2416.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T12:51:04Z","timestamp":1688129464000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/15\/2416\/3096434"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,3,30]]},"references-count":9,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2017,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx185","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,1]]},"published":{"date-parts":[[2017,3,30]]}}}