{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:26Z","timestamp":1753875806110,"version":"3.41.2"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,2,21]],"date-time":"2023-02-21T00:00:00Z","timestamp":1676937600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Characterizing all steady-state flux distributions in metabolic models remains limited to small models due to the explosion of possibilities. Often it is sufficient to look only at all possible overall conversions a cell can catalyze ignoring the details of intracellular metabolism. Such a characterization is achieved by elementary conversion modes (ECMs), which can be conveniently computed with ecmtool. However, currently, ecmtool is memory intensive, and it cannot be aided appreciably by parallelization.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We integrate mplrs\u2014a scalable parallel vertex enumeration method\u2014into ecmtool. This speeds up computation, drastically reduces memory requirements and enables ecmtool\u2019s use in standard and high-performance computing environments. We show the new capabilities by enumerating all feasible ECMs of the near-complete metabolic model of the minimal cell JCVI-syn3.0. Despite the cell\u2019s minimal character, the model gives rise to 4.2\u00d7109 ECMs and still contains several redundant sub-networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>ecmtool is available at https:\/\/github.com\/SystemsBioinformatics\/ecmtool.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad095","type":"journal-article","created":{"date-parts":[[2023,2,21]],"date-time":"2023-02-21T17:30:08Z","timestamp":1677000608000},"source":"Crossref","is-referenced-by-count":4,"title":["<tt>ecmtool<\/tt>: fast and memory-efficient enumeration of elementary conversion modes"],"prefix":"10.1093","volume":"39","author":[{"given":"Bianca","family":"Buchner","sequence":"first","affiliation":[{"name":"acib GmbH, Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria"}]},{"given":"Tom J","family":"Clement","sequence":"additional","affiliation":[{"name":"Systems Biology Lab, Vrije Universiteit , 1081HV Amsterdam, The Netherlands"}]},{"given":"Daan H","family":"de Groot","sequence":"additional","affiliation":[{"name":"Biozentrum, Swiss Institute of Bioinformatics, University of Basel , 4056 Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1964-2455","authenticated-orcid":false,"given":"J\u00fcrgen","family":"Zanghellini","sequence":"additional","affiliation":[{"name":"Department of Analytical Chemistry, University of Vienna , 1090 Vienna, Austria"}]}],"member":"286","published-online":{"date-parts":[[2023,2,21]]},"reference":[{"first-page":"267","year":"2018","author":"Avis","key":"2023030308030530500_"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"e36842","DOI":"10.7554\/eLife.36842","article-title":"Essential metabolism for a minimal cell","volume":"8","author":"Breuer","year":"2019","journal-title":"eLife"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1186\/s12859-021-04417-9","article-title":"EFMlrs: a Python package for EFM enumeration via lexicographic reverse search","volume":"22","author":"Buchner","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"100177","DOI":"10.1016\/j.patter.2020.100177","article-title":"Unlocking elementary conversion modes: ecmtool unveils all capabilities of metabolic networks","volume":"2","author":"Clement","year":"2021","journal-title":"Patterns"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.tibtech.2004.07.007","article-title":"Bow ties, metabolism and disease","volume":"22","author":"Csete","year":"2004","journal-title":"Trends Biotechnol"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/srep00580","article-title":"Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks","volume":"2","author":"Kelk","year":"2012","journal-title":"Sci. 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Syst"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1093\/bioinformatics\/btn401","article-title":"Large-scale computation of elementary flux modes with bit pattern trees","volume":"24","author":"Terzer","year":"2008","journal-title":"Bioinformatics"},{"key":"2023030308030530500_","doi-asserted-by":"crossref","first-page":"4176","DOI":"10.1093\/bioinformatics\/bti674","article-title":"Functional stoichiometric analysis of metabolic networks","volume":"21","author":"Urbanczik","year":"2005","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad095\/49284954\/btad095.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/3\/btad095\/49407400\/btad095.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/3\/btad095\/49407400\/btad095.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,25]],"date-time":"2023-03-25T23:48:47Z","timestamp":1679788127000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad095\/7049479"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,2,21]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad095","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,3,1]]},"published":{"date-parts":[[2023,2,21]]},"article-number":"btad095"}}