{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:06:14Z","timestamp":1760709974461,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,30]],"date-time":"2019-07-30T00:00:00Z","timestamp":1564444800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"EU H2020","award":["686070","814408"],"award-info":[{"award-number":["686070","814408"]}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["UID\/BIO\/04469\/2019","NORTE-01-0145-FEDER-000004"],"award-info":[{"award-number":["UID\/BIO\/04469\/2019","NORTE-01-0145-FEDER-000004"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["SFRH\/BD\/118657\/2016"],"award-info":[{"award-number":["SFRH\/BD\/118657\/2016"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https:\/\/github.com\/BioSystemsUM\/cobamp.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz598","type":"journal-article","created":{"date-parts":[[2019,7,25]],"date-time":"2019-07-25T19:11:15Z","timestamp":1564081875000},"page":"5361-5362","source":"Crossref","is-referenced-by-count":11,"title":["CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9604-9586","authenticated-orcid":false,"given":"V\u00edtor","family":"Vieira","sequence":"first","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8439-8172","authenticated-orcid":false,"given":"Miguel","family":"Rocha","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2019,7,29]]},"reference":[{"key":"2023020108351786500_btz598-B1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/bioinformatics\/btr674","article-title":"Minimal cut sets in a metabolic network are elementary modes in a dual network","volume":"28","author":"Ballerstein","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020108351786500_btz598-B2","doi-asserted-by":"crossref","first-page":"3158","DOI":"10.1093\/bioinformatics\/btp564","article-title":"Computing the shortest elementary flux modes in genome-scale metabolic networks","volume":"25","author":"de Figueiredo","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020108351786500_btz598-B3","doi-asserted-by":"crossref","first-page":"74.","DOI":"10.1186\/1752-0509-7-74","article-title":"COBRApy: COnstraints-Based Reconstruction and Analysis for Python","volume":"7","author":"Ebrahim","year":"2013","journal-title":"BMC Syst. 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