{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:31:43Z","timestamp":1773966703549,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T00:00:00Z","timestamp":1610928000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["814408"],"award-info":[{"award-number":["814408"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Metabolic Engineering aims to favour the overproduction of native, as well as non-native, metabolites by modifying or extending the cellular processes of a specific organism. In this context, Computational Strain Optimization (CSO) plays a relevant role by putting forward mathematical approaches able to identify potential metabolic modifications to achieve the defined production goals. We present MEWpy, a Python workbench for metabolic engineering, which covers a wide range of metabolic and regulatory modelling approaches, as well as phenotype simulation and CSO algorithms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MEWpy can be installed from PyPi (pip install mewpy), the source code being available at https:\/\/github.com\/BioSystemsUM\/mewpy under the GPL license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab013","type":"journal-article","created":{"date-parts":[[2021,1,5]],"date-time":"2021-01-05T22:31:42Z","timestamp":1609885902000},"page":"2494-2496","source":"Crossref","is-referenced-by-count":28,"title":["MEWpy: a computational strain optimization workbench in Python"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8661-9626","authenticated-orcid":false,"given":"V\u00edtor","family":"Pereira","sequence":"first","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2468-7364","authenticated-orcid":false,"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057, 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 4710-057, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"2023051609140579500_btab013-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s12859-019-3329-9","article-title":"Automatic construction of metabolic models with enzyme constraints","volume":"21","author":"Bekiaris","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2023051609140579500_btab013-B2","author":"Ben\u00edtez-Hidalgo","year":"2019"},{"key":"2023051609140579500_btab013-B3","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/bit.10803","article-title":"Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization","volume":"84","author":"Burgard","year":"2003","journal-title":"Biotechnol. Bioeng"},{"key":"2023051609140579500_btab013-B4","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1021\/acssynbio.7b00423","article-title":"Cameo: A Python library for computer aided metabolic engineering and optimization of cell factories","volume":"7","author":"Cardoso","year":"2018","journal-title":"ACS Synth. Biol"},{"key":"2023051609140579500_btab013-B5","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. Biol"},{"key":"2023051609140579500_btab013-B6","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/1752-0509-4-53","article-title":"OptORF: optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains","volume":"4","author":"Kim","year":"2010","journal-title":"BMC Syst. Biol"},{"key":"2023051609140579500_btab013-B7","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/ncomms1928","article-title":"In silico method for modelling metabolism and gene product expression at genome scale","volume":"3","author":"Lerman","year":"2012","journal-title":"Nat. Commun"},{"key":"2023051609140579500_btab013-B8","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1128\/MMBR.00014-15","article-title":"In silico constraint-based strain optimization methods: the quest for optimal cell factories","volume":"80","author":"Maia","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev"},{"key":"2023051609140579500_btab013-B9","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1186\/1471-2105-9-499","article-title":"Natural computation meta-heuristics for the in silico optimization of microbial strains","volume":"9","author":"Rocha","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023051609140579500_btab013-B10","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/1752-0509-4-45","article-title":"OptFlux: an open-source software platform for in silico metabolic engineering","volume":"4","author":"Rocha","year":"2010","journal-title":"BMC Syst. Biol"},{"key":"2023051609140579500_btab013-B11","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/s41467-019-13818-7","article-title":"The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models","volume":"11","author":"Salvy","year":"2020","journal-title":"Nat. Commun"},{"key":"2023051609140579500_btab013-B12","doi-asserted-by":"crossref","first-page":"935","DOI":"10.15252\/msb.20167411","article-title":"Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints","volume":"13","author":"Sanchez","year":"2017","journal-title":"Mol. Syst. Biol"},{"key":"2023051609140579500_btab013-B13","doi-asserted-by":"crossref","first-page":"e1006835","DOI":"10.1371\/journal.pcbi.1006835","article-title":"OptRAM: in-silico strain design via integrative regulatory-metabolic network modeling","volume":"15","author":"Shen","year":"2019","journal-title":"PLoS Comput. Biol"},{"key":"2023051609140579500_btab013-B14","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s10710-019-09367-z","article-title":"Inspyred: bio-inspired algorithms in Python","volume":"21","author":"Tonda","year":"2020","journal-title":"Genet. Program Evol. Mach"},{"key":"2023051609140579500_btab013-B15","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1016\/j.asoc.2014.08.025","article-title":"A comparative review of approaches to prevent premature convergence in GA","volume":"24","author":"Pandey","year":"2014","journal-title":"Appl. Soft Comput"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab013\/35940336\/btab013.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2494\/50339580\/btab013.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2494\/50339580\/btab013.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T09:17:04Z","timestamp":1684228624000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/16\/2494\/6103790"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,1,18]]},"references-count":15,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2021,8,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab013","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,8,15]]},"published":{"date-parts":[[2021,1,18]]}}}