merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Detalhes bibliográficos
Autor(a) principal: Capela, João
Data de Publicação: 2021
Outros Autores: Lagoa, D., Rodrigues, Rúben, Cunha, Emanuel, Cruz, Fernando, Barbosa, Ana, Bastos, J., Lima, Diogo, Ferreira, Eugénio C., Rocha, Miguel, Dias, Oscar
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/77153
Resumo: merlin is an open-source application currently available for Linux, Windows, and macOS. It is distributed under the GNU General Public License at the website https://www.merlin-sysbio.org. Moreover, merlin source code, including plugins, is fully available at https://github.com/merlin4-sysbio. The draft models assessment scripts and files are available at https://github.com/BioSystemsUM/merlinv4_paper. Comprehensive documentation is provided at https://merlin-sysbio.org/documentation/. Animated snapshots of merlin’s interface and clear descriptions of each step in the reconstruction are therein provided.
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spelling merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic modelsmerlin is an open-source application currently available for Linux, Windows, and macOS. It is distributed under the GNU General Public License at the website https://www.merlin-sysbio.org. Moreover, merlin source code, including plugins, is fully available at https://github.com/merlin4-sysbio. The draft models assessment scripts and files are available at https://github.com/BioSystemsUM/merlinv4_paper. Comprehensive documentation is provided at https://merlin-sysbio.org/documentation/. Animated snapshots of merlin’s interface and clear descriptions of each step in the reconstruction are therein provided.Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures while leveraging the users expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and non-template based draft reconstructions, while achieving top performance compared to state-of-the art tools both for well and less-studied organisms.Centre of Biological Engineering (CEB, UMinho) for financial and equipment support and Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. This work is a result of the project 22231/01/SAICT/2016: Biodata.pt Infraestrutura Portuguesa de Dados Biológicos, supported by the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). The authors would also like to acknowledge the Portuguese Foundation for Science and Technology (FCT) for the Strategic Funding FCT 2020-2023 (PEst UIDB/04469/2020). FCT for providing PhD scholarships to J. Capela (DFA/BD/08789/2021), E. Cunha (DFA/BD/8076/2020), F. Cruz (SFRH/BD/139198/2018) and R. Rodrigues (SFRH/BD/131916/2017). FCT for the Assistant Research contract of Oscar Dias obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersionCold Spring Harbor LaboratoryUniversidade do MinhoCapela, JoãoLagoa, D.Rodrigues, RúbenCunha, EmanuelCruz, FernandoBarbosa, AnaBastos, J.Lima, DiogoFerreira, Eugénio C.Rocha, MiguelDias, Oscar2021-02-252021-02-25T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/77153engCapela, João; Lagoa, D.; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, Diogo; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models. bioRxiv - the Preprint Server for Biology, 202110.1101/2021.02.24.432752https://www.biorxiv.org/info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:52:20Zoai:repositorium.sdum.uminho.pt:1822/77153Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:51:25.297808Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
title merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
spellingShingle merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
Capela, João
title_short merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
title_full merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
title_fullStr merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
title_full_unstemmed merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
title_sort merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models
author Capela, João
author_facet Capela, João
Lagoa, D.
Rodrigues, Rúben
Cunha, Emanuel
Cruz, Fernando
Barbosa, Ana
Bastos, J.
Lima, Diogo
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
author_role author
author2 Lagoa, D.
Rodrigues, Rúben
Cunha, Emanuel
Cruz, Fernando
Barbosa, Ana
Bastos, J.
Lima, Diogo
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Capela, João
Lagoa, D.
Rodrigues, Rúben
Cunha, Emanuel
Cruz, Fernando
Barbosa, Ana
Bastos, J.
Lima, Diogo
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
description merlin is an open-source application currently available for Linux, Windows, and macOS. It is distributed under the GNU General Public License at the website https://www.merlin-sysbio.org. Moreover, merlin source code, including plugins, is fully available at https://github.com/merlin4-sysbio. The draft models assessment scripts and files are available at https://github.com/BioSystemsUM/merlinv4_paper. Comprehensive documentation is provided at https://merlin-sysbio.org/documentation/. Animated snapshots of merlin’s interface and clear descriptions of each step in the reconstruction are therein provided.
publishDate 2021
dc.date.none.fl_str_mv 2021-02-25
2021-02-25T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/77153
url http://hdl.handle.net/1822/77153
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Capela, João; Lagoa, D.; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, Diogo; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models. bioRxiv - the Preprint Server for Biology, 2021
10.1101/2021.02.24.432752
https://www.biorxiv.org/
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory
publisher.none.fl_str_mv Cold Spring Harbor Laboratory
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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