A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information

Detalhes bibliográficos
Autor(a) principal: Vilaça, Paulo
Data de Publicação: 2011
Outros Autores: Rocha, I., Rocha, Miguel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/14326
Resumo: Background and scope Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events. Implementation and performances This work proposes a novel software tool that implements methods for the simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community. Availability The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation.
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spelling A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory informationMetabolic engineeringIntegrated modelsRegulatory modelsOpen-source softwareMetabolic modelsSoftware toolOpen-sourceScience & TechnologyBackground and scope Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events. Implementation and performances This work proposes a novel software tool that implements methods for the simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community. Availability The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation.Portuguese FCT (MIT-Portugal Program) - project MIT-PT/BS-BB/0082/2008.ElsevierUniversidade do MinhoVilaça, PauloRocha, I.Rocha, Miguel2011-032011-03-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/14326eng0303-264710.1016/j.biosystems.2010.11.01221144882http://www.sciencedirect.com/science/article/pii/S0303264710002145info: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:RCAAP2023-07-21T12:40:36Zoai:repositorium.sdum.uminho.pt:1822/14326Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:37:27.443629Repositório 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 A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
title A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
spellingShingle A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
Vilaça, Paulo
Metabolic engineering
Integrated models
Regulatory models
Open-source software
Metabolic models
Software tool
Open-source
Science & Technology
title_short A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
title_full A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
title_fullStr A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
title_full_unstemmed A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
title_sort A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/ regulatory information
author Vilaça, Paulo
author_facet Vilaça, Paulo
Rocha, I.
Rocha, Miguel
author_role author
author2 Rocha, I.
Rocha, Miguel
author2_role author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Vilaça, Paulo
Rocha, I.
Rocha, Miguel
dc.subject.por.fl_str_mv Metabolic engineering
Integrated models
Regulatory models
Open-source software
Metabolic models
Software tool
Open-source
Science & Technology
topic Metabolic engineering
Integrated models
Regulatory models
Open-source software
Metabolic models
Software tool
Open-source
Science & Technology
description Background and scope Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events. Implementation and performances This work proposes a novel software tool that implements methods for the simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community. Availability The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation.
publishDate 2011
dc.date.none.fl_str_mv 2011-03
2011-03-01T00:00:00Z
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/1822/14326
url http://hdl.handle.net/1822/14326
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0303-2647
10.1016/j.biosystems.2010.11.012
21144882
http://www.sciencedirect.com/science/article/pii/S0303264710002145
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 Elsevier
publisher.none.fl_str_mv Elsevier
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
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