CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/31907 |
Resumo: | Background Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full portfolio of flux analysis methods. Results This work presents Constraint-based Flux Analysis (CBFA), an open-source software application for flux analysis in metabolic models that implements several methods for phenotype prediction, allowing users to define constraints associated with measured fluxes and/or flux ratios, together with environmental conditions (e.g. media) and reaction/gene knockouts. CBFA identifies the set of applicable methods based on the constraints defined from user inputs, encompassing algebraic and constraint-based simulation methods. The integration of CBFA within the OptFlux framework for ME enables the utilization of different model formats and standards and the integration with complementary methods for phenotype simulation and visualization of results. Conclusions A general-purpose and flexible application is proposed that is independent of the origin of the constraints defined for a given simulation. The aim is to provide a simple to use software tool focused on the application of several flux prediction methods. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental dataConstraint-based modelingMetabolic Flux analysisMetabolic engineeringOpen-source softwareScience & TechnologyBackground Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full portfolio of flux analysis methods. Results This work presents Constraint-based Flux Analysis (CBFA), an open-source software application for flux analysis in metabolic models that implements several methods for phenotype prediction, allowing users to define constraints associated with measured fluxes and/or flux ratios, together with environmental conditions (e.g. media) and reaction/gene knockouts. CBFA identifies the set of applicable methods based on the constraints defined from user inputs, encompassing algebraic and constraint-based simulation methods. The integration of CBFA within the OptFlux framework for ME enables the utilization of different model formats and standards and the integration with complementary methods for phenotype simulation and visualization of results. Conclusions A general-purpose and flexible application is proposed that is independent of the origin of the constraints defined for a given simulation. The aim is to provide a simple to use software tool focused on the application of several flux prediction methods.The work is partially funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within project ref. COMPETE FCOMP-01-0124-FEDER-015079. RC's work is funded by a Ph.D. grant from the Portuguese FCT (ref. SFRH/BD/66201/2009).The authors would also like to thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Projects "BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes", REF. NORTE-07-0124-FEDER-000028 and "PEM - Metabolic Engineering Platform", project number 23060, both co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER.BioMed Central (BMC)Universidade do MinhoCarreira, RafaelEvangelista, PedroMaia, PauloVilaça, PauloPont, M.Tomb, J. F.Rocha, I.Rocha, Miguel20142014-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/31907engCarreira, R.; Evangelista, Pedro; Maia, P.; Vilaça, P.; Pont, Marcellinus; Tomb, Jean-François; Rocha, I.; Rocha, Miguel, CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Systems Biology, 8(123), 20141752-05091752-050910.1186/s12918-014-0123-125466481info: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:RCAAP2023-07-21T11:54:50Zoai:repositorium.sdum.uminho.pt:1822/31907Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:44:18.327940Repositório 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 |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
title |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
spellingShingle |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data Carreira, Rafael Constraint-based modeling Metabolic Flux analysis Metabolic engineering Open-source software Science & Technology |
title_short |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
title_full |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
title_fullStr |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
title_full_unstemmed |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
title_sort |
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data |
author |
Carreira, Rafael |
author_facet |
Carreira, Rafael Evangelista, Pedro Maia, Paulo Vilaça, Paulo Pont, M. Tomb, J. F. Rocha, I. Rocha, Miguel |
author_role |
author |
author2 |
Evangelista, Pedro Maia, Paulo Vilaça, Paulo Pont, M. Tomb, J. F. Rocha, I. Rocha, Miguel |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Carreira, Rafael Evangelista, Pedro Maia, Paulo Vilaça, Paulo Pont, M. Tomb, J. F. Rocha, I. Rocha, Miguel |
dc.subject.por.fl_str_mv |
Constraint-based modeling Metabolic Flux analysis Metabolic engineering Open-source software Science & Technology |
topic |
Constraint-based modeling Metabolic Flux analysis Metabolic engineering Open-source software Science & Technology |
description |
Background Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full portfolio of flux analysis methods. Results This work presents Constraint-based Flux Analysis (CBFA), an open-source software application for flux analysis in metabolic models that implements several methods for phenotype prediction, allowing users to define constraints associated with measured fluxes and/or flux ratios, together with environmental conditions (e.g. media) and reaction/gene knockouts. CBFA identifies the set of applicable methods based on the constraints defined from user inputs, encompassing algebraic and constraint-based simulation methods. The integration of CBFA within the OptFlux framework for ME enables the utilization of different model formats and standards and the integration with complementary methods for phenotype simulation and visualization of results. Conclusions A general-purpose and flexible application is proposed that is independent of the origin of the constraints defined for a given simulation. The aim is to provide a simple to use software tool focused on the application of several flux prediction methods. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014 2014-01-01T00:00:00Z |
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/1822/31907 |
url |
http://hdl.handle.net/1822/31907 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Carreira, R.; Evangelista, Pedro; Maia, P.; Vilaça, P.; Pont, Marcellinus; Tomb, Jean-François; Rocha, I.; Rocha, Miguel, CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Systems Biology, 8(123), 2014 1752-0509 1752-0509 10.1186/s12918-014-0123-1 25466481 |
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 |
BioMed Central (BMC) |
publisher.none.fl_str_mv |
BioMed Central (BMC) |
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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1799132191930712064 |