Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model

Autores
Alberton, Kese Pontes Freitas; Alberton, André Luís; Di Maggio, Jimena Andrea; Estrada, Vanina Gisela; Díaz, María Soledad; Resende Secchi, Argimiro
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in themodeling of such systems. As case study, the complex real problem of parameters identifiability of the Escherichia coli K-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved formost of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions.The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.
Fil: Alberton, Kese Pontes Freitas. Universidade Federal do Rio de Janeiro; Brasil
Fil: Alberton, André Luís. Universidade Do Estado de Rio Do Janeiro; Brasil
Fil: Di Maggio, Jimena Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Estrada, Vanina Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Díaz, María Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Resende Secchi, Argimiro. Universidade Federal do Rio de Janeiro; Brasil
Materia
PARAMETERS IDENTIFIABILITY
COMPLEX DYNAMIC MODELS
SCARCE EXPERIMENTAL DATA
METABOLIC NETWORKS
ESCHERICHIA COLI
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/24451
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/24451
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network ModelAlberton, Kese Pontes FreitasAlberton, André LuísDi Maggio, Jimena AndreaEstrada, Vanina GiselaDíaz, María SoledadResende Secchi, ArgimiroPARAMETERS IDENTIFIABILITYCOMPLEX DYNAMIC MODELSSCARCE EXPERIMENTAL DATAMETABOLIC NETWORKSESCHERICHIA COLIhttps://purl.org/becyt/ford/2.4https://purl.org/becyt/ford/2This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in themodeling of such systems. As case study, the complex real problem of parameters identifiability of the Escherichia coli K-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved formost of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions.The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.Fil: Alberton, Kese Pontes Freitas. Universidade Federal do Rio de Janeiro; BrasilFil: Alberton, André Luís. Universidade Do Estado de Rio Do Janeiro; BrasilFil: Di Maggio, Jimena Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; ArgentinaFil: Estrada, Vanina Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; ArgentinaFil: Díaz, María Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; ArgentinaFil: Resende Secchi, Argimiro. Universidade Federal do Rio de Janeiro; BrasilHindawi Publishing Corporation2015-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/24451Alberton, Kese Pontes Freitas; Alberton, André Luís; Di Maggio, Jimena Andrea; Estrada, Vanina Gisela; Díaz, María Soledad; et al.; Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model; Hindawi Publishing Corporation; Biomed Research International; 2015; 2-2015; 1-21; 4547652314-61332314-6141CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1155/2015/454765info:eu-repo/semantics/altIdentifier/url/https://www.hindawi.com/journals/bmri/2015/454765/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:02:24Zoai:ri.conicet.gov.ar:11336/24451instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:02:25.037CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
title Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
spellingShingle Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
Alberton, Kese Pontes Freitas
PARAMETERS IDENTIFIABILITY
COMPLEX DYNAMIC MODELS
SCARCE EXPERIMENTAL DATA
METABOLIC NETWORKS
ESCHERICHIA COLI
title_short Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
title_full Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
title_fullStr Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
title_full_unstemmed Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
title_sort Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model
dc.creator.none.fl_str_mv Alberton, Kese Pontes Freitas
Alberton, André Luís
Di Maggio, Jimena Andrea
Estrada, Vanina Gisela
Díaz, María Soledad
Resende Secchi, Argimiro
author Alberton, Kese Pontes Freitas
author_facet Alberton, Kese Pontes Freitas
Alberton, André Luís
Di Maggio, Jimena Andrea
Estrada, Vanina Gisela
Díaz, María Soledad
Resende Secchi, Argimiro
author_role author
author2 Alberton, André Luís
Di Maggio, Jimena Andrea
Estrada, Vanina Gisela
Díaz, María Soledad
Resende Secchi, Argimiro
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv PARAMETERS IDENTIFIABILITY
COMPLEX DYNAMIC MODELS
SCARCE EXPERIMENTAL DATA
METABOLIC NETWORKS
ESCHERICHIA COLI
topic PARAMETERS IDENTIFIABILITY
COMPLEX DYNAMIC MODELS
SCARCE EXPERIMENTAL DATA
METABOLIC NETWORKS
ESCHERICHIA COLI
purl_subject.fl_str_mv https://purl.org/becyt/ford/2.4
https://purl.org/becyt/ford/2
dc.description.none.fl_txt_mv This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in themodeling of such systems. As case study, the complex real problem of parameters identifiability of the Escherichia coli K-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved formost of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions.The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.
Fil: Alberton, Kese Pontes Freitas. Universidade Federal do Rio de Janeiro; Brasil
Fil: Alberton, André Luís. Universidade Do Estado de Rio Do Janeiro; Brasil
Fil: Di Maggio, Jimena Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Estrada, Vanina Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Díaz, María Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Fil: Resende Secchi, Argimiro. Universidade Federal do Rio de Janeiro; Brasil
description This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in themodeling of such systems. As case study, the complex real problem of parameters identifiability of the Escherichia coli K-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved formost of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions.The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.
publishDate 2015
dc.date.none.fl_str_mv 2015-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/24451
Alberton, Kese Pontes Freitas; Alberton, André Luís; Di Maggio, Jimena Andrea; Estrada, Vanina Gisela; Díaz, María Soledad; et al.; Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model; Hindawi Publishing Corporation; Biomed Research International; 2015; 2-2015; 1-21; 454765
2314-6133
2314-6141
CONICET Digital
CONICET
url http://hdl.handle.net/11336/24451
identifier_str_mv Alberton, Kese Pontes Freitas; Alberton, André Luís; Di Maggio, Jimena Andrea; Estrada, Vanina Gisela; Díaz, María Soledad; et al.; Simultaneous Parameters Identifiability and Estimation of an E. coli Metabolic Network Model; Hindawi Publishing Corporation; Biomed Research International; 2015; 2-2015; 1-21; 454765
2314-6133
2314-6141
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1155/2015/454765
info:eu-repo/semantics/altIdentifier/url/https://www.hindawi.com/journals/bmri/2015/454765/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Hindawi Publishing Corporation
publisher.none.fl_str_mv Hindawi Publishing Corporation
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1846781231279112192
score 12.982451

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