BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models

Bibliographic Details
Main Author: Cruz, Fernando
Publication Date: 2021
Other Authors: Capela, João, Ferreira, Eugénio C., Rocha, Miguel, Dias, Oscar
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/1822/77020
Summary: BioISO was implemented as a webserver available at https://bioiso.bio.di.uminho.pt; and integrated into merlin as a plugin. BioISOs implementation as a Python package can also be retrieved from: https://github.com/BioSystemsUM/BioISO
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spelling BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic modelsBioISO was implemented as a webserver available at https://bioiso.bio.di.uminho.pt; and integrated into merlin as a plugin. BioISOs implementation as a Python package can also be retrieved from: https://github.com/BioSystemsUM/BioISOAs the reconstruction of Genome-Scale Metabolic Models becomes standard practice in systems biology, the number of organisms having at least one metabolic model at the genome-scale is peaking at an unprecedented scale. The automation of several laborious tasks, such as gap-finding and gap-filling, allowed to develop GSMMs for poorly described organisms. However, such models quality can be compromised by the automation of several steps, which may lead to erroneous phenotype simulations. The Biological networks constraint-based In Silico Optimization (BioISO) is a computational tool aimed at accelerating the reconstruction of Genome-Scale Metabolic Models. This tool facilitates the manual curation steps by reducing the large search spaces often met when debugging in silico biological models. BioISO uses a recursive relation-like algorithm and Flux Balance Analysis to evaluate and guide debugging of in silico phenotype simulations. The potential of BioISO to guide the debugging of model reconstructions was showcased using GSMMs available in literature and compared with the results of two other state-of-the-art gap-filling tools (Meneco and fastGapFill). Furthermore, BioISO was used as Menecos gap-finding algorithm to reduce the number of proposed solutions (reaction sets) for filling the gaps.info:eu-repo/semantics/publishedVersionCold Spring Harbor LaboratoryUniversidade do MinhoCruz, FernandoCapela, JoãoFerreira, Eugénio C.Rocha, MiguelDias, Oscar2021-03-122021-03-12T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/77020engCruz, Fernando; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. bioRxiv - the Preprint Server for Biology, 202110.1101/2021.03.07.434259https://www.biorxiv.org/content/10.1101/2021.03.07.434259v2info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-11T05:19:47Zoai:repositorium.sdum.uminho.pt:1822/77020Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T15:14:46.211767Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
title BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
spellingShingle BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
Cruz, Fernando
title_short BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
title_full BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
title_fullStr BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
title_full_unstemmed BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
title_sort BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models
author Cruz, Fernando
author_facet Cruz, Fernando
Capela, João
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
author_role author
author2 Capela, João
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Cruz, Fernando
Capela, João
Ferreira, Eugénio C.
Rocha, Miguel
Dias, Oscar
description BioISO was implemented as a webserver available at https://bioiso.bio.di.uminho.pt; and integrated into merlin as a plugin. BioISOs implementation as a Python package can also be retrieved from: https://github.com/BioSystemsUM/BioISO
publishDate 2021
dc.date.none.fl_str_mv 2021-03-12
2021-03-12T00:00:00Z
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/1822/77020
url http://hdl.handle.net/1822/77020
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Cruz, Fernando; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar, BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. bioRxiv - the Preprint Server for Biology, 2021
10.1101/2021.03.07.434259
https://www.biorxiv.org/content/10.1101/2021.03.07.434259v2
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:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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