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dc.contributor.authorMartyushenko, Nikolay
dc.contributor.authorAlmaas, Eivind
dc.identifier.citationBMC Bioinformatics. 2019, 20 (56),nb_NO
dc.description.abstractBackground Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of computational approaches. The link between a metabolic network model and an organisms’ higher-level behaviour is usually found using a constraint-based analysis approach, such as FBA (Flux Balance Analysis). However, the process of model reconstruction rarely proceeds without error. Often, considerable parts of a model cannot carry flux under any condition. This is termed model inconsistency and is caused by faulty topology and/or stoichiometry of the underlying reconstructed network. While there exist several automated gap-filling tools that may solve some of the inconsistencies, much of the work still needs to be carried out manually. The common “linear list” format of writing biochemical reactions makes it difficult to intuit what is at the root of the inconsistent behaviour. Unfortunately, we have frequently observed that model builders do not correct their models past the abilities of automated tools, leaving many widely used models significantly inconsistent. Results We have developed the software ModelExplorer, which main purpose is to fill this gap by providing an intuitive and visual framework that allows the user to explore and correct inconsistencies in genome-scale metabolic models. The software will automatically visualize metabolic networks as graphs with distinct separation and delineation of cellular compartments. ModelExplorer highlights reactions and species that are unable to carry flux (blocked), with several different consistency checking modes available. Our software also allows the automatic identification of neighbours and production pathways of any species or reaction. Additionally, the user may focus on any chosen inconsistent part of the model on its own. This facilitates a rapid and visual identification of reactions and species responsible for model inconsistencies. Finally, ModelExplorer lets the user freely edit, add or delete model elements, allowing straight-forward correction of discovered issues. Conclusion Overall, ModelExplorer is currently the fastest real-time metabolic network visualization program available. It implements several consistency checking algorithms, which in combination with its set of tracking tools, gives an efficient and systematic model-correction process.nb_NO
dc.publisherBioMed Centralnb_NO
dc.rightsNavngivelse 4.0 Internasjonal*
dc.titleModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructionsnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewednb_NO
dc.source.journalBMC Bioinformaticsnb_NO
dc.relation.projectNorges forskningsråd: 271585nb_NO
dc.relation.projectStiftelsen Kristian Gerhard Jebsen: SKGJ-MED-015nb_NO
dc.description.localcodeOpen Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( applies to the data made available in this article, unless otherwise stated.nb_NO
cristin.unitnameInstitutt for bioteknologi og matvitenskap
cristin.unitnameInstitutt for samfunnsmedisin og sykepleie

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Navngivelse 4.0 Internasjonal
Except where otherwise noted, this item's license is described as Navngivelse 4.0 Internasjonal