dc.contributor.author | Martyushenko, Nikolay | |
dc.contributor.author | Almaas, Eivind | |
dc.date.accessioned | 2019-12-16T10:24:52Z | |
dc.date.available | 2019-12-16T10:24:52Z | |
dc.date.created | 2019-10-23T15:42:05Z | |
dc.date.issued | 2019 | |
dc.identifier.issn | 1367-4803 | |
dc.identifier.uri | http://hdl.handle.net/11250/2633367 | |
dc.description.abstract | Motivation: The number and complexity of genome-scale metabolic models is steadily increasing, empowered by automated model-generation algorithms. The quality control of the models, however, has always remained a significant challenge, the most fundamental being reactions incapable of carrying flux. Numerous automated gap-filling algorithms try to address this problem, but can rarely resolve all of a model’s inconsistencies. The need for fast inconsistency checking algorithms has also been emphasized with the recent community push for automated modelvalidation before model publication. Previously, we wrote a graphical software to allow the modeller to solve the remaining errors manually. Nevertheless, model size and complexity remained a hindrance to efficiently tracking origins of inconsistency. Results: We developed the ErrorTracer algorithm in order to address the shortcomings of existing approaches: ErrorTracer searches for inconsistencies, classifies them and identifies their origins. The algorithm is 2 orders of magnitude faster than current community standard methods, using only seconds even for large-scale models. This allows for interactive exploration in direct combination with model visualization, markedly simplifying the whole error-identification and correction work flow. Availability and implementation: Windows and Linux executables and source code are available under the EPL 2.0. Licence at https://github.com/TheAngryFox/ModelExplorer and https://www.ntnu.edu/almaaslab/downloads. Contact: nikolay.martyushenko@ntnu.no or eivind.almaas@ntnu.no. Supplementary information: Supplementary data are available at Bioinformatics online | nb_NO |
dc.language.iso | eng | nb_NO |
dc.publisher | Oxford University Press | nb_NO |
dc.rights | Navngivelse-Ikkekommersiell 4.0 Internasjonal | * |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/deed.no | * |
dc.title | ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models | nb_NO |
dc.type | Journal article | nb_NO |
dc.type | Peer reviewed | nb_NO |
dc.description.version | publishedVersion | nb_NO |
dc.source.journal | Bioinformatics | nb_NO |
dc.identifier.doi | 10.1093/bioinformatics/btz761 | |
dc.identifier.cristin | 1739965 | |
dc.relation.project | Norges forskningsråd: 271585 | nb_NO |
dc.relation.project | Stiftelsen Kristian Gerhard Jebsen: SKGJ-MED-015 | nb_NO |
dc.description.localcode | © The Author(s) 2019. Published by Oxford University Press. 1 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | nb_NO |
cristin.unitcode | 194,66,15,0 | |
cristin.unitname | Institutt for bioteknologi og matvitenskap | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 2 | |