ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models

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