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EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models

1
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
2
Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands
3
Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128, Germany
4
Preventive Cardiology and Preventive Medicine—Center for Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
5
Department of Epidemiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
*
Author to whom correspondence should be addressed.
Metabolites 2020, 10(2), 66; https://doi.org/10.3390/metabo10020066 (registering DOI)
Received: 31 December 2019 / Revised: 6 February 2020 / Accepted: 7 February 2020 / Published: 12 February 2020
(This article belongs to the Special Issue Metabolic Networks)
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1260) and large (human, Recon 2.2) genome-scale metabolic models. EFMviz is open-source and integrated into COBRA Toolbox. The analysis workflows used for the two use cases are detailed in the two tutorials provided with EFMviz along with the data used in this study.
Keywords: Elementary Flux Modes; Genome-Scale Metabolic Models; data visualization; network visualization; SBML Elementary Flux Modes; Genome-Scale Metabolic Models; data visualization; network visualization; SBML
MDPI and ACS Style

Sarathy, C.; Kutmon, M.; Lenz, M.; Adriaens, M.E.; Evelo, C.T.; Arts, I.C. EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models. Metabolites 2020, 10, 66.

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