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

Chaitra Sarathy; Martina Kutmon; Michael Lenz; Michiel E Adriaens; Chris T Evelo; Ilja C W Arts

doi:10.3390/metabo10020066

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

Chaitra Sarathy^*, Martina Kutmon, Michael Lenz, Michiel E Adriaens, Chris T Evelo, Ilja C W Arts

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

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.

Original language	English
Article number	66
Number of pages	14
Journal	Metabolites
Volume	10
Issue number	2
DOIs	https://doi.org/10.3390/metabo10020066
Publication status	Published - 12 Feb 2020

Keywords

elementary flux modes
genome-scale metabolic models
data visualization
network visualization
SBML
ESCHERICHIA-COLI
PATHWAY ANALYSIS
GENE-EXPRESSION
CELL
DEFINITION
CYTOSCAPE
ACETATE
GROWTH
SET

Access to Document

10.3390/metabo10020066Licence: CC BY

Cite this

@article{1c689d1199d44243ac0aa546e1d419da,

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

abstract = "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, ESCHERICHIA-COLI, PATHWAY ANALYSIS, GENE-EXPRESSION, CELL, DEFINITION, CYTOSCAPE, ACETATE, GROWTH, SET",

author = "Chaitra Sarathy and Martina Kutmon and Michael Lenz and Adriaens, {Michiel E} and Evelo, {Chris T} and Arts, {Ilja C W}",

note = "Publisher Copyright: {\textcopyright} 2020 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2020",

month = feb,

day = "12",

doi = "10.3390/metabo10020066",

language = "English",

volume = "10",

journal = "Metabolites",

issn = "2218-1989",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "2",

}

TY - JOUR

T1 - EFMviz

T2 - A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models

AU - Sarathy, Chaitra

AU - Kutmon, Martina

AU - Lenz, Michael

AU - Adriaens, Michiel E

AU - Evelo, Chris T

AU - Arts, Ilja C W

PY - 2020/2/12

Y1 - 2020/2/12

N2 - 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.

AB - 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.

KW - elementary flux modes

KW - genome-scale metabolic models

KW - data visualization

KW - network visualization

KW - SBML

KW - ESCHERICHIA-COLI

KW - PATHWAY ANALYSIS

KW - GENE-EXPRESSION

KW - CELL

KW - DEFINITION

KW - CYTOSCAPE

KW - ACETATE

KW - GROWTH

KW - SET

U2 - 10.3390/metabo10020066

DO - 10.3390/metabo10020066

M3 - Article

C2 - 32059585

SN - 2218-1989

VL - 10

JO - Metabolites

JF - Metabolites

IS - 2

M1 - 66

ER -