6533b85bfe1ef96bd12baa8a

RESEARCH PRODUCT

EFMviz

Chris T. EveloMichael LenzMichael LenzIlja C. W. ArtsChaitra SarathyMartina KutmonMichiel E. Adriaens

subject

0301 basic medicineComputer scienceEndocrinology Diabetes and Metabolismgenome-scale metabolic modelslcsh:QR1-502computer.software_genreBiochemistryData typelcsh:MicrobiologySBML03 medical and health sciences0302 clinical medicineData visualizationGraph drawingProtocolACETATEdata visualizationCELLSBMLCYTOSCAPEMolecular BiologyGENE-EXPRESSIONSoftware visualizationbusiness.industryPATHWAY ANALYSISnetwork visualizationelementary flux modesToolboxVisualization030104 developmental biologyWorkflowDEFINITIONESCHERICHIA-COLIGROWTHData miningbusinesscomputerSET030217 neurology & neurosurgery

description

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.

yearjournalcountryeditionlanguage
2020-02-12Metabolites
10.3390/metabo10020066https://doi.org/10.3390/metabo10020066