FLUX and pathways viewER
FLUX and pathways viewER
Fluxer is a web application for the computation and interactive visualization of metabolic flux networks. Fluxer can perform Flux Balance Analysis (FBA) and create visualizations of the resulting flux network with spanning trees, k-shortest paths, or complete graphs in a user-friendly interface. Fluxer also allows any number of reactions to be knocked-out, simulating the deletion of specific enzymes and their resultant effects on the fluxes and growth rates. Currency and cofactor metabolites, such as ATP and H2O, or reactions carrying zero-flux can be excluded from the graph computations. Users can upload their own metabolic models for visualization, retrieve a model from BioModels, and choose one preloaded from the BiGG Models, AGORA, and Metabolic Atlas databases or curated from papers. The Tutorial page provides detailed information on how to use Fluxer and customize the graphs it generates.
Fluxer uses Flask for the backend, SQLite for database storage, and HTML5 and Javascript for the front end. The libSBML package is used to read SBML layouts. Flux Balance Analysis is computed with COBRApy. Genome-scale metabolic models are merged with mergem. FROG reports are generated with fbc_curation. Metabolite and reaction information were pooled from KEGG, MetaNetX, ModelSEED, BiGG Models, AGORA, Metabolic Atlas, and ChEBI for names, crosslinks, and molecular weights. When available, metabolite structures are displayed from KEGG. Fluxer uses D3 during the layout calculations. Users can download the graphs generated as PNG and SVG files.
Archana Hari, Arveen Zarrabi, and Daniel Lobo
Fluxer: a web application to compute and visualize genome-scale metabolic flux
networks
A. Hari, D. Lobo
Nucleic Acids Research, 48, pp. 427-435, 2020
mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers
A. Hari, A. Zarrabi, D. Lobo
NAR Genomics & Bioinformatics, 6(1), lqae010, 2024
Fluxer is provided ‘as-is’, without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, subject to the following restrictions: