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Open AccessArticle

FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks

by Tim Daniel Rose 1,2,3 and Jean-Pierre Mazat 2,3,*
1
Institute for Quantitative and Theoretical Biology, Heinrich-Heine-University, 40225 Duesseldorf, Germany
2
IBGC-CNRS UMR 5095, 1 rue Camille Saint Saens, CS 61390, 33077 Bordeaux-cedex, France
3
University of Bordeaux France, 33076 Bordeaux-cedex, France
*
Author to whom correspondence should be addressed.
Processes 2018, 6(5), 39; https://doi.org/10.3390/pr6050039
Received: 2 March 2018 / Revised: 10 April 2018 / Accepted: 17 April 2018 / Published: 24 April 2018
(This article belongs to the Special Issue Methods in Computational Biology)
FluxVisualizer (Version 1.0, 2017, freely available at https://fluxvisualizer.ibgc.cnrs.fr) is a software to visualize fluxes values on a scalable vector graphic (SVG) representation of a metabolic network by colouring or increasing the width of reaction arrows of the SVG file. FluxVisualizer does not aim to draw metabolic networks but to use a customer’s SVG file allowing him to exploit his representation standards with a minimum of constraints. FluxVisualizer is especially suitable for small to medium size metabolic networks, where a visual representation of the fluxes makes sense. The flux distribution can either be an elementary flux mode (EFM), a flux balance analysis (FBA) result or any other flux distribution. It allows the automatic visualization of a series of pathways of the same network as is needed for a set of EFMs. The software is coded in python3 and provides a graphical user interface (GUI) and an application programming interface (API). All functionalities of the program can be used from the API and the GUI and allows advanced users to add their own functionalities. The software is able to work with various formats of flux distributions (Metatool, CellNetAnalyzer, COPASI and FAME export files) as well as with Excel files. This simple software can save a lot of time when evaluating fluxes simulations on a metabolic network. View Full-Text
Keywords: metabolic network visualization; metabolic modelling; elementary flux modes visualization; flux balance analysis metabolic network visualization; metabolic modelling; elementary flux modes visualization; flux balance analysis
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Rose, T.D.; Mazat, J.-P. FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks. Processes 2018, 6, 39.

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