AltFluxes

Visualization of flux variability analysis (FVA) results of COBRA Toolbox.

 

About

 

AltFluxes (Alternative Fluxes) is an open source (under the GPL v3 license) the COBRA Toolbox extension for flux variability analysis (FVA) with a graphical representation of alternative flux rates for constraints-based reconstruction and analysis (COBRA) models in the MATLAB environment.

The first version of AltFluxes was released on 03.02.2012.

AltFluxes is developed with funding sources of a project of European Structural Fund Nr. 2009/0207/1DP/1.1.1.2.0/09/APIA/VIAA/128 "Latvian Interdisciplinary Interuniversity Scientific Group of Systems Biology"

 

Installation

The installation of the extension consists of unpacking the archived scripts (M files) to the desired location and setting a path to these files in MATLAB.

AltFluxes User Manual

AltFluxes has one function:

fluxes=altfluxes(model,rxns)

where model stands for COBRA model and rxns stands for a list of reactions of interest. The model must contain all the necessary data for FBA and FVA processing. The list of reactions of interest can be a predefined variable in the MATLAB workspace or a string of reactions abbreviations in brackets {} separated by commas, for example:

{'R01','R02',...,'Rn'}

 

Screenshots from AltFluxes

Graphical results:

 

Results in the MATLAB command window:

Citation

Kostromins A. Altfluxes: COBRA Toolbox extension for flux variability analysis of stoichiometric models of metabolism. In Proceedings of the International Scientific Conference "Applied Information and Communication Technologies", April 26–27, 2012, Jelgava, Latvia, ISBN 978-9984-48-065-7, pp. 294–299. View full text.

 

Institute of Microbiology and Biotechnology, University of Latvia Jelgavas iela 1, Riga
LV-1004, Latvia

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