AltFluxes: Cobra Toolbox extension for flux variability analysis of stoichiometric models of metabolism
2012
Kostromins, A., Latvia Univ. of Agriculture, Jelgava (Latvia). Faculty of Information Technology. Dept. of Computer Systems. Biosystems Group
The size and number of available constraint-based genome scale metabolic reconstructions and models is rapidly growing. Flux Balance Analysis (FBA) is an important analysis for these models to investigate possible steady state conditions for particular constraints sets in the models. FBA is based on linear algebra and it returns only one feasible set of distribution of fluxes. In the model there is possible infinite number of unique solutions depending on constraints set in the model. The COBRA Toolbox is a powerful tool with expanding functionality for analysis of stoichiometric models. The COBRA Toolbox offers the function to calculate alternative flux rates for each reaction in the model, however there is a lack of visual representation of the obtained results. Therefore the AltFluxes extension for the COBRA Toolbox is developed to visualize the flux variability results in the graph. The AltFluxes represents the numerical results in more transparent structure in the MATLAB command window as well. Moreover, proposed function returns not only alternative fluxes for each reaction in the model, but the set of the other fluxes of reactions in the extreme flux rates of corresponding reaction. The function AltFluxes is written in the MATLAB scripting language ensuring the cross-platform approach. It is an open source software under the GPL v3 license and available at http://www.biosystems.lv/altfluxes.
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