Statistics, Department of

 

The R Journal

Date of this Version

6-2017

Document Type

Article

Citation

The R Journal (June 2017) 9(1); Editor: Roger Bivand

Comments

Copyright 2017, The R Foundation. Open access material. License: CC BY 4.0 International

Abstract

A genome-scale metabolic reconstruction is a compilation of all stoichiometric reactions that can describe the entire cellular metabolism of an organism, and they have become an indispensable tool for our understanding of biological phenomena, covering fields that range from systems biology to bioengineering. Interrogation of metabolic reconstructions are generally carried through Flux Balance Analysis, an optimization method in which the biological sense of the optimal solution is highly sensitive to thermodynamic unbalance caused by the presence of stoichiometric reactions whose compounds are not produced or consumed in any other reaction (orphan metabolites) and by mass unbalance. The minval package was designed as a tool to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

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