minval : an R package for MINimal VALidation of stoichiometric reactions

The genome-scale metabolic reconstructions, a compilation of all stoichiometric reactions that can describe the entire cellular metabolism of an organism, have become an indispensable tool for our understanding of biological phenomena, covering fields that range from systems biology to bioengineering. Evaluation of metabolic reconstructions are generally carried through Flux Balance Analysis, an optimization method where the biological sense of optimal solution is 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 unbalanced stoichiometric reactions. The MINVAL package was designed as a tool to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. MINVAL 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.


This package required R version 2.10 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.

The official release of MINVAL is available on CRAN. To install from CRAN, use the following command:

install.packages("minval", dependencies = TRUE)

If you have devtools installed, install the latest stable version this package directly from GitHub:

# Install 'minval' package

Available functions:

Function Description
characterizeReactions Characterize stoichiometric reactions by compartments and reaction type
checkBalance Evaluate the mass or charge balance for a set of stoichiometric reactions
compartments Extract the compartments associated to metabolites of a set of stoichiometric reactions
downloadChEBI Download the ChEBI database
metabolites Identify the list of metabolites for a set of stoichiometric reactions
orphanMetabolites Identify the orphan metabolites of a set of stoichiometric reactions
products Identify the products of a stoichometric reaction
reactants Identify the reactants of a stoichometric reaction
stoichiometricMatrix Build the stoichiometric matrix for a set of stoichiometric reactions
validateSyntax Evaluate if a stoichiometric reaction has a valid syntax
writeSBMLmod Write a model in SBML format
writeTSVmod Write a model in TSV format for the ‘sybil’ R package


Daniel Osorio, Janneth Gonzalez and Andres Pinzon (2016). minval: MINimal VALidation for Stoichiometric Reactions. R package version 0.8. https://CRAN.R-project.org/package=minval