MINimal VALidation for Stoichiometric Reactions

For a given set of stoichiometric reactions, this package evaluates the mass and charge balance, extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to characterize and write models in TSV and SBML formats.


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.

Install:

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:

devtools::install_github("gibbslab/minval")
library("minval")

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

Citation

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

News

NEWS

minval v.0.8-1

  • An error with the downloadChEBI function when it was used in Windows OS was solved.
  • The citation file was added.
  • The link with sybilSBML was removed due the package was removed from CRAN

minval v.0.8

  • validateSyntax function now returns FALSE values instead error return
  • Minor changes in writeSBMLmod function were made

minval v.0.7

  • A bug related to unmapped metabolites in checkBalance function was solved

minval v.0.6

  • downloadChEBI function was added. This function can download any user-defined release of the ChEBI database.
  • checkBalance function now includes support for decimal coefficients in stoichiometric reactions.
  • characterizeReactions function was added.
  • The RECON 2.04 and an unbalanced Glycolysis model in a human-readable format were included.
  • The writeTSV and writeSBML functions were rewritten, the XML package dependency was removed and the support to convert modelOrg objects was added.
  • Two vignettes were included
  • The orphanMetabolites function was included and the orphanReactants and orphanProducts functions were added as wrappers.

minval v.0.5

  • All functions were vectorized
  • Functions to write TSV and SBML models were added
  • A function to download the different releases of the ChEBI database was added

minval v.0.4

  • A bug in reactants function was solved. It also affected the orphan.reactants function.

minval v.0.3

  • A bug in products function was solved
  • A bug related with spaces between metabolites was solved in several functions

minval v.0.2

  • Some functions were rewrited
  • A bug in the compartments function was solved.

minval v.0.1

  • ChEBI database release 136 was added.
  • The stoichiometric reactions from the reconstructon of the glutamate/glutamine cycle were added.

Reference manual

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install.packages("minval")

0.8-1 by Daniel Osorio, 10 months ago


https://github.com/gibbslab/minval


Browse source code at https://github.com/cran/minval


Authors: Daniel Osorio [aut, cre] , Janneth Gonzalez [aut, ths] , Andres Pinzon [aut, ths]


Documentation:   PDF Manual  


GPL (>= 2) license


Suggests testthat, knitr, rmarkdown, sybil, glpkAPI


Imported by g2f.


See at CRAN