The R Journal: article published in 2017, volume 9:1

minval: An R package for MINimal VALidation of Stoichiometric Reactions
Daniel Osorio, Janneth González and Andrés Pinzón , The R Journal (2017) 9:1, pages 114-123.

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.

Received: 2016-03-10; online 2017-06-08
CRAN packages: sybil, abcdeFBA, minval, gdata, readxl, xlsx, sybilSBML, sybil

This article is licensed under a Creative Commons Attribution 4.0 International license.

@article{RJ-2017-031,
  author = {Daniel Osorio and Janneth González and Andrés Pinzón},
  title = {{minval: An R package for MINimal VALidation of
          Stoichiometric Reactions}},
  year = {2017},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2017-031},
  url = {https://doi.org/10.32614/RJ-2017-031},
  pages = {114--123},
  volume = {9},
  number = {1}
}