minval: An R package for MINimal VALidation of Stoichiometric Reactions

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.

Daniel Osorio , Janneth González , Andrés Pinzón

CRAN packages used

sybil, abcdeFBA, minval, gdata, readxl, xlsx, sybilSBML, sybil

CRAN Task Views implied by cited packages


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For attribution, please cite this work as

Osorio, et al., "The R Journal: minval: An R package for MINimal VALidation of Stoichiometric Reactions", The R Journal, 2017

BibTeX citation

  author = {Osorio, Daniel and González, Janneth and Pinzón, Andrés},
  title = {The R Journal: minval: An R package for MINimal VALidation of Stoichiometric Reactions},
  journal = {The R Journal},
  year = {2017},
  note = {https://doi.org/10.32614/RJ-2017-031},
  doi = {10.32614/RJ-2017-031},
  volume = {9},
  issue = {1},
  issn = {2073-4859},
  pages = {114-123}