The R Journal: article published in 2021, volume 13:2

g2f as a Novel Tool to Find and Fill Gaps in Metabolic Networks
Daniel Osorio, Kelly Botero, Andrés Pinzón Velasco, Nicolás Mendoza-Mejía, Felipe Rojas- Rodríguez, George Barreto and Janneth González , The R Journal (2021) 13:2, pages 28-37.

Abstract During the building of a genome-scale metabolic model, there are several dead-end metabo lites and substrates which cannot be imported, produced, nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from dead-end metabolites and fill them from the stoichiometric reactions of a reference, filtering candidate reactions using a weighting function. Additionally, this algorithm allows downloading all the sets of gene-associated stoichiometric reactions for a specific organism from the KEGG database. Our package is compatible with both 4.0.0 and 3.6.0 R versions.

Received: 2019-10-20; online 2021-07-15, supplementary material, (11.1 KiB)
CRAN packages: g2f, sybil

This article and supplementary materials are licensed under a Creative Commons Attribution 4.0 International license.

@article{RJ-2021-064,
  author = {Daniel Osorio and Kelly Botero and Andrés Pinzón Velasco and
          Nicolás Mendoza-Mejía and Felipe Rojas- Rodríguez
          and George Barreto and Janneth González},
  title = {{g2f as a Novel Tool to Find and Fill Gaps in Metabolic
          Networks}},
  year = {2021},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2021-064},
  url = {https://doi.org/10.32614/RJ-2021-064},
  pages = {28--37},
  volume = {13},
  number = {2}
}