Supplementary code - Peiro et al., 2019.
Content
This R script performs genome-scale flux balance analysis and flux variability analysis of Escherichia coli K-12 during aerobic growth on DHA, as detailed in the following publication:
Chemical and metabolic controls on dihydroxyacetone metabolism lead to a suboptimal growth of E. coli
Peiro et al., submitted
All calculations are performed using the E. coli genome scale metabolic model iJO1366 (Orth et al., 2011, DOI: 10.1038/msb.2011.65). This model can be found in Biomodels database (http://www.ebi.ac.uk/biomodels/ ; ID MODEL1108160000) and BiGG database (http://bigg.ucsd.edu ; ID iJO1366). It is also provided in folder 'iJO1366' in three different formats (SBML, TSV, and modelorg object provided in an RData file)
Details on the calculations can be found in the code (DHA.R).
Dependencies
Some R packages (lattice, glpkAPI, Matrix, sybil) are required. They can be installed with the following command in an R console:
$ install.packages(c("lattice", "glpkAPI", "Matrix", "sybil"))Usage
To run flux calculations as detailed in the publication:
- go to the code directory, e.g.:
$ cd /home/usr/data/Peiro_2019/- open an R session:
$ R- run calculations:
$ source("DHA.R")The code is open-source, and available under GPLv3 license.
Authors
Pierre Millard, Stéphanie Heux