These R scripts perform all analyses detailed in the following publication:

Control and regulation of acetate overflow in Escherichia coli

Millard et al., 2021, eLife, doi: 10.7554/eLife.63661

All models are available in COPASI format in the directory /model/cps/, with the experimental data used for model calibration. The final kinetic model is also available in SBML format in the directory /model/sbml/ and from the Biomodels database (http://www.ebi.ac.uk/biomodels/) under identifier MODEL2005050001.

Details on the calculations can be found in the original publication and in the R scripts.

Some R packages are required.

RColorBrewer, stringr and gplots can be installed by running the following command in an R console:

install.packages(c("RColorBrewer", "gplots", "stringr"))

CoRC can be installed using the following command:

install.packages("remotes")
library(remotes)
remotes::install_github("jpahle/CoRC")
library(CoRC)
CoRC::getCopasi()

Additional information on CoRC installation and usage are available from the CoRC repository (https://github.com/jpahle/CoRC) an in the associated publication (Föster et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btab033).

To run all analyses detailed in the publication and reproduce Figures 1, 3-6 and all Supplementary figures:

• go to the code directory, e.g.:

cd /home/usr/data/acetate_regulation/

• open an R session:

R

• run calculations, starting from model construction to regulation analyses:

source("1-Model_construction.R")

source("2-Model_validation.R")

source("3-Metabolic_control_analyses.R")

source("4-Regulation_analyses.R")

The code is open-source and available under GPLv3 license.

Millard P., Enjalbert B., Uttenweiler-Joseph S., Portais J.C., and Letisse F. Control and regulation of acetate overflow in Escherichia coli. eLife, 2021, doi: 10.7554/eLife.63661

Pierre Millard

📧 Pierre Millard, [email protected]