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Kinetic modeling of glucose and acetate metabolisms in Escherichia coli

Overview

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.

Dependencies

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).

Usage

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.

How to cite

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

Authors

Pierre Millard

Contact

📧 Pierre Millard, [email protected]