This R code perform all analyses detailed in the following publication:
From toxic waste to beneficial nutrient: acetate boosts Escherichia coli growth at low glycolytic flux.
Millard P., Gosselin-Monplaisir T. Uttenweiler-Joseph S., Enjalbert B. Acetate is a beneficial nutrient for E. coli at low glycolytic flux. EMBO J., 2023, doi: 10.15252/embj.2022113079
The model is available in COPASI format in the ./model/ directory, and in SBML format from the Biomodels database (http://www.ebi.ac.uk/biomodels/) under identifier MODEL2005050001. Details on the model can be found in Millard et al. 2021 (eLife, doi: 10.7554/eLife.63661) and at https://github.com/MetaSys-LISBP/acetate_regulation. Experimental data are provided in the ./data/ directory. Calculation results and figures are saved in the ./results/ directory.
Details on the calculations can be found in the original publication and in the Rmd notebook.
We distribute an HTML file showing the notebook’s output after execution
The code is open-source and available under GPLv3 license.
If not yet done, download and install Rstudio.
Some R packages are also required.
RColorBrewer, gplots, pso, colorspace and optimx can be installed
by running the following command in the Rstudio console:
install.packages(c("RColorBrewer", "gplots", "pso", "optimx", "colorspace"))CoRC can be installed
using the following commands:
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) and the associated publication (Föster et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btab033).
To run all analyses detailed in the publication and reproduce Figures 1-4, 6-7 and EV1-2:
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download the GitHub repository tarball and unpack it somewhere on your disk
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start Rstudio
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open the file
./notebook.Rmd
The notebook will open in Rstudio, in each cell you can read/modify/execute the code as well as read accompanying comments.
If you have any question, please open a new issue to our GitHub issue tracker so we could discuss together.
Millard P., Gosselin-Monplaisir T. Uttenweiler-Joseph S., Enjalbert B. Acetate is a beneficial nutrient for E. coli at low glycolytic flux. EMBO J., 2023, doi: 10.15252/embj.2022113079
Pierre Millard
📧 Pierre Millard, pierre.millard@insa-toulouse.fr