Chemostat_EColi

This is the main package for reproducing the results published at:

Pereiro-Morejón, José Antonio, Jorge Fernandez-de-Cossio-Diaz, and Roberto Mulet. “Inference of Metabolic Fluxes in Nutrient-Limited Continuous Cultures: A Maximum Entropy Approach with the Minimum Information.” IScience 25, no. 12 (December 22, 2022): 105450. https://doi.org/10.1016/j.isci.2022.105450.

Installation (macOs or linux)

The installation expect you to have git and julia (version >= 1.6) installed and on the PATH with those names. For testing run:

git version && echo && julia -e 'println(VERSION)' && echo "Test Passed"

For installing all required repositories (this part require internet on the terminal) run the follow command in an empty folder.

git clone --depth 1 --branch main --single-branch \
https://github.com/josePereiro/Chemostat_EColi.jl Chemostat_EColi && \
cd Chemostat_EColi && \
julia --startup-file=no scripts/0.1_install.jl

To reproduce the results (WARNING: this takes ~ 2 days in a core i5 cpu 2019 MacBook Air), run the follow command (in the Chemostat_EColi folder):

julia --startup-file=no scripts/0.2_make.jl

If bibtex and pdflatex are installed and in the PATH the make script should produce all the figures (contained at Chemostat_EColi/plots) and the paper's .pdf (at MaxEnt_EColi_paper/MaxEnt_EColi.pdf).