Compute growth rates of an organism through its metabolic niche. One can compute the niche of an organism through its metabolic model with the script here: https://gitlab.univ-nantes.fr/aregimbeau/metabolic-niche. (associated paper: https://onlinelibrary.wiley.com/doi/10.1111/ele.13954)
To be able to run the script your environment need to have numpy and netCDF4 python packages. Numpy and netCDF4 are available through pip, or conda.
This script is aimed to be used with environmental conditions and a metabolic niche description
python minimo.py --help
usage: minimo.py [-h] [-d DIRECTORY] [-s STRESS] [-a AUX] environmental_fluxes niche_file flux_name carbon
positional arguments:
environmental_fluxes File with environmental fluxes in HDF4 format (.nc), temporal unit is second
niche_file File with the niche description in .ine (h-format), see lrslib for detail on the format. Unit of flux should be in molXX.gDW-1.h-1
flux_name File where flux names are stored, one per line, corresponding to the niche fluxes.
carbon Carbon composition of the considered system in mole. In a GSM, this is the stoichiometry of C in the biomass reaction.
options:
-h, --help show this help message and exit
-d DIRECTORY, --directory DIRECTORY
Directory where result will be written, if not provided nothing will be written.
-s STRESS, --stress STRESS
Nutrient on which to compute the stress
-a AUX, --aux AUX Auxiliary metabolite niche file computation
The outputs of the script will be in DIRECTORY: growth.npy, stress.npy and auxiliary.npy.