A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes

This repository contains code to simulate microbial growth on carbon and nitrogen using a coarse-grained resource allocation model. It also includes code to generate the figures for our associated manuscript (Kleijn et al., bioRxiv 2023).

Folder structure

General Julia code for simulating the models is provided in src/. The Julia code under scripts/ was used to generate simulation data in data/ketoacid-excretion/, which were aggregated manually as data/results.csv. The R code in scripts/ was used to generate the figures in plots/. For Figure 5B, supplementary data was taken from Kleijn, Martínez-Segura et al. (Life Science Alliance 2022), it is included here in data/pomballoc/.

Citation

Kleijn, I.T., Marguerat, S. and Shahrezaei, V. (2023) ‘A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes’. bioRxiv, p. 2023.04.04.535571. Available at: https://doi.org/10.1101/2023.04.04.535571.

Reference

Kleijn, I.T., Martínez-Segura A., et al. (2022) ‘Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast’, Life Science Alliance, 5(5), p. e202101223. Available at: https://doi.org/10.26508/lsa.202101223.