Scripts to study the effect of ribosome composition on growth rate using resource balance analysis (RBA) and elementary growth vectors (EGVs).
- model_functions.py - functions and classes used by other scripts
- fit_kdegmax.py - fit rRNA degradation rate (kdeg_max) so the optimal R composition is xrP=36%
- run_all_conditions.py - RBA simulations that find max. growth rate at each ribosome composition for different parameter sets (specified in parameters.csv)
- fluxes_vs_growth_rate.py - vary growth rate at fixed xrP = 36%; save RNAP fluxes with or without excess accumulation of R or rRNA / excess RNA degradation
- plot_growth_rates.R - plot growth rate vs. ribosome composition
- plot_allocations.R - plot ribosome allocation vs. ribosome composition
- plot_RNAP_fluxes.R - plot RNAP fluxes vs. growth rate at fixed xrP=36%
- plot_RP_ratios.R - plot RNA/protein ratios at different growth rates
- plot_RNase_RNAP_ratios.R - plot ratios of RNA degradation flux to RNAP flux at max. growth rates
- outputs of the simulations
- fitted_kdegmax.txt - printed output from fit_kdegnax.py
- RBA_[xy].csv - outputs of run_all_conditions.py (xy: growth_rates, fluxes, allocations, mass_fractions)
- fluxes_x0.36.csv - output of fluxes_vs_growth_rate.py
- parameters.csv - parameters for simulations (see class Model() in model_functions.py for explanations)
- gausing_RNA_deg.csv - fraction of degraded RNA at different growth rates from Gausing 1977 extracted with WebPlotDigitizer
- fluxes_bremer.csv - fluxes from Bremer 2008, converted to mmol/gh with fluxes_vs_growth_rate.py
- stats.csv - optimal xrP for each condition & growth rate at xrP = 36%, output of plot_growth_rates.R
Plots generated by R scripts in the section 'Plots'