Computing and analyzing ME-model predicted biomass compositions

Scripts to reproduce results in "Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth"

Running simulations

python submit_media_edison.py

• Runs ME-model simulations for all possible carbon, nitrogen, phosphorus, and sulfur sources, aerobically and anaerobically

python run_auxotroph_titration

• Runs ME-model simulations for amino acid and cofactor auxotroph from excess to 1/20th the optimal amount of the essential metabolite

Perform analysis

part_1.ipynb

• Recreate Figures 2 through 5

part_2.ipynb

• Recreate Figure 6