Custom code for constraining and solving COBRAme models
run_simulations.ipynb: constrains a COBRAme model with measured growth and exchange rates, applies gene knockouts, and adds proteome sector constraints from RNA-seq. Each sector's transcript mass fraction, relative to ribosomal proteins, sets a lower bound on the protein the model allocates to that sector.run_simulations_w_cap.ipynb: the same, plus an oxygen uptake band (mean ± SD) andset_expression_cap, an upper bound on a sector's protein allocation at a multiple of its transcript-implied ratio. The floor only says "at least this much", so the cap is what stops the model from over-allocating a sector. The example caps the D-lactate dehydrogenases (ldhA, dld).
Both need cobrame, ecolime and qminospy.