This is the code for Oftadeh, O., and Hatzimanikatis, V., "Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression." Metabolic Engineering 84 (2024).
You will need pyTFA and ETFL to run it. We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
For further details, see ETFL's instruction.
The data to reconstruct the wild-type model is adopted from Salvy, P., Hatzimanikatis, V., "The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models" Nat Commun 11, 30 (2020).