GECKO
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Incorportate GECKO Light into the GECKO repo
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GECKO Light does the following
- Makes the model irreversible (same as original GECKO)
- It penalizes each reaction with a protein cost that is MW/kcat
- For complexes, the MWs are summed up
- For isozymes, the lowest protein cost is used for the reaction. This is what the optimizer would select anyway.
I hereby confirm that I have:
- [X] Done this analysis in the
masterbranch of the repository - [X] Checked that a similar issue does not exist already
Point 4 (isoenzymes) should still be addressed in #170, while the unit of MW/kcat is probably also not yet correct in that PR. Note that in generic GECKO, we'll redefine the enzyme usage fluxes as umol/gDW/h (instead of previously mmol/gDW/h), to prevent very low fluxes and issues with scaling when solving the LP.
Implemented with #180.