GECKO icon indicating copy to clipboard operation
GECKO copied to clipboard

Incorportate GECKO Light into the GECKO repo

Open johan-gson opened this issue 3 years ago • 1 comments
trafficstars

GECKO Light does the following

  1. Makes the model irreversible (same as original GECKO)
  2. It penalizes each reaction with a protein cost that is MW/kcat
  3. For complexes, the MWs are summed up
  4. 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 master branch of the repository
  • [X] Checked that a similar issue does not exist already

johan-gson avatar Jun 23 '22 19:06 johan-gson

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.

edkerk avatar Jul 08 '22 22:07 edkerk

Implemented with #180.

edkerk avatar Dec 19 '22 23:12 edkerk