Tags: SBRG/ecolime
Tags
Clean up model building - Unlump iron sulfur cluster forming reactions - broaden definition of enzyme 'carriers' to include all enzymes used as reactants in metabolic reaction - update mRNA degradation constraint - Allow building directly from E. coli M-model - Fix NGAM bug - Account for mu=0 case with degradation constraintsPlease enter the commit message for your changes. Lines starting
Refine surface area constraints
- Moved biomass allocation characterization functions to ecolime
- added get_SASA_keffs function to set SASA based keff approximations
- bug fixes for determining translocate costs
- moved translation and transcription building functions to dedicated
scripts
- added function for calculating gr dependent DNA concentrations as in
iOL1650
- functions for MPI parallel simulation
Big update: Implement surface area constraints 1)Reformulated surface area capacity constraint to ensure unit consistency 2)Added protein/nonprotein segregation to inner/outer membrane 3)Updated parameter sweeps to enable probing of linear acetate overflow metabolism trends 4)Move translocation formation reactions for prototype notebook to translocation.py 5)Correction of keff temperature scaling and small protein groEL folding 6)Replaced dummy_protein with dummy_protein_biomass for unmodeled protein dilution reaction 7)Corrected bug that allowed model to cheat by overproducing mRNA biomass. This should allow the enyzme efficiency increase with growth rate effect 8)Updated binary search to allow minimization of enzyme_efficiency_scaling 9)Models can now be saved as a json