The following bugs have been identified:
growth.m: the XY-axes labels of the growth plot are swapped (since release 8.3.5).scaleBioMass does not balance out to 1 g/gDCW, it only balances the biomass changes that is applied in that particular run. This becomes a problem if scaleBioMass is run multiple times without balancing (as is done in growth.m followed by balancing to one biomass component: the behaviour is not as reported (since release 8.3.5.anaerobicModel modifies the protein component of the biomass composition to 0.461 g/gDCW (reflecting carbon-limiting conditions), which becomes a problem if the biomass composition had just been changed to reflect nitrogen-limiting conditions). Additionally, modifying protein content to 0.461 for anaerobic conditions is not necessary, as it was already set to 0.46 release 8.1.0.
The above bugs mispresent growth predictions under anaerobic conditions.
Corrected growth prediction for yeast-GEM 9.0.2
Correcting the above bugs, without any further conceptual changes to how anaerobic conditions are simulated, gives a R2 of 0.8369.
Currently reported growth prediction for yeast-GEM 9.0.2
The above bugs that have existed since yeast 8.1.0 has resulted in inaccurate represented of nitrogen-limited anaerobic conditions, and gives a misleading R2 of 0.8798.
The following bugs have been identified:
growth.m: the XY-axes labels of the growth plot are swapped (since release 8.3.5).scaleBioMassdoes not balance out to 1 g/gDCW, it only balances the biomass changes that is applied in that particular run. This becomes a problem ifscaleBioMassis run multiple times without balancing (as is done ingrowth.mfollowed by balancing to one biomass component: the behaviour is not as reported (since release 8.3.5.anaerobicModelmodifies the protein component of the biomass composition to 0.461 g/gDCW (reflecting carbon-limiting conditions), which becomes a problem if the biomass composition had just been changed to reflect nitrogen-limiting conditions). Additionally, modifying protein content to 0.461 for anaerobic conditions is not necessary, as it was already set to 0.46 release 8.1.0.The above bugs mispresent growth predictions under anaerobic conditions.
Corrected growth prediction for yeast-GEM 9.0.2
Correcting the above bugs, without any further conceptual changes to how anaerobic conditions are simulated, gives a R2 of 0.8369.
Currently reported growth prediction for yeast-GEM 9.0.2
The above bugs that have existed since yeast 8.1.0 has resulted in inaccurate represented of nitrogen-limited anaerobic conditions, and gives a misleading R2 of 0.8798.