problems in manualModifications.m #72
Description
It has been found that in the manualModifications function not all of the introduced changes to Kcat values are saved and given as an output. It actually happens that the first set of modifications (coming from: manual_data.txt and mostly for central carbon metabolism) are not saved at all. For the sake of consistency and in order to avoid weird results in later curation steps (automated) ALL of the modifications are needed to be saved.
Another aspect that has popped up when discussing with @feiranl, when introducing manually curated values we should make sure that the introduced value is not lower than the rest of available values for the reaction's isoenzymes, because if so the optimizer is always gonna choose the "cheapest" options.
We think that if lower Kcats are desired to be introduced in any manual curation then we need to make sure that modification applies to all of the isoenzymes for a given reaction.