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TrinhLab / ctherm-gem

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Secretion product configuration #45

Closed sergarcia closed 6 years ago

sergarcia commented 6 years ago

Many options, have big impact on model prediction.

For instance for GAM/NGAM configuration ( or fitting experimental data more generally, without leading to an infeasible model) it is important to relax secretion constraints (anything can be secreted). On the other hand it is well known that certain products are only made under some very specific condtions (e.g. overflow metabolites, or trace metabolites).

Related with #44 #43 #17

sergarcia commented 6 years ago

This was thoroughly evaluated in step 9 (9f80e2383e9f52f46f75052e74f5a16a4d9b104e), essentially allowing the secretion of metabolites which are not commonly observed in significant amounts leads to incorrect predictions.