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CovertLab / wcEcoli

Whole Cell Model of E. coli
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Very low oxygen usage in sims with new flat files #1077

Open tahorst opened 3 years ago

tahorst commented 3 years ago

With the updated files from EcoCyc (#1065), the model consumes very little oxygen during simulations as seen with external_exchange_fluxes single analysis plots below.

Before EcoCyc files (768d8d7342): external_exchange_fluxes

After (3fb36325): external_exchange_fluxes

This might be linked to ubiquinone and ubiquinol since reactions that convert between and consume oxygen are much lower in the new sims.

ggsun commented 3 years ago

I'm looking into this right now - thanks for pointing this out. There were a lot of metabolic redox reactions that started using different cofactors, so this might be easy as adding a single different version of a metabolic reaction.

ggsun commented 3 years ago

Based on what I've looked at so far, I'm suspecting that this issue is connected to the lower GLC[p] import that we can also see in the same plot. There's something funny going on in the first few reactions of glycolysis that imports GLC[p] and phosphorylates it to get G6P that I'm not fully grasping yet.