many of fba's external exchange molecules have a [c] tag

CovertLab / wcEcoli

Whole Cell Model of E. coli

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many of fba's external exchange molecules have a [c] tag #471

Open eagmon opened 5 years ago

eagmon commented 5 years ago

About a third of the external exchange molecules have a [c] tag, which the rest have a [p] tag. Ideally, they should all be coming from the periplasm and so have a [p]. I plan to fix this, possibly by adding some new reactions that have a stoic of {mol[p]: -1, mol[c]: 1}.

eagmon commented 5 years ago

CPD-10774 is a secretion molecule that gets secreted both as CPD-10774[p] and CPD-10774[c]. There is a reaction, TRANS-RXN0-453, with stoich {"CPD-10774[p]": 1, "CPD-10774[c]": -1}. I would think that secreting only CPD-10774[p] would suffice given this export reaction.

eagmon commented 5 years ago

4FE-4S is secreted as 4FE-4S[c] it is not in any reaction listed in reactions.tsv as either [c] or [p] . It is only present in equilibrium. I'm not sure what this means for FBA.