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CovertLab / wcEcoli

Whole Cell Model of E. coli
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Unnecessary complexation reactions in simData #210

Open ggsun opened 6 years ago

ggsun commented 6 years ago

While building up the causal network nodes and edges, I noticed that a total of 5 complexation reactions included in simData have reactants that are products of equilibrium reactions in rawData, but these equilibrium reactions are removed in simData since the ligand metabolite is modeled as having zero counts. These reactants cannot be produced in any other way other than the deleted equilibrium reaction, so I think it would be safe to just remove these reactions from complexation as well.

tahorst commented 6 years ago

What are the reactions?

ggsun commented 6 years ago

CPLX0-7639_RXN (CPLX0-7620), CPLX0-7672_RXN (CPLX0-7701), CPLX0-7678_RXN (CPLX0-7677), CPLX0-7707_RXN (MONOMER0-1781), and CPLX0-7708_RXN (CPLX0-7702). The complexes in parenthesis are the ones that are formed by deleted equilibrium reactions.

tahorst commented 6 years ago

At what point would you want to remove them? If they're not affecting the sim at all, I think it's best to leave them in there so we don't need to remember to go back and add them if we ever add information like the ligand metabolite concentration. If you want to programmatically remove them if there are 0 counts, that would be a little safer but also introduce extra complexity.

jmason42 commented 6 years ago

Generally speaking, it sounds like we should be automatically documenting which complexation reactions can never occur consequent of missing metabolites. "Stub" submodels i.e. submodels that don't actually connect to some other model inputs and outputs should be regarded with skepticism and documented thoroughly, since there is no empirical evidence that they will work if the inputs and outputs are eventually connected.