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fix-gene: remove non-transporter genes - updated #450
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See my comment in #444 - I'm worried that we might be moving too fast here. |
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It was difficult to see the exact changes from last time, but I think you thought it through - I will not go over everything again. Good job!
as suggested in #426, simulation checks with models before and after these deletions were conducted and showed exactly the same growth rates. |
Why would removing genes change simulation results? Unless you're using an enzyme-constrained model, I don't quite understand how it would influence flux at all (assuming by "simulation" you mean FBA). |
@JonathanRob yes, now it's just FBA that gave the same results since stoichiometric was not changed. As just commented in #426, a systematic checking code would be needed as reaction addition/removal may happen in the future. |
Gene essentiality analysis should performed in terms of removing genes? The check function is coming. |
agree |
If you want I can do the gene essentiality part - I recently did this for the single-cell modeling paper, so I know how to do it and have the code on the cluster etc. set up for this. I can do it in 1-2 weeks (or later), I don't know the status of the model, when it will be ready. |
But don't expect any large changes to the prediction power :) |
Main improvements in this PR:
Transporter reactions
, as proposed in remove non-transporter genes from transport reactions #444I hereby confirm that I have:
develop
as a target branch