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C-CoMP-STC / GEM-mit1002

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Come up with algorithm for iterative gap filling #30

Open hgscott opened 9 months ago

hgscott commented 9 months ago

We want to gap fill for a whole bunch of carbon sources, how should we do it?

hgscott commented 9 months ago

Daniel says to look at what Alan did.

Here's the paper: https://doi-org.ezproxy.bu.edu/10.1126/science.adf5121

And an excerpt specifically about the gap filling procedure: Image

hgscott commented 9 months ago

What is the MS2 improved gap filling app doing? You can add multiple media to gap fill for, is it doing it sequentially or something else?

hgscott commented 9 months ago

The documentation for the app doesn't say anything about when there are multiple media provided: https://narrative.kbase.us/#appcatalog/app/ModelSEEDReconstruction/gapfill_metabolic_models/beta

So I still have no idea if it is iterative or not.

Daniel says to reach out to the KBase team.