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C-CoMP-STC / GEM-mit1002

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Revisit the biomass equation #19

Open hgscott opened 12 months ago

hgscott commented 12 months ago

All of the gap filling is based on the biomass components from the standard gram-negative equation, so we may be gap filling for nothing if those components aren't really there.

hgscott commented 12 months ago

Looked at the Biomass components for P. simiae (gram-negative) on KBase.

Daniel is worried about apo-ACP, unsure why it is in the equation.

hgscott commented 12 months ago

Just to understand central carbon metabolism and nitrogen metabolism it may be enough to simplify the biomass reaction to amino acids and cofactors we know are there, it may make the model much simpler, but that may be fine.

hgscott commented 12 months ago

Daniel says not to use the core model biomass reaction, that is too small.

hgscott commented 12 months ago

Instead of making a new biomass reaction, gap fill when maximizing for each biomass component individually (the way we check for blocked biomass components).