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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Alternative universe curation #50

Closed fairquestion closed 5 years ago

fairquestion commented 5 years ago

Dear Daniel,

Finally I am working regularly with Carveme and I would like to reconstruct an Alternative Universe for the bacterial genus Nitrospira since the gramm- universe is not enough in order to obtain a proper reconstruction (which is something expected, due to the life style reactions in this genus).

I would like to know which hints and recomendations can you provide before starting the manual curation for this universal model, since it is an intense time consuming work.

Best and thanks, Fair.

cdanielmachado commented 5 years ago

The hardest part for me curating the currently available universal models was the thermodynamics. Using the Gibbs free energy values (you can find them in the data files) gives an initial rough estimation on reversibility, but after that, it requires a lot of fine-tuning until you find a good balance between avoiding futile cycles and not over-constraining the solution space.