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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Eukaryotic model #53

Closed yunha closed 5 years ago

yunha commented 5 years ago

Hi,

I know that the original paper states that Eukaryote universal model isn't yet supported. Has there been any effort in building one recently? if not, where can I find the procedure to build a universal model for, say, yeast strains? Thanks!

cdanielmachado commented 5 years ago

We are considering the possibility of using a pan-genomic yeast reconstruction from the Mahadevan lab as a universal model for yeast:

https://www.biorxiv.org/content/10.1101/412593v1.abstract

Unfortunately, we haven't had the time to test it yet. I'd be happy to hear your feedback if you wanna try it.

cdanielmachado commented 5 years ago

The model is in this repository from @kcorreia :

https://github.com/LMSE/aybraham

kcorreia commented 5 years ago

We are revising the manuscript. Hope to have some updates within the next week.

I should stress that it is more of a fungal/Dikarya pan-model than eukaryotic since it doesn't have information about animal/plant models. But many reactions are conserved like amino acid metabolism, ETC, etc.

At the last COBRA meeting, I tried to get a couple of groups to develop separate animal and plant models in a similar approach. Would be nice to see standardization.

yunha commented 5 years ago

Thanks! @kcorreia will the revision be published on biorxiv? and @cdanielmachado I will try out carveme with the yeast model as a universal model and will let you know if it worked!

bcoltman commented 4 years ago

Was there any success with using the yeast model as a universal model @yunha?