Eukaryotic model about carveme

[cdanielmachado]

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]

The model is in this repository from @kcorreia :

https://github.com/LMSE/aybraham

[kcorreia]

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]

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]

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