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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Is carveme able to reconstruct genome scale models for fungies? #44

Closed amirfeizi closed 5 years ago

amirfeizi commented 5 years ago

Reading the paper, the core reaction database is built upon BiGG models. Therefore, in principal carveme should be able to reconstruct genome-scale models for fungies or eukaryotes. However, the implementation has been done on the gut microbial community. So, it would be nice to know if it is possible to use carveme for reconstruction in eukaryotes and if there is any specific parameters needed to be used in doing so.

Thanks,

Amir

cdanielmachado commented 5 years ago

Hi @amirfeizi,

Unfortunately for the moment eukaryotes are not supported as we don't have yet a universal model for them.

cdanielmachado commented 5 years ago

By the way, we are currently exploring the possibility of using this pan-genomic fungi reconstruction from the Mahadevan lab as a universal model for fungi:

https://www.biorxiv.org/content/early/2018/09/10/412593

amirfeizi commented 5 years ago

Thanks, Daniel! that was useful!