Finally getting a chance to check out q2-micom and it’s looking really cool so far! And thanks for the excellent documentations and tutorials!
I have a few quasi related questions about the starting input files to use in micom. I couldn’t find a clear answer to these throughout the documentations (both q2, and stand-alone version).
- In the q2-micom tutorial, you use a pre-built western diet environment and mention the VMH database can be used for other diets. However, I couldn’t find how these other diets (or a custom one made on VMH) should be imported. For ex. your prebuilt
western_diet_gut.qzaartifact has 4 columns:
While the diets I download directly from VMH have only 2:
What is the intermediary process exactly to go from one to the other?
The AGORA taxonomy, I think appears to be in NCBI taxonomy format, however the taxonomy you use in the q2-micom tutorial is based on SILVA. What magic is being used under the hood to map these 2 together? On that note, are other databases supported? Namely Greengenes and GTDB?
In a situation where we have information about each individual’s diet, we can produce a specific environment model for each individual, assuming this will increase accuracy of flux estimates. Is there an easy way to run the growth simulations by providing a manifest file of sorts that would map each subject with their own diet
.qza, rather them running them individually? If not, how would you recommend importing, running growth simulations, and merging a bunch of samples with their own unique diets?
I’m sure more questions will be heading your way soon