Model Diet Input: VMH (Virtual Metabolic Human) Diet Designer Questions

[Andrew Culhane]

Hello all! Many of you might be very familiar with using the VMH to generate input diets for models. I had a few questions about VMH. 

1. Are you able to upload a list of food items (that exactly match your database) instead of just drag and drop to create a diet? If so, how does one do this? 
2. Once you generate a flux list for metabolites in your diet, can you edit it on the site, or do you have to download it and make your own changes? If so, how does one do this? 
3. You can pre-load a standard diet on the site. Can a user save and re-load custom diets they have created? 
4. How does VMH go from food -> list of metabolites? Does anyone know what databases they draw on aside from USDA? 
   
   Thank you! 
   
   Andrew 

[Bram Nap]

Hi Andrew,

To the best of my knowledge

1. Currently, it is not possible to drag a premade list of food items in the VMH itself. You will have to create each diet manually by selecting and adding individual food items.
2. The flux list generated by the VMH is not editable on the VMH itself. In order to edit it, you will need to download the file by "generate fluxes" and then "download". You will get a txt file with the dietary exchange reaction and its associated flux. To modify a value, just adjust the value in the .txt file. To add a new dietary reaction add a newline. For your metabolite of interest, find the metabolite ID on the VMH and set the ID of the rxn as :Diet_EX_metabolite ID of interest[d]. Add a tab or other delimiter used in your file, and then the value of the flux you want. To find out which dietary exchange reactions are in the WBMs, load a WBM in MATLAB, run dietRxns = model.rxns(contains(model.rxns, 'Diet_EX_')).
3. This is currently not possible on the VMH
4. The VMH uses the USDA database. It maps the metabolites measured in the USDA to VMH metabolites and translates the measured values in grams, milligrams or micrograms to mmol based on the amount of food consumed and molecular weight of the metabolite (found in the VMH as well).

I hope this helps you!

As an FYI we will submit a preprint to bioRxiv next week on a software package to create in silico diets, if you want we can let you know when that is online.

Cheers,

Bram