Questions about DEMETER

[Nicholas Y]

Hi,

My name is Nick, and I am using DEMETER to create genome-scale models of strains of Bifidobacteria and Lactobacillus bacteria. I have a couple of questions about using DEMETER to create these reconstructions.

1) I am running into the following issue. When I run my reconstructions on a custom diet I want to use, the biomass reactions for the final reconstructions are forced to zero. However, the biomass reactions are not forced to zero in DEMETER's built-in testing (i.e. when running runTestSuiteTools or in the results after running runDebuggingTools). I was wondering what is the best way to resolve issues like this? This issue occurs, for example, when I try to run FBA on my refined models using a breastmilk diet consisting of "Milk, human, mature, fluid (100g)" in VMH.

2) Is there a way for me to do gap filling in DEMETER on a custom pre-specified diet? I would like to run gap-filling using my custom diet (the breast milk diet mentioned above, plus some metabolites from experimental data) if possible to make sure the models can grow on it.

3) There are certain reactions in my models that I know should have nonzero flux, but which are being forced to zero. Is it possible for me to provide a list of reactions to DEMETER that I want to ensure can carry nonzero flux in the final models?

4) I want to add reactions and metabolites to my model that I know are present in my strains based on experimental data, but which are not present in the VMH database. Currently, I am translating my KBase draft models to VMH nomenclature. Then, I am adding these reactions. Finally, I am running DEMETER on the resulting translated models with the custom reactions. However, DEMETER seems to be removing the reactions and metabolites I am trying to add, which are not present in VMH. Is there a way for me to prevent DEMETER from removing these?

Thank you for your time and assistance. It is much appreciated. Please let me know if you need any more information to better answer my questions.

Best regards,

Nick Yousefi