I need help understanding the activeGenesApproach in XomicsToModel

[Juan Sepulveda]

Dear community,

I'm using XomicsToModel, and I'm trying to understand how genes and reaction weights are used in ThermoKernel to extract a tissue model. However, I'm struggling to understand the activeGeneApproach and the dummyMetabolites and dummyReactions.

From what I understand:

From reading the methods paper and the code, I understand that every active gene is turned into a dummy metabolite.

My questions:

1. The createDummyModel function says that the dummy metabolite will be destroyed in the corresponding dummyReaction but does this mean that there is a dummyMetabolite sink reaction for its intake? 
2. Does this also mean that the dummy metabolite is added to the reaction as a reactant? Or that a separate reaction is created (and in that case how is the activity of the dummy reaction connected to that of the active reaction)? 
3. And, how is this more beneficial than simply using model.expressionRxns as weights for thermokernel (which is already implemented)?

I appreciate any help in answering these questions.

Best,

Juan