Reactions to Initial Model

Once we have determined which reactions are implemented by an organism's annotated genes, we can construct the initial model: this is essentially a stoichiometric matrix and a biomass objective function, essentially the parts list that a cell needs to produce the biomass it needs to grow.

However, in most cases this model is not yet functional. If we attempt to grow it on complete media, i.e. LB, it will fail to produce all the parts needed for the biomass function. This is where model gap-filling comes in. We insert candidate transport and standard reactions until the cell successfully grows on complete media. These reactions are clearly labeled in the initial model. In the Model View Tutorial, you can search for gap-filled reactions in the Reaction table.