Just based on the Times article, I think the idea is, define a simulation of a cell and subject it to a bunch (100s) of simulated experiments, based on real experiments that have been run on real versions of the cell. If you get the same results from your simulated cell that other researchers got from watching real cells, then your simulation is potentially accurate enough to run new experiments on that will generate useful information about the actual organism. The fact that it predicts the outcome of previous experiments we were interested in suggests (hopefully) that it has sufficient resolution to predict new stuff we're interested in.
So in this case, it sounds like they're simulating the interaction of genes and molecules, since they think that's sufficient to model cell behavior (and/or it's the best we can do). But it doesn't really matter what technical level of detail they went to -- the only useful definition of a "proper" simulation is whether it behaves the same as the real thing in the context you care about. For example, this simulation would be totally insufficient if I wanted to model a hydrogen bomb -- but totally excessive if I wanted to model gravitational forces on independent objects in space. If it's good enough to tell us anything new about the actual cell, that'll be pretty cool.
So in this case, it sounds like they're simulating the interaction of genes and molecules, since they think that's sufficient to model cell behavior (and/or it's the best we can do). But it doesn't really matter what technical level of detail they went to -- the only useful definition of a "proper" simulation is whether it behaves the same as the real thing in the context you care about. For example, this simulation would be totally insufficient if I wanted to model a hydrogen bomb -- but totally excessive if I wanted to model gravitational forces on independent objects in space. If it's good enough to tell us anything new about the actual cell, that'll be pretty cool.