This is cool, but as I read it here (and someone correct me if I'm wrong), it's no substitute for doing a real experiment. I'm going to launch into a long explanatory diatribe - models like this one can be VERY useful for hypothesis generation, or to try and understand seemingly disconnected results that (very often) arise in a biological experiment. They are especially useful when you have some hypothesis/theory of how a complex system is governed and you need to generate some prediction which you can experimentally test based on your theory.
But not a substitute for the real experiment, no way no how. Why? Because living things aren't designed, and they don't respect your modularity, abstract data typing, etc. etc.
For example, suppose your bacterium starts making some huge amount of a membrane protein (a common thing you do in the lab, for reasons outside the scope of this example). What's going to happen?
Well, that protein is going to try and fold up in the membrane, but as you make more and more of it, the protein is going to fail to get there. Other proteins destined for the membrane are going to experience the same problem. Are you going to update every single module that contains something membrane bound, to reflect this? As they accumulate in the membrane, the membrane curvature is going to change, and this in turn is going to change the relative concentrations of various lipids on each leaf of the membrane, which alters the chemistry of everything that interacts with the membrane in any way (a whole bunch more modules.)
Even if you have those effects covered, they're going to have indirect (and non-linear) effects on the concentration of various ions in the cytosol (all of which, just for starters, interact with the inner membrane with different affinities), the excess protein is going to start accumulating in inclusion bodies which are going to start taking up physical space inside the cell. These two changes alter the likelihood of interaction and the energy of interaction of every single other thing going on in the cell (!). So good luck with that.
That's just one example. The same thing would happen if you sheared the DNA, or heat shocked the cell, or put the cell in an environment of rapidly changing nutrient concentrations. To put all that in CS terms - the actual cell isn't object oriented, there's all sorts of cross-talk between the different components (because they're physical objects in a little tiny soap bubble, they're bumping into each other) and no abstraction layer or anything of that kind.
To be quite honest, I am of the opinion that a living cell is an irreducible system, and the only way you'd get a real substitute for experiments on actual cells would be JUST MAYBE if you ran a molecular dynamics simulation on all 10^14 or so atoms; and if you did so with a much better physics engine than we have now.