[ohblahitsme]

There's this project by Stanford to simulate Mycoplasma genitalium: http://wholecellviz.stanford.edu

There's also this, which is part of the project above: http://www.cell.com/abstract/S0092-8674(12)00776-3

The problem is you need to know about tons of stuff before doing anything useful with it. For example, you need to know the biology of M. genitalium (or even what the hell it is) and you need to know at least a little bit about how the biology works (i.e. what is the metabolome? etc.). Then you need to know enough about software to be able to install and get everything running (often with poor documentation). Sometimes you need access to expensive software like Matlab.

So I guess that means it's coming, but very slowly and only for people who are in the field, not DIY biologists.

This is actually something I'm interested in working in (once I get to grad school).