To start with you only need to study input-response pairs (sensory input causing motor commands). You enter the neural inputs from a real fly into the simulation, and compare responses of the real fly and the simulated one. Once you understand what's going on, proceed to do sequence of inputs, and compare the sequence of responses. The goal is not to produce the identical sequence of actions by tuning the simulation, it's understanding how the actions are being computed from the inputs.

Having a detailed simulation like this would greatly accelerate Numenta's style research, where instead of piecing together information from published papers, you would get it straight from the experiments you control.