Have you considered looking at things like Matlab or Stella or Neurosolutions? As I understand your thread you want to have an element of simulation in there that can be displayed or modified during the simulation. Matlab does provide a means to generate the algorithm to run the data through. There may also be a windowing environment other than your offerings that it can run on. Stella is another simulation offering that comes with a runtime viewer. Perhaps worth checking out what they do and some research on how they were developed. on the few occasions I have done this I've usually gone outside of Perl to another windowing environment.
in reply to The browser as a (simple) window manager. (Updated)
yet another biologist hacking perl....