I was at EBI last week for PhD interview (though I unfortunately failed the IAA test, and did not enter), but in addition to the opportunity to see EBI, I got to know some interesting stuff.
Agent based simulation seems highly interesting for biological and/or molecular systems, which are too complex and "high dimensional" to be successfully simulated solely by mathematical means.
Stochastic simulation use to be the way to go then, but it seems agent based computing provide an even more general, and powerful paradigm for simulating this kind of systems.
In light of this, I was delighted to find Mason, a free (how does the "academic free licence" compare against LGPL etc.?) Java based software for agent based simulations, seemingly with many characteristics that make it good for integration in other software (Of course I'm pondering bioclipse integration here)
It seems to be quite working ... see the Conway's "Game Of Life" implementation, further down on the page :)
And, in case MASON is not the right answer to every question, they provide a shortlist of other interesting agent-based simulation software.
This site is candy for anyone interested in computational molecular biology in general and developmental biology in particular:
Haven't assessed the usefulness versus "eye candy" ratio though ... :) ("don't go for what the eyes see ..."). But at least they have developed a (seemingly) nice network analytic tool (they claim it is the first general purpose one, for constructing and anlyzing gene regulatory networks), Ingeneue, that is Java based and Open Sourced, so could be a nice Bioclipse plugin too sometime in the future! :)