Organelle (GitHub) is an agent-based modeling engine that is used for a number of our cell simulations at the Concord Consortium. The challenge was to create an engine that would allow us to simulate a wide variety of cells using simple rules, and also to bring some of the rules from model to model, so that common pieces of the cell (organelles) could just be defined once, and work in similar ways across cells.
I made a demo page here to let people play around with the rules of a very simple model.
I also wrote an article about the engine for the newsletter @Concord, which describes more of the thinking behind it: Under the Hood: A New Engine for Modeling Biological Processes
