This Beta version incorporates the additional bond perturbation functionality that was developed for the paper "Non-Template Molecules Designed For Open-Ended Evolution" that was published in the proceedings of ECAL 2011 (Eleventh European Conference on the Synthesis and Simulation of Living Systems).
A few usability issues remain; a couple of the displays are not complete (eg with values shown as 'Unknown'), and there is no user manual yet. Hence the beta status.
The main improvement has been to ensure that the user interface remains active while the simulation is running. Without this, it is not possible to interrupt the simulation to enable the status to be investigated. Various solutions had been tried previously, but none had been ideal. A robust solution based on multi-threading is now in place. The user interface runs as one thread, and the simulation runs as another. The user interface can respond to user input, even while the simulation thread is performing the intensive processing that is required when a new Molecule Type appears to determine how it can interact with existing Molecule Types.