Automata and visualisation

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breve - 3D swarm simulation environment (OS X and Linux).
framsticks - 3D evolution and simulation of artificial life (Windows).

Mirek's Cellebration - 1-D and 2-D Cellular Automata (Windows).
Lifelab - 1-D and 2-D Cellular Automata (OS X).

VMD - molecular visualisation (Windows, OS X and Linux)