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If you post more detail about the custom rule, the complicated function, or what it means to "change the state of the automaton", it might be possible to come up with more specific suggestions. Thanks for the suggestions dvgrn! Scripting inside Golly does sound like a better idea. Since you suggest...

I am trying to run a custom rule in Golly for n steps, evaluate a complicated function of the final state, and change the state of the automaton based on this function. I want to repeat this process a few billion times, so performance is quite important. Would you suggest that I run the loop in anot...