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Add to those NEURON (http://www.neuron.yale.edu/neuron/) which is the most popular for compartmental neuron simulations. It's a terribly old program (1990) with horrible limitations yet people still use it.

Terribly old - But is being updated constantly, they are adding in the capabilities to explicitly (in hoc or python) add in chemical reaction schemes. Some interesting research is being worked on in that regard at the moment.

If there are horrible limitations, email Dr. Mike Hines or write some code that will fix it. It is open source.

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