Compile the connection-deciding process in NEURON

As mentioned in a previous post, you can compile frequently used functions to save time when running your NEURON code. For my code, this made a huge difference when it came to connecting the model cells. The process used to be coded in hoc, and it took hours. Now it takes about a minute in NMODL for my largest model size. Continue reading

Speed up your NEURON code

I use NEURON for my neural simulations and I recommend it. Not only is it well documented, but it is consistently well supported – Michael Hines and Ted Carnevale (NEURON developers) are always quick to respond to questions on the NEURON forum or by email. NEURON has been used in well over a thousand publications.

Most every programmer is interested in having their program execute as quickly as possible. This concern is held by computational neuroscientists as well. Most important is your time: the faster you can get results, the faster your research progresses and the sooner you can get published. But computing time is also an issue – people often run their simulations on shared machines and can only get (or afford) a limited amount of computing time. Continue reading