NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.
Neuron was developed at Yale University. Neuron website
On Helix, Neuron can be run either via the GUI or the command line.
You should have an X-windows connection to Helix.
You will need to set up environment variables as follows.
helix% module load neuron
As a first test, try 'neurondemo'.
To make Neuron read your input file 'foo.hoc', type 'nrngui foo.hoc'.
Neuron can potentially multithread -- use multiple cores on Helix. However, this will only help if your simulations have cells with lots of compartments and mechanisms, i.e. requiring at least a couple thousand ODEs per cell? If no, multithreaded won't help. It is recommended that you start by using the GUI RunControl panel and the Neuron Main Menu -> Tools -> Parallel Computing tool -- to run a few interactive tests to decide on appropriate simulation parameters. See for more info.
On Helix, you should use a maximum of 8 threads. If you want more parallelization, use Biowulf.