hnn-core

This is a leaner and cleaner version of the code based off the HNN repository. However, a Graphical User Interface is not supported at the moment in this repository.

It is early Work in Progress. Contributors are very welcome.

Dependencies

• Neuron: installation instructions here: https://neuron.yale.edu/neuron/
• scipy
• numpy
• matplotlib
• joblib (optional for parallel processing)

Installation

We recommend the Anaconda Python distribution. To install hnn-core, you first need to install its dependencies:

$ conda install numpy matplotlib scipy

For joblib, you can do:

$ pip install joblib

Additionally, you would need Neuron which is available here: https://neuron.yale.edu/neuron/

Since hnn-core does not yet have a stable release, we recommend installing the nightly version. This may change in the future if more users start using it.

To install the latest version of the code (nightly) do:

$ git clone https://github.com/jonescompneurolab/hnn-core.git
$ cd hnn-core/
$ python setup.py develop

A final step to the installation process is to compile custom ionic channel mechanisms using nrnivmodl from Neuron. To do this, simple do:

$ cd mod/ && nrnivmodl

inside the hnn-core directory. It should create the compiled custom mechanism files.

To check if everything worked fine, you can do:

$ python -c 'import hnn_core'

and it should not give any error messages.

Bug reports

Use the github issue tracker to report bugs.