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.

• numpy
• scipy
• matplotlib
• Neuron: installation instructions here: https://neuron.yale.edu/neuron/

• joblib (for simulating trials simultaneously)
• mpi4py (for simulating the cells in parallel for a single trial). Also depends on:
  • openmpi or other mpi platform installed on system
  • psutil

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

$ conda install numpy matplotlib scipy

Additionally, you would need Neuron which is available here: https://neuron.yale.edu/neuron/. It can also be installed via pip now:

$ pip install 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:

$ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master

To check if everything worked fine, you can do:

$ python -c 'import hnn_core'

and it should not give any error messages.

For further instructions on installation and usage of parallel backends for using more than one core, refer to parallel_backends

Use the github issue tracker to report bugs.

Read our contributing guide.