HNN “Python” install (CentOS)

The script below assumes that it can update OS packages for python and prerequisites for NEURON and HNN.

Start HNN

  1. From the command-line, type following commands

     cd hnn_source_code
     python3 hnn.py
    
  2. The HNN GUI should show up. Make sure that you can run simulations by clicking the ‘Run Simulation’ button. This will run a simulation with the default configuration. After it completes, graphs should be displayed in the main window.

  3. You can now proceed to running the tutorials at https://hnn.brown.edu/index.php/tutorials/ . Some things to note:

    • A directory called “hnn_out” exists in your home directory in Ubuntu where the results from your simulations (data and param files) will be stored.

Upgrading to a new version of HNN

HNN Releases can be seen on the GitHub releases page. You can also be notified of new releases by watching the hnn repository on GitHub.

To download the latest release, use the following commands within an Ubuntu terminal:

curl --remote-name https://github.com/jonescompneurolab/hnn/releases/latest/download/hnn.tar.gz
tar -x --strip-components 1 -f hnn.tar.gz -C hnn_source_code
cd hnn_source_code
make
python3 hnn.py

Troubleshooting

If you run into other issues with the installation, please open an issue on our GitHub. Our team monitors these issues and will investigate possible fixes.

Another option for users that are running into problems with the above methods, we provide a VirtualBox VM pre-installed with HNN.