5. Install Simulations

  1. Start the virtual machine and log in:

    ssh -p 8015 hjc@dynamicshjc.case.edu

  2. Check for and install system updates on the virtual machine:

    sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get autoremove

  3. Download JSNeuroSim, the JavaScript code for the neural simulations:

    git clone https://github.com/CWRUChielLab/JSNeuroSim.git /var/www/html/JSNeuroSim

  4. Download executables for the Nernst Potential Simulator:

    mkdir -p /var/www/html/nernst
sudo wget -O /var/www/html/nernst/nernst-v1-0-1-mac-intel.zip https://github.com/CWRUChielLab/nernst/releases/download/v1.0.1/nernst-v1-0-1-mac-intel.zip
sudo wget -O /var/www/html/nernst/nernst-v1-0-1b-win.zip https://github.com/CWRUChielLab/nernst/releases/download/v1.0.1b/nernst-v1-0-1b-win.zip
sudo wget -O /var/www/html/nernst/nernst-v1-0-1-linux.tar.gz https://github.com/CWRUChielLab/nernst/releases/download/v1.0.1/nernst-v1-0-1-linux.tar.gz

  5. Give the web server ownership of and access to the new files:

    sudo chown -R www-data:www-data /var/www/
sudo chmod -R ug+rw /var/www/

  6. The JavaScript simulations should now be accessible. Verify this by visiting

    The Nernst Potential Simulator should also be accessible. Verify that these links work:

  7. Shut down the virtual machine:

    sudo shutdown -h now

  8. Using VirtualBox, take a snapshot of the current state of the virtual machine. Name it “Simulations installed”.