dmiyamoto/neuron repository overview

⁠docker-neuron

docker containers for NEURON simulator

⁠Basic Usage

⁠run NERUON GCC+OpenMPI+Python version

$ docker run -it dmiyamoto/neuron:gcc-ompi

• you could run neuron or python with neuron in the docker image

  $ nrniv
  NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
  Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
  See http://www.neuron.yale.edu/neuron/credits
  oc>
  

  Copy

  $ python
  Python 2.7.12 (default, Nov 19 2016, 06:48:10)
  [GCC 5.4.0 20160609] on linux2
  Type "help", "copyright", "credits" or "license" for more information.
  >>> import neuron
  NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
  Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
  See http://www.neuron.yale.edu/neuron/credits
  
  >>>
  

  Copy

⁠run built-in benchmark of the multi-compartment hodgkin-huxley model

• single core condition

  $ docker run dmiyamoto/neuron:bench ./run.sh
  

  Copy

• multi-core conditions

  • 2 core

    $ docker run dmiyamoto/neuron:bench ./run.sh 2
    

    Copy

  • 4 core

    $ docker run dmiyamoto/neuron:bench ./run.sh 4
    

    Copy

⁠run NEURON with Jupyter Notebook

1. run docker image

   $ docker run -p 8888:8888 dmiyamoto/neuron:jupyter
   /usr/local/lib/python2.7/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '/home/neuron' is not a writable location, using a temp directory.
     " using a temp directory.".format(parent))
   [I 14:20:39.322 NotebookApp] Writing notebook server cookie secret to /home/neuron/.local/share/jupyter/runtime/notebook_cookie_secret
   [W 14:20:39.331 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
   [I 14:20:39.335 NotebookApp] Serving notebooks from local directory: /work
   [I 14:20:39.336 NotebookApp] 0 active kernels 
   [I 14:20:39.336 NotebookApp] The Jupyter Notebook is running at: http://[all ip addresses on your system]:8888/?token=4683????????????????????????????
   [I 14:20:39.336 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
   [C 14:20:39.336 NotebookApp] 
       
       Copy/paste this URL into your browser when you connect for the first time,
       to login with a token:
           http://localhost:8888/?token=4683????????????????????????????????
   

   Copy

2. Access to the printed URL by a browser

3. You could find some NEURON+Python examples in examples directory.

• example1⁠: single cell (1 compartment) with current clamp stimulation
• example2⁠: single cell (some compartments) with current clamp stimulation
• example3⁠: single cell (some sompartments) with synaptic stimulation
• example4⁠: many cells with synfire chain network

⁠run NEURON dpkg distributed version

$ docker run -it dmiyamoto/neuron:dpkg

⁠Reference

• https://hub.docker.com/r/dmiyamoto/neuron/⁠
• http://neuron.yale.edu⁠