README.md

Software repository for OIST Computational Neuroscience Course (OCNC)

This repository provides Docker image with pre-compiled computational neuroscience software and usage instructions for the OIST Computational Neuroscience Course (OCNC). For more information of the course, please visit https://groups.oist.jp/ocnc.

For Optinist tutorial docker image installation, please follow the instructions in

https://github.com/oist/OCNC_tutorial_optinist/

For NEST tutorial, clone the following repository inside your docker system

git clone  https://github.com/sunzhe839/ocnc2024NEST

Prerequisites

Download and install Docker Desktop https://www.docker.com/products/docker-desktop/. For Mac users, please note that Docker provides different installers for Intel and Apple silicon cpu.

Fetch and use the OCNC docker image

1. start the Docker Desktop application.

2. Open a Terminal/Command prompt/PowerShell.

3. In the Terminal, prepare a directory for storing your exercise files, and cd to this directory. e.g.:

   mkdir ocnc_tutorial
   cd ocnc_tutorial
   

4. In the Terminal, execute the following command to fetch and start the OCNC docker container, note that -v `pwd`/:/work mount your current directory (in the above case, ocnc_tutorial) as /work in your Docker container system, and --rm set the container to be destroyed automatically after use (i.e. any change to the docker system will not be saved except the files stored in /work). For more information about the Docker commands, please visit https://docs.docker.com/engine/reference/commandline/run/.

   For Mac/Linux machine with x86 cpu:

   docker pull cnsoist/ocnc:2024
   docker run -p 6080:80 --rm -v `pwd`:/work cnsoist/ocnc:2024
   

   For Mac machine with Apple Silicon cpu:

   docker pull cnsoist/ocnc:2024_apple_silicon
   docker run -p 6080:80 --rm -v `pwd`:/work cnsoist/ocnc:2024_apple_silicon
   

   for Windows, you may need to specify the path of your directory, e.g.

   docker run -p 6080:80 --rm -v C:\Users\YOUR_USER_NAME\ocnc_tutorial:/work cnsoist/ocnc:2024
   

   You should see similar information as below from the Terminal.

   

5. Open a web browser and enter: http://127.0.0.1:6080/. The following interface should be shown in the browser.

   

6. Double click the LXTerminal icon to open a terminal in the docker system. You can also double click the ocnc icon to access this repository page for future references.

   

7. In the LXTerminal, cd to \work.

   cd /work
   

   You can store and exchange files between your host system and the docker system here.

   Then clone the ocnc github repository.

   git clone https://github.com/CNS-OIST/ocnc.git
   

   Go into the directory, and start Jupyter notebook

   cd ocnc
   jupyter notebook --allow-root
   

   A Jupyter notebook interface should pop up, within it, open the simulator_tests.ipynb, and from the top menu select Cell->Run All. Jupyter may ask for the password you've just set from time to time. Please check the default behaviors of this test from the video below, if yours behave differently, please contact [email protected].

8. At the tutorial sessions, start the computational neuroscience software according to your tutorial instructions from the LXTerminal. Here are some general commands for different software.

   • update the ocnc github repository.

     cd /work/ocnc
     git pull
     

   • Copying and Pasting
     • General e.g. in Firefox: ctrl + c, ctrl + v
     • In LXTerminal: ctrl + shift + c, ctrl + shift + v
     • Between the host system and the docker system: Click the clipboard button in the left novnc sidebar, it contains the clipboard content of the docker system.
   • Starting Jupyter notebook

     jupyter notebook --allow-root
     

   • Starting Jupyterlab

     jupyter lab --allow-root
     

   • Python3

     python
     

     and with in Python
     • NEURON https://neuron.yale.edu/neuron/

       import neuron
       

     • NEST https://nest-simulator.readthedocs.io/

       import nest
       

     • STEPS http://steps.sourceforge.net/

       import steps
       

     • Brian2 https://brian2.readthedocs.io/en/stable/

       import brian2
       

     • pystan https://pystan.readthedocs.io/en/latest/

       import stan
       

   • NEURON with GUI and hoc interpreter

     nrngui
     

9. Once you finish your work, make sure your files have been saved to /work (aka ocnc_tutorial in your host system), then go back to the Terminal/Command prompt/PowerShell of your host system, and press ctrl + c to stop the docker container.

Connect to the docker system using vnc viewer

If you want to connect to the docker system using a vnc viewer such as https://www.realvnc.com/en/connect/download/viewer/ instead of the browser, start the docker with

docker run -p 6080:80 -p 5900:5900 --rm -v `pwd`:/work cnsoist/ocnc:2024

Open your vnc viewer and enter 127.0.0.1:5900 as the address

a vnc connection to the docker system should then be displayed.