Biological neuronal network simulations with Python

What it gives you

• shell environment with NEST, NEURON, Brian and PyNN installed (for specific versions see Dockerfile).
• The Python 2 version provides Brian 1.4, the Python 3 version provides Brian 2.
• IPython, scipy, matplotlib and OpenMPI are also installed.
• use directly or as a base for your own project-specific Docker images.

Basic use

The following command starts a container with the bash shell, running as user docker, in a Python virtual environment named "neurosci"

docker run -i -t neuralensemble/simulation /bin/bash

after which you can run simulations with Python and MPI. This will use Python 3.5 as the Python version; if you'd prefer Python 2.7 use:

docker run -i -t neuralensemble/simulation:py2 /bin/bash

Note that this image does not provide an X11 graphical environment, so GUI tools will not work; use the neuralensemble/simulationx image if you need X11.

Docker Hub

More information on the various images which have been released can be found at: https://hub.docker.com/r/neuralensemble/

Documentation for simulators

For documentation of the simulation tools installed in the image, see http://neuralensemble.org/projects/