Friday, August 28, 2015

Docker images for neuronal network simulation

I've created some Docker images for biological neuronal network simulations with Python.

The images contain NEST 2.6, NEURON 7.3, Brian 1.4 and PyNN 0.8.0rc1, together with IPython, numpy, scipy and matplotlib.

The images are intended as a quick way to get simulation projects up-and-running on Linux, OS X and Windows (the latter two via the Docker Toolbox, which runs Docker in a VM). They can be used for teaching or as the basis for reproducible research projects that can easily be shared with others.

The images are available on Docker Hub.

To quickly get started, once you have Docker installed, run

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

then inside the container

source ~/env/simulation/bin/activate

For ssh/X11 support, use the "simulationx" image instead of "simulation". Full instructions are available here.

I plan to add further images for neuroscience data analysis, providing Neo, Elephant, OpenElectrophy, SpykeViewer, the G-Node Python tools, KlustaSuite, etc. If anyone would like to help out, or suggest other tools that should be installed, please contact me, or open a ticket on Github.


Unknown said...
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Unknown said...

This seems like an interesting project...There's a network simulator with a nice GUI that uses Docker for nodes: IMUNES

Technically, it can use any kind of Docker image to run with a bit of tweaking. Would you be interested in creating an image that fits nicely into IMUNES?

Andrew Davison said...

While I'm sure there are similarities between computer/telecommunication networks and brain networks, I don't really see what the application would be of running biological neuronal network simulations within IMUNES.