Thursday, May 26, 2016

Updated Docker images for biological neuronal network simulations with Python

The NeuralEnsemble Docker images for biological neuronal network simulations with Python have been updated to contain NEST 2.10, NEURON 7.4, Brian 2.0rc1 and PyNN 0.8.1.

In addition, the default images (which are based on NeuroDebian Jessie) now use Python 3.4. Images with Python 2.7 and Brian 1.4 are also available (using the "py2" tag). There is also an image with older versions (NEST 2.2 and PyNN 0.7.5).

The images are intended as a quick way to get simulation projects up-and-running on Linux, OS X and Windows. 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

For Python 2.7:

docker pull neuralensemble/simulation:py2

For older versions:

docker pull neuralensemble/pynn07

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

If anyone would like to help out, or suggest other tools that should be installed, please contact me, or open a ticket on Github.

PyNN 0.8.1 released

Having forgotten to blog about the release of PyNN 0.8.0, here is an announcement of PyNN 0.8.1!

For all the API changes between PyNN 0.7 and 0.8 see the release notes for 0.8.0. The main change with PyNN 0.8.1 is support for NEST 2.10.

PyNN 0.8.1 can be installed with pip from PyPI.

What is PyNN?

PyNN (pronounced 'pine' ) is a simulator-independent language for building neuronal network models.

In other words, you can write the code for a model once, using the PyNN API and the Python programming language, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST and Brian as well as the SpiNNaker and BrainScaleS neuromorphic hardware systems).

Even if you don't wish to run simulations on multiple simulators, you may benefit from writing your simulation code using PyNN's powerful, high-level interface. In this case, you can use any neuron or synapse model supported by your simulator, and are not restricted to the standard models.

The code is released under the CeCILL licence (GPL-compatible).