News

  • G-Node Workshop on Neuronal GPU Computing [more]
    Friday 17th February 2012
  • Neo, a base library for handling electrophysiology data in Python [more]
    Friday 10th February 2012
  • BrainScaleS/FACETS CodeJam #5 registration now open [more]
    Friday 27th January 2012
  • 5th INCF Congress of Neuroinformatics: Call for Workshop Proposals [more]
    Wednesday 7th December 2011
  • Sumatra 0.3 released [more]
    Monday 14th March 2011

About

Trends in programming language development and adoption point to Python as the high-level systems integration language of choice. Python leverages a vast developer-base external to the Neuroscience community, and promises leaps in simulation complexity and maintainability to any neural simulator which adopts it. As more and more simulators support Python, model development times can be drastically reduced by promoting code sharing and reuse across simulator communities. As a result, modellers can devote their software development time to innovating new simulation tools such as network topology databases, stimulus programming, analysis and visualisation tools, and simulation accounting, to name a few.


NeuralEnsemble
is a multilateral effort to coordinate and organise Neuroscience software development efforts into a larger meta-simulator software system, a natural and alternate approach to incrementally address what is known as the complexity bottleneck, presently a major roadblock for neural modelling. While a solution here is arguably a necessary condition for resolving the present stalemate for understanding the complexities of brain-like computing, a successful initiative could also end up being a major innovation of the field for the larger computing community.

Community

There is a NeuralEnsemble Google group for discussion of collaborative neuroscience software development in Python and to provide software support. If you have any questions about any of the software listed below, please join the group and post a message in one of the forums.

Software

NeuralEnsemble hosts Trac/Subversion servers for a number of open-source neuroscience tools:

The Brian Simulator
Brian is a simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists. Brian is easy to learn and use, highly flexible and easily extensible. The Brian package itself and simulations using it are all written in the Python programming language.
NeuroTools
a set of tools written in Python to manage, store and analyse computational neuroscience simulations.
OpenElectrophy
OpenElectrophy is a tool written in Python and based on a MySQL database for organising, computing, and visualising neural data from intra- and extra-cellular recording. It can be used, for example, both for studying spike and local field oscillations.
PyNN
a Python package for simulator-independent specification of neuronal network models. In other words, you can write the code for a model once, using the PyNN API, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST, Brian and PCSIM).