Sunday, February 14, 2010

PyNN 0.6.0 released

PyNN 0.6.0 is available for download from the INCF Software Center or from PyPI.


There have been three major changes to the API in this version.
  1. Spikes, membrane potential and synaptic conductances can now be saved to file in various binary formats. To do this, pass a PyNN File object to Population.print_X(), instead of a filename. There are various types of PyNN File object, defined in the recording.files module, e.g., StandardTextFile, PickleFile, NumpyBinaryFile, HDF5ArrayFile.
  2. Added a reset() function and made the behaviour of setup() consistent across simulators. reset() sets the simulation time to zero and sets membrane potentials to their initial values, but does not change the network structure. setup() destroys any previously defined network.
  3. The possibility of expressing distance-dependent weights and delays was extended to the AllToAllConnector and FixedProbabilityConnector classes. To reduce the number of arguments to the constructors, the arguments affecting the spatial topology (periodic boundary conditions, etc.) were moved to a new Space class, so that only a single Space instance need be passed to the Connector constructor.

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, PCSIM and Brian).

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).

For an in-depth explanation of the motivations behind PyNN and the guiding principles behind its design, see this article in Frontiers in Neuroinformatics. For a briefer overview, see this recent article in the Neuromorphic Engineer.

Thursday, February 4, 2010

3rd INCF Congress of Neuroinformatics

The 3rd INCF Congress of Neuroinformatics will take place in Kobe, Japan, from 30th August - 1st September 2010.

I'm particularly looking forward to the keynotes from Upi Bhalla ("Multiscale models of the synapse: a self-modifying memory machine") and Colin Ingram ("Working in the clouds: creating an e-science collaborative environment for neurophysiology"), and to the workshop on model description languages.

Abstract submission (for posters and demos) is open until 21st April. Hopefully I'll be able to present our Django-based framework for neuroscience databases.