Thursday, December 4, 2008

Python 3.0 final released

"Python 3.0 (a.k.a. "Python 3000" or "Py3k") is a new version of the language that is incompatible with the 2.x line of releases. The language is mostly the same, but many details, especially how built-in objects like dictionaries and strings work, have changed considerably, and a lot of deprecated features have finally been removed. Also, the standard library has been reorganized in a few prominent places."

For what's new, go here.

Given the extent of the syntax changes, it may be a while before Python 3.0 is officially supported by NeuralEnsemble projects.

Thursday, November 13, 2008

NeuroTools 0.1 (Asynchronous Astrocyte) released

NeuroTools is a Python package for analysis, visualization and management of real and simulated neuroscience data, built on top of numpy and matplotlib.

Inspired by Ubuntu, the first release is code-named "Asynchronous Astrocyte". Suggestions for names for future releases are welcome!

It is available for download from:

or just

  easy_install NeuroTools

The NeuroTools homepage, with full documentation, is at:

Wednesday, November 12, 2008

NeuroTools Live Demo @ INCF Booth, SfN 2008. (Nov 16; 9:30-12:30)

NeuroTools Live Demo @ SfN 2008

Time: Nov 16; 9:30-12:30
Location: INCF Booth #3227

NeuroTools: Analysis, visualization and management of real and
simulated neuroscience data.

Jens Kremkow, Thierry Brizzi, Daniel Bruederle, Andrew Davison,
Eilif Muller, Laurent Perrinet, Michael Schmuker, Pierre Yger

Friday, June 13, 2008

BCCN/FACETS Student Workshop: Using Python for Computational Neuroscience

Thanks to Jens Kremkow, Jochen Eppler, Bernd Wiebelt, the BCCN Freiburg staff and all the motivated students and lecturers for making the first BCCN/FACETS Student Workshop on Using Python for Computational Neuroscience a great success! Lecture material can be found here.

Monday, June 9, 2008

Cookbook launched

Thanks to Dan Goodman and the Neural Ensemble googlegroup for the impetus, a cookbook for computational neuroscience recipies can now be found at

Tuesday, June 3, 2008

Call for Contributions - Python in Neuroscience Special Section


Special Section: "Python in Neuroscience"
Journal: Frontiers in Neuroinformatics []

Associate Editor:
Rolf Kötter (Radboud University Medical Centre Nijmegen, Netherlands)

Guest Editors:

James A. Bednar (University of Edinburgh, UK)
Andrew Davison (UNIC, CNRS, France)
Markus Diesmann (RIKEN Brain Science Institute, Japan)
Marc-Oliver Gewaltig (Honda Research Institute Europe GmbH, Germany)
Michael Hines (Yale University, USA)
Eilif Muller (LCN-EPFL, Switzerland)

Important Dates:

Abstract/outline submission deadline: June 14th, 2008.
Invitations for full paper submissions sent by June 21st, 2008.
Invited full paper submission deadline: September 14th, 2008.

Special Section Abstract:

Python is rapidly becoming the de facto standard language for systems
integration. Python has a large user and developer-base external to
the neuroscience community, and a vast module library that facilitates
rapid and maintainable development of complex and intricate systems.

In this special section, we highlight recent efforts to develop Python
modules for the domain of neuroscience software and neuroinformatics:

- simulators and simulator interfaces
- data collection and analysis
- sharing, re-use, storage and databasing of models and data
- stimulus generation
- parameter search and optimization
- visualization
- VLSI hardware interfacing
- ...

Moreover, we seek to provide a representative overview of existing
mature Python modules for neuroscience and neuroinformatics, to
demonstrate a critical mass and show that Python is an appropriate
choice of interpreter interface for future neuroscience software

Submission Procedure:

Researchers and practitioners are invited to submit on or before June
14th, 2008 a max. 1 page abstract/outline of work related to the focus
of the special section to, CC'd to
for consideration for inclusion as an elaborated full article in the
special section.

Please include a provisional title, a full author list, and format the
subject of your email as follows: "[python SI] outline - Your Name".

Authors will be notified whether their contribution has been accepted
by June 21st, 2008.

Full Article Information:

* Full articles will be solicited by invitation only, based on the
abstracts/outlines we receive by June 14th, 2008.

* The deadline for submission of invited full articles will be
September 14th, 2008.

* Article formatting will be as for standard Frontiers "Original
Research Articles". Guidelines and instructions for their preparation
can be found at

* General author instructions for Frontiers in Neuroinformatics can be
found at

* Frontiers in Neuroinformatics is an open access journal, following a
pay-for-publication model. Details of the publication fees can be found

* Further details will be provided to authors of accepted abstracts by
June 21st, 2008.