Advanced Scientific Programming in Python G-Node Summer School

When: August 31st, 2009 - September 4th, 2009.
Where: Berlin, Germany.

Many scientists spend much of their time writing, debugging, and
maintaining software. But while techniques for doing this efficiently
have been developed, only few scientists actually use them. As a
result, they spend far too much time writing deficient code and
reinventing the wheel instead of doing research. In this course we
present a selection of advanced programming techniques with
theoretical lectures and practical exercises tailored to the needs of
the programming scientist. To spice up theory and foster our new
skills in a real-world programming project, we will team up to develop
an entertaining scientific computer game.

We will use the Python programming language for the entire
course. With a large collection of open-source scientific modules and
all features of a full-fledged programming language, Python is rapidly
gaining popularity in the neuroscience community. It enables the
scientist to quickly develop powerful, efficient, and structured
software and is becoming an essential tool for scientific computing.

The summer school is targeted at Post-docs and PhD students from all
areas of neuroscience. Substantial proficiency in Python or in
another language (e.g. Java, C/C++, MATLAB, Mathematica) is absolutely
required. An optional, one-day pre-course is offered to participants
without Python experience to familiarize with the language.

Preliminary Program
-------------------
Day 0 (Mon Aug 31) -- [Optional] Dive into Python

Day 1 (Tue Sep 1) -- Software Carpentry
- Documenting code and using version control
- Test-driven development & unit testing
- Debugging, profiling and benchmarking techniques
- Object-oriented programming, design patterns and Extreme Programming

Day 2 (Wed Sep 2) -- Scientific Tools for Python
- NumPy, SciPy, Matplotlib, IPython
- Neuroscience libraries
- Programming project in the afternoon

Day 3 (Thu Sep 3) -- Parallelization
- Python multiprocessing for SMP machines
- Distributed parallelization for cluster computing
- Programming project in the afternoon

Day 4 (Fri Sep 4) -- Practical Software Development
- Software design
- Efficient programming in teams
- Quality Assurance
- Finalizing the programming project

Applications
------------
Applications should be sent before May 31st, 2009 to
pythonsummerschool@bccnberlin.de. No fee is charged but participants
should take care of travel, living, and accommodation expenses.

Applications should include full contact information (name,
affiliation, email & phone), a short CV and a short statement
addressing the following questions (maximum 500 words):
- What is your educational background?
- What experience do you have in programming?
- Why do you think "Advanced Scientific Programming in Python" is an
appropriate course for your skill profile?

Candidates will be selected based on their profile. Places are
limited: early application is recommended.

Faculty
-------
Pietro Berkes, Volen Center for Complex Systems, Brandeis University, USA
Jens Kremkow, Bernstein Center for Computational Neuroscience Freiburg, Germany
Eilif Muller, Laboratory of Computational Neuroscience, Ecole Polytechnique Fédérale de Lausanne, Switzerland
Michael Schmuker, Neurobiology, Freie Universität Berlin, Germany
Bartosz Telenczuk, Charité Universitätsmedizin Berlin, Germany
Niko Wilbert, Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Germany
Tiziano Zito, Bernstein Center for Computational Neuroscience Berlin, Germany

Organized by Michael Schmuker and Tiziano Zito for the German
Neuroinformatics Node of the INCF.

Website: http://www.g-node.org/Teaching
Contact: python-summerschool@bccn-berlin.de

2nd INCF Congress of Neuroinformatics

The 2nd INCF Congress of Neuroinformatics will take place in Pilsen, Czech Republic, from September 6th-8th 2009.

Last year's meeting in Stockholm was excellent - check out the videos of the keynote talks.

The deadline for abstract submission is April 17th.

When will NumPy and SciPy move to Python 3.0?

http://jarrodmillman.blogspot.com/2009/01/when-will-numpy-and-scipy-migrate-to.html

Python 2.6 by March 2009

Python 3.0 by mid-to-late 2010?

Once Numpy and Scipy hit 3.0, we can port NeuroTools: this shouldn't be a very difficult task, since NeuroTools is pure Python, with no C-extensions. Porting PyNN depends on the simulator backends - NEURON, NEST, PCSIM, Brian - being ported, but again, PyNN itself should be a straightforward task.

Hot off the press: PyNN, PyNEST, NEURON+Python, Brian

Hot off the press!

Several new publications of interest for NeuralEnsemblers to appear in the Frontiers in Neuroinformatics special section "Python in Neuroscience" are already available in provisional form at

http://www.frontiersin.org/neuroinformatics/specialtopics/8/

including but not limited papers on large-scale simulation technologies like PyNN, PyNEST, NEURON+Python, and Brian:


Hines M, Davison AP and Muller E (2009) NEURON and Python. Front. Neuroinform. doi:10.3389/neuro.11.013.2009

http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/013.2009/



Eppler JM, Helias M, Muller E, Diesmann M and Gewaltig M (2008) PyNEST: A convenient interface to the NEST simulator. Front. Neuroinform. doi:10.3389/neuro.11.012.2008

http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/012.2008/



Davison AP, Brüderle D, Eppler JM, Kremkow J, Muller E, Pecevski DA, Perrinet L and Yger P (2008) PyNN: a common interface for neuronal network simulators. Front. Neuroinform. doi:10.3389/neuro.11.011.2008

http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/011.2008/



Goodman D and Brette R (2008) Brian: a simulator for spiking neural networks in Python. Front. Neuroinform. (2008) 2:5. doi:10.3389/neuro.11.005.2008

http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/005.2008/

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."

http://www.python.org/download/releases/3.0/

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.

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:

  http://software.incf.org/software/neurotools/home/download

or just

  easy_install NeuroTools

The NeuroTools homepage, with full documentation, is at:

  http://neuralensemble.org/NeuroTools

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

http://neuralensemble.org/NeuroTools
http://www.incf.org