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Advanced Scientific Programming in Python

a Summer School by the G-Node, the Bernstein Center for Computational
Neuroscience Munich and the Graduate School of Systemic Neurosciences


Scientists spend more and more time writing, maintaining, and debugging software. While techniques for doing this efficiently have evolved, only few scientists have been trained to use them. As a result, instead of doing their research, they spend far too much time writing deficient code and reinventing the wheel. In this course we will present a selection of advanced programming techniques, incorporating theoretical lectures and practical exercises tailored to the needs of a programming scientist. New skills will be tested in a real programming project: we will team up to develop an entertaining scientific computer game.

We use the Python programming language for the entire course. Python works as a simple programming language for beginners, but more importantly, it also works great in scientific simulations and data analysis. We show how clean language design, ease of extensibility, and the great wealth of open source libraries for scientific computing and data visualization are driving Python to become a standard tool for the programming scientist.

This school is targeted at Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or Mathematica is absolutely required. Basic knowledge of Python is assumed. Participants without any prior experience with Python should work through the proposed introductory materials before the course.

Download the original announcement: pdf

Date & Location


You can apply on-line. Here is a preview of the application form.

Applications must be submitted before 23:59 UTC, March 31, 2015. The application process is closed: We received 300 applications and are in the process of reviewing them to select the 30 participants! Notifications of acceptance will be sent by May 1, 2015. Participants have been selected. If you missed the deadline, write to to be put on the announcement list for next year.

No fee is charged but participants should take care of travel, living, and accommodation expenses.

FENS and IBRO-PERC provide 4 stipends of 750€ for master and/or PhD students interested in attending this course. Through these stipends FENS and IBRO-PERC aim to encourage and promote international experience of students; hence, students that are currently residing or studying in Germany are not eligible for a FENS and IBRO-PERC stipend. You can apply for the FENS and IBRO-PERC directly in our application form.

Candidates will be selected on the basis of their profile and motivation. Places are limited: acceptance rate this year was 10%.


You are supposed to know the basics of Python to participate in the lectures!

You are encouraged to go through the introductory material.



Day-by-day schedule with links to lecture and exercise materials

Day0 (Mon Aug 31): Best Programming Practices

  • Best Practices for Scientific Computing
  • Version control with git and how to contribute to Open Source with github
  • Object-oriented programming & design patterns

Day1 (Tue Sep 1): Software Carpentry

  • Test-driven development, unit testing & quality assurance
  • Debugging, profiling and benchmarking techniques
  • Advanced Python: generators, decorators, and context managers

Day2 (Wed Sep 2): Scientific Tools for Python

  • Advanced NumPy
  • The Quest for Speed (intro): Interfacing to C with Cython
  • Contributing to Open Source Software/Programming in teams

Day3 (Thu Sep 3): The Quest for Speed

  • Writing parallel applications in Python
  • Python 3: why should I care
  • Programming project

Day4 (Fri Sep 4): Efficient Memory Management

  • When parallelization does not help: the starving CPUs problem
  • Programming project

Day5 (Sat Sep 5): Practical Software Development

  • Programming project
  • The Pelita Tournament

Lectures start at 8:30 sharp and finish around 18:30. During the day we will have short breaks (coffee & tea provided), and a long lunch break. The last half hour every evening is dedicated to tutors' consultation: Tutors will answer your questions and give suggestions for your own projects.

On Saturday, September 5, we are going to have a little closing party that you should not miss: book your return travel not before Sunday, September 6 ;-)


Evaluation Survey Results

Previous Schools


Organized by Tiziano Zito (head) and Zbigniew Jędrzejewski-Szmek for the German Neuroinformatics Node of the INCF Germany, Christopher Roppelt for the German Center for Vertigo and Balance Disorders (DSGZ) and the Graduate School of Systemic Neurosciences (GSN) of the Ludwig-Maximilians-Universität Munich Germany, Christoph Hartmann for the Frankfurt Institute for Advanced Studies (FIAS) and International Max Planck Research School (IMPRS) for Neural Circuits, Frankfurt Germany, and Jakob Jordan for the Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Jülich Research Centre and JARA, Germany. Additional funding provided by the Bernstein Center for Computational Neuroscience (BCCN) Munich.


For any further questions please write to


Machines for parallel computing exercises are graciously provided by S3IT - Services and Support for Science IT of the University of Zürich.
start.txt · Last modified: 2015/10/13 16:11 by tiziano

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