FACETS CodeJam Workshop #3

7th-9th October 2009, Freiburg, Germany

Freiburger Rathaus - source: Luidger with permission under terms of GFDL

The first CodeJam focused on adding or improving Python support for different neuroscience simulators, and on the PyNN common simulator API.

The focus for the second CodeJam was expanded to include the next stages in the simulation workflow - analysis and visualisation of simulation results, and management of simulation projects to promote reproducibility and reliability.

The third CodeJam, aimed to catalyze development on a broad range of topics, including simulator interoperability, modeling langauge standardization, parallelizaion, Python tool-chain & abstraction development to further erode the complexity barrier facing computational neuroscientists, and much more ...

The general format of the workshop was to dedicate the mornings to invited and contributed talks on topics relating to simulation and collaborative software development in computational and systems neuroscience, leaving the afternoons free for discussions and code sprints.


The meeting was held at the Bernstein Center for Computational Neuroscience, located at Hansastr. 9A in Freiburg, Germany. The meeting was organised by Andrew Davison, Abigail Morrison, Eilif Muller and Bernd Wiebelt.


Group photo from the FACETS CodeJam Workshop #3

Meeting Program

Wed. 7th Oct.

09:00 Welcome
09:10 NeuroTools I
09:10Andrew Davison An overview of NeuroTools
09:15Luc Estebanez and Pierre Yger Data analysis with the "signals" and "analysis" modules
09:50Luc Estebanez and Jens Kremkow Importing data in text, NEX and Spike2 formats
10:05Eilif Muller Generating spike sequences with the "stgen" module
10:10Andrew Davison Managing model parameters with the "parameters" module
10:15Andrew Davison Caching intermediate results with the datastore module
10:20 Parallel Computation I
10:20Mikael Djurfeldt MUSIC [PDF]
11:10 Coffee break
11:40 Simulator updates I
11:40Jochen Martin Eppler NEST [PDF]
12:00Michael Hines NEURON [PDF]
12:20 Parallel Computation II
12:20Eilif Muller mpi4py tutorial I
12:50 Lunch
14:10-18:30 Code sprints and discussions

Thu. 8th Oct.

09:00 Parallel Computation III
09:00Andreas Klöckner PyOpenCl [PDF]
10:00Eilif Muller mpi4py tutorial II
10:30 Reproducible Research I
10:30Marc-Oliver Gewaltig Reproducible network descriptions
11:10 Coffee Break
11:40 Reproducible Research II
11:40Andrew Davison Sumatra, an electronic lab book for simulation projects [PDF]
12:10Philipp Rautenberg Python, Neuron and the SQLdatabase
12:25Hans Ekkehard Plesser Graphical network descriptions [PDF]
12:50 Lunch
14:10 Code sprints and discussions
14:10Andreas Klöckner PyOpenCl Hands-on Exercises [PDF]
16:00 code sprints and discussions
19:00- Banquet

Fri. 9th Oct.

09:00 Faster and better Python
09:00Stefan Behnel Using the Cython compiler to write fast Python code [link to slides]
10:00Chris Ball Parameters and traits: extending Python attributes
10:20 NeuroTools II
10:20Moritz Schilling Development status of the "plotting" and "utilities" modules [PDF]
10:30Samuel Garcia The architecture of OpenElectrophy and coordination with NeuroTools [PDF]
10:45Christian Garbers FIND - A unified framework for neural data analysis
11:00 Coffee break
11:30 Simulator updates II
11:30Dejan Pecevski PCSIM [PDF]
11:45Stefan Lang NeuroDune
12:00Andrew Davison PyNN
12:10 Hardware
12:10Eric Müller The PyNN module for the FACETS wafer- scale neuromorphic hardware system [PDF]
12:30Mihai Petrovici The FACETS Demonstrator [PDF]
13:00 Lunch
14:20-18:30 Code sprints and discussions
16:50Stefan Behnel Cython Hands-on Exercises

Creative Commons License
Unless mentioned otherwise, all the downloadable talks are licenced under a Creative Commons Attribution-Noncommercial-No Derivative Works License.


The meeting organizers gratefully acknowledge the support of the European Union through the FACETS Project (grant no. IST-2005-15879) and the INCF. We also wish to express our great appreciation to the Bernstein Center for Computational Neuroscience in Freiburg for providing us with a great location and much assistance.