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.

Organization

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.

Participants



Group photo from the FACETS CodeJam Workshop #3

Meeting Program

Wed. 7th Oct.

07:00 Welcome
07:10 NeuroTools I
07:10Andrew Davison An overview of NeuroTools
07:15Luc Estebanez and Pierre Yger Data analysis with the "signals" and "analysis" modules
07:50Luc Estebanez and Jens Kremkow Importing data in text, NEX and Spike2 formats
08:05Eilif Muller Generating spike sequences with the "stgen" module
08:10Andrew Davison Managing model parameters with the "parameters" module
08:15Andrew Davison Caching intermediate results with the datastore module
08:20 Parallel Computation I
08:20Mikael Djurfeldt MUSIC [PDF]
09:10 Coffee break
09:40 Simulator updates I
09:40Jochen Martin Eppler NEST [PDF]
10:00Michael Hines NEURON [PDF]
10:20 Parallel Computation II
10:20Eilif Muller mpi4py tutorial I
10:50 Lunch
12:10-16:30 Code sprints and discussions
 

Thu. 8th Oct.

07:00 Parallel Computation III
07:00Andreas Klöckner PyOpenCl [PDF]
08:00Eilif Muller mpi4py tutorial II
08:30 Reproducible Research I
08:30Marc-Oliver Gewaltig Reproducible network descriptions
09:10 Coffee Break
09:40 Reproducible Research II
09:40Andrew Davison Sumatra, an electronic lab book for simulation projects [PDF]
10:10Philipp Rautenberg Python, Neuron and the SQLdatabase
10:25Hans Ekkehard Plesser Graphical network descriptions [PDF]
10:50 Lunch
12:10 Code sprints and discussions
12:10Andreas Klöckner PyOpenCl Hands-on Exercises [PDF]
14:00 code sprints and discussions
17:00- Banquet
 

Fri. 9th Oct.

07:00 Faster and better Python
07:00Stefan Behnel Using the Cython compiler to write fast Python code [link to slides]
08:00Chris Ball Parameters and traits: extending Python attributes
08:20 NeuroTools II
08:20Moritz Schilling Development status of the "plotting" and "utilities" modules [PDF]
08:30Samuel Garcia The architecture of OpenElectrophy and coordination with NeuroTools [PDF]
08:45Christian Garbers FIND - A unified framework for neural data analysis
09:00 Coffee break
09:30 Simulator updates II
09:30Dejan Pecevski PCSIM [PDF]
09:45Stefan Lang NeuroDune
10:00Andrew Davison PyNN
10:10 Hardware
10:10Eric Müller The PyNN module for the FACETS wafer- scale neuromorphic hardware system [PDF]
10:30Mihai Petrovici The FACETS Demonstrator [PDF]
11:00 Lunch
12:20-16:30 Code sprints and discussions
14:50Stefan 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.

Support

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.