FACETS CodeJam Workshop #2

5th-8th May 2008, Gif sur Yvette, France

Château du CNRS, Gif sur Yvette

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 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 informal discussions and code sprints.


The meeting was held at the Château du CNRS, located in Gif sur Yvette, France. The meeting was organised by Andrew Davison and Eilif Muller.


Group photo from the FACETS CodeJam Workshop #2

Meeting Program

Mon. 5th May

09:00 Simulators I
09:00Andrew Davison and Eilif Muller Welcome
09:15Subhasis Ray MOOSE to PyMOOSE: Interfacing MOOSE with Python [PDF]
10:45 Break
11:15 Simulators I (continued)
11:15Romain Brette and Dan Goodman Brian: a pure Python simulator [PDF]
12:00Abigail Morrison What's new with NEST
12:45 Lunch
14:00 Lightning talks
14:00Raphael Ritz The Zope Component Architecture
14:10Dan Goodman Sphinx: Python 3.0's documentation system [PDF]
14:20Moritz Helias f2py: Python's interface to the world of number crunching [PDF]
14:30 Code sprints and general discussion
16:00 Break
16:30-18:00 Code sprints and general discussion

Tue. 6th May

09:00 Simulators II and Meta-simulators
09:00Michael Hines What's new with NEURON + Python [PDF]
09:45Stefan Wils STEPS (STochastic Engine for Pathway Simulation)
10:30 Break
11:00 Simulators II and Meta-simulators (continued)
11:00Mikael Djurfeldt and Örjan Ekeberg MUSIC [PDF]
11:45Andrew Davison What's new with PyNN [PDF]
12:15Daniel Brüderle PyNN and the FACETS hardware [PDF]
12:45 Lunch
14:00 Lightning talks
14:00Bernhard Kaplan Boost::Python [PDF]
14:10Eric Müller Git: a fast, distributed revision control system [PDF]
14:20Johannes Bill The FACETS Graph Model [PDF]
14:30 Code sprints and general discussion
16:00 Break
16:30 Code sprints and general discussion
19:00- Banquet dinner ("Les Saveurs Sauvages")

Wed. 7th May

09:00 Stimulus generation, data storage and data analysis
09:00Jonathan Peirce PsychoPy [PDF]
09:45Padraig Gleeson NeuroML and Python/HDF5 support in neuroConstruct
10:30 Break
11:00 Stimulus generation, data storage and data analysis (continued)
11:00Laurent Perrinet NeuroTools I: SpikeTrains and SpikeLists
11:20Eilif Muller NeuroTools II: ParameterSets
11:40Thierry Brizzi NeuroTools III: HDF5
12:00Samuel Garcia OpenElectrophy: database storage for neural data [PDF]
12:45 Lunch
14:00 Discussion: Collaborative development of data analysis, storage and visualisation tools
16:00 Break
16:30- Code sprints and general discussion

Thu. 8th May

09:00 Managing complexity
09:00Eilif Muller Reflections on managing complexity
09:45Andrew Davison Simulation project management with Sumatra [PDF]
10:30 Break
11:00 Discussion: What's next? Where do we go from here? CodeJam #3?
12:30 Lunch
14:00 Code sprints and general discussion
16:00 Break
16:30- Code sprints and general discussion

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).