FACETS CodeJam Workshop #2

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

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.

Organization

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.

Participants

• Michael Hines⁴
• Andrew Davison¹
• Eilif Muller⁵
• Johannes Bill⁵
• Romain Brette^3,10
• Thierry Brizzi¹
• Daniel Brüderle⁵
• Mikael Djurfeldt¹¹
• Örjan Ekeberg¹¹
• Samuel Garcia³
• Padraig Gleeson⁹
• Dan Goodman¹⁰
• Moritz Helias²
• Bernhard Kaplan⁵
• Jens Kremkow^2,7
• Susanne Kunkel²
• Abigail Morrison^2,6
• Eric Müller⁵
• Jonathan Peirce¹²
• Laurent Perrinet⁷
• Subhasis Ray¹³
• Raphael Ritz⁸
• Michelle Rudolph¹
• Bernd Wiebelt²
• Stefan Wils^14,15
• Pierre Yger¹

Meeting Program

Mon. 5th May
09:00	Simulators I
09:00	Andrew Davison and Eilif Muller	Welcome
09:15	Subhasis Ray	MOOSE to PyMOOSE: Interfacing MOOSE with Python [PDF]
10:45	Break
11:15	Simulators I (continued)
11:15	Romain Brette and Dan Goodman	Brian: a pure Python simulator [PDF]
12:00	Abigail Morrison	What's new with NEST
12:45	Lunch
14:00	Lightning talks
14:00	Raphael Ritz	The Zope Component Architecture
14:10	Dan Goodman	Sphinx: Python 3.0's documentation system [PDF]
14:20	Moritz 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
09:00	Michael Hines	What's new with NEURON + Python [PDF]
09:45	Stefan Wils	STEPS (STochastic Engine for Pathway Simulation)
10:30	Break
11:00	Simulators II and Meta-simulators (continued)
11:00	Mikael Djurfeldt and Örjan Ekeberg	MUSIC [PDF]
11:45	Andrew Davison	What's new with PyNN [PDF]
12:15	Daniel Brüderle	PyNN and the FACETS hardware [PDF]
12:45	Lunch
14:00	Lightning talks
14:00	Bernhard Kaplan	Boost::Python [PDF]
14:10	Eric Müller	Git: a fast, distributed revision control system [PDF]
14:20	Johannes 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
09:00	Jonathan Peirce	PsychoPy [PDF]
09:45	Padraig Gleeson	NeuroML and Python/HDF5 support in neuroConstruct
10:30	Break
11:00	Stimulus generation, data storage and data analysis (continued)
11:00	Laurent Perrinet	NeuroTools I: SpikeTrains and SpikeLists
11:20	Eilif Muller	NeuroTools II: ParameterSets
11:40	Thierry Brizzi	NeuroTools III: HDF5
12:00	Samuel 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
09:00	Eilif Muller	Reflections on managing complexity
09:45	Andrew 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

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).