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
- Johannes Bill3
- Romain Brette4,5
- Thierry Brizzi2
- Daniel Brüderle3
- Andrew Davison2
- Mikael Djurfeldt6
- Örjan Ekeberg6
- Samuel Garcia4
- Padraig Gleeson7
- Dan Goodman5
- Moritz Helias8
- Michael Hines1
- Bernhard Kaplan3
- Jens Kremkow8,9
- Susanne Kunkel8
- Abigail Morrison8,10
- Eilif Muller3
- Eric Müller3
- Jonathan Peirce11
- Laurent Perrinet9
- Subhasis Ray12
- Raphael Ritz13
- Michelle Rudolph2
- Bernd Wiebelt8
- Stefan Wils14,15
- Pierre Yger2
- 1Yale University, New Haven, USA
- 2UNIC, CNRS, Gif sur Yvette, France
- 3Kirchoff-Institut für Physik, Ruprecht-Karls-Universität, Heidelberg, Germany
- 4Université Claude Bernard Lyon 1, France
- 5Ecole normale supérieure, Paris, France
- 6KTH, Stockholm, Sweden
- 7Dept. of Physiology, UCL, London, UK
- 8Bernstein Centre for Computational Neuroscience, Albert-Ludwigs-Universität, Freiburg, Germany
- 9INCM, Marseille, France
- 10Diesmann Research Unit, RIKEN, Japan
- 11School of Psychology, Nottingham University, Nottingham, UK
- 12NCBS, Bangalore, India
- 13INCF Secretariat, Stockholm, Sweden
- 14Computational Neuroscience Unit, OIST, Okinawa, Japan
- 15Theoretical Neurobiology, University of Antwerp, Antwerp, Belgium
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).