FACETS CodeJam Workshop #4

22nd-24th June 2010, Marseille, France

la Cité Radieuse

la Cité Radieuse, Le Corbusier's vision of a high-rise residential building as a "vertical city" in Marseille. Image by Dom Dada (Creative Commons Licence)

The goal of the FACETS CodeJam workshops is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics, by bringing together researchers, students and engineers to share ideas, present their work, and write code together. The general format of the workshops is to dedicate the mornings to invited and contributed talks, leaving the afternoons free for discussions and code sprints.

For the 4th FACETS CodeJam, the main theme of the meeting was workflows: what are the best practices for combining different tools (simulators, analysis tools, visualization tools, databases etc.) to ensure the efficient and reproducible flow of data and information from experiment conception to publication and archiving?


The meeting was held at the International Center for Mathematical Research, located in Marseille, France. The meeting was organised by Andrew Davison, Abigail Morrison, Eilif Muller and Laurent Perrinet.


Group photo from the FACETS CodeJam Workshop #4

Meeting Program

Tue. 22nd June

08:30 Session 1
08:30Laurent Perrinet Welcome
08:45Gaël Varoquaux Analyzing and modelling spontaneous brain activity in neuroimaging with Python [PDF]
09:30David Koop VisTrails: Using Provenance for Scientific Exploration through Workflows
10:15 Coffee Break
11:00 Session 2
11:00Michele Mattioni Sumatra and Neuronvisio. Run, Store, Search, Locate and Reload simulations' results [ODP]
11:30Mike Hull Morphforge - Biophysical Simulation In Python [PDF]
12:00Tom Schaul PyBrain: a machine learning perspective on neural networks and learning tools [PPTX]
12:30 Lunch
14:00 Code sprints, tutorials and discussions
20:00- Banquet

Wed. 23rd June

09:00 Session 3
09:00Raphael Ritz INCF Digital Atlasing Infrastructure Initiative
09:45Hugo Cornelis GENESIS 3/Neurospaces
10:30 Coffee Break
11:00 Session 4
11:00Philipp Rautenberg and Andrey Sobolev Development of tools for neurophysiology data management and sharing at the German Neuroinformatics Node [PDF]
11:30 Lightning Talks
11:30Samuel Garcia NEO : base and integration in OpenElectrophy [PDF]
11:50John Kenyon PLY (Python Lex-Yacc)
12:10Anthony Mouraud Spiking Neuron Networks Distributed Simulations with DAMNED [PDF]
12:30 Lunch
14:00-18:00 Code sprints, tutorials and discussions

Thu. 24th June

09:00 Session 5
09:00Mihai Petrovici Neuroscientific modeling with large-scale and highly accelerated neuromorphic hardware devices: methods, problems and perspectives [PDF]
09:45Erik Anderson Using VisTrails to Analyze and Visualize MRI and EEG Data
10:30 Coffee Break
11:00 Session 6
11:00Andrew Davison What's new with PyNN, what's new with Sumatra? [PDF]
11:30 Lightning Talks
11:30Laurent Perrinet Hooking together the pieces to build a neuroscience demo [link to slides]
11:50Sebastian Jeltsch The WAF build system [PDF]
12:10Eilif Muller Working with neuroscience ontologies using Python & rdflib [PDF]
12:30 Lunch
14:00-18:00 Code sprints, tutorials and discussions

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 International Neuroinformatics Co-ordinating Facility (INCF). We also wish to express our great appreciation to the DyVA team at the Institut de Neurosciences Cognitives de la Méditerranée for providing us with a great location and much assistance.