FACETS CodeJam Workshop #4

22nd-24th June 2010, Marseille, France

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?

Organization

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.

Participants

• Erik Anderson⁷
• Javier Baladron⁹
• Thierry Brizzi¹
• Hugo Cornelis
• Andrew Davison¹
• Diego Fasoli⁹
• Samuel Garcia³
• Mike Hull¹⁰
• Florent Jaillet¹¹
• Sebastian Jeltsch⁴
• Philippe Katz¹¹
• John Kenyon
• David Koop
• Susanne Kunkel²
• Michele Mattioni¹²
• Abigail Morrison⁵
• Simon Moré¹⁶
• Anthony Mouraud⁸
• Eilif Muller⁶
• Eric Müller⁴
• Laurent Perrinet¹¹
• Laurent Pezard¹³
• Philipp Rautenberg¹⁴
• Raphael Ritz¹⁵
• Paula Sanz Leon¹¹
• Tom Schaul¹⁷
• Andrey Sobolev¹⁴
• Sylvain Takerkart¹¹
• Gaël Varoquaux
• Liang Wang
• Bernd Wiebelt²
• Sarah Wirtssohn¹¹
• Pierre Yger¹
• Yury V. Zaytsev²

Meeting Program

Tue. 22nd June
08:30	Session 1
08:30	Laurent Perrinet	Welcome
08:45	Gaël Varoquaux	Analyzing and modelling spontaneous brain activity in neuroimaging with Python [PDF]
09:30	David Koop	VisTrails: Using Provenance for Scientific Exploration through Workflows
10:15	Coffee Break
11:00	Session 2
11:00	Michele Mattioni	Sumatra and Neuronvisio. Run, Store, Search, Locate and Reload simulations' results [ODP]
11:30	Mike Hull	Morphforge - Biophysical Simulation In Python [PDF]
12:00	Tom 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
09:00	Raphael Ritz	INCF Digital Atlasing Infrastructure Initiative
09:45	Hugo Cornelis	GENESIS 3/Neurospaces
10:30	Coffee Break
11:00	Session 4
11:00	Philipp Rautenberg and Andrey Sobolev	Development of tools for neurophysiology data management and sharing at the German Neuroinformatics Node [PDF]
11:30	Lightning Talks
11:30	Samuel Garcia	NEO : base and integration in OpenElectrophy [PDF]
11:50	John Kenyon	PLY (Python Lex-Yacc)
12:10	Anthony 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
09:00	Mihai Petrovici	Neuroscientific modeling with large-scale and highly accelerated neuromorphic hardware devices: methods, problems and perspectives [PDF]
09:45	Erik Anderson	Using VisTrails to Analyze and Visualize MRI and EEG Data
10:30	Coffee Break
11:00	Session 6
11:00	Andrew Davison	What's new with PyNN, what's new with Sumatra? [PDF]
11:30	Lightning Talks
11:30	Laurent Perrinet	Hooking together the pieces to build a neuroscience demo [link to slides]
11:50	Sebastian Jeltsch	The WAF build system [PDF]
12:10	Eilif Muller	Working with neuroscience ontologies using Python & rdflib [PDF]
12:30	Lunch
14:00-18:00	Code sprints, tutorials and discussions

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 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.