"Increasingly, the real limit on what
computational scientists can accomplish is how quickly and reliably they
can translate their ideas into working code."
Gregory V. Wilson, Where's
the Real Bottleneck in Scientific Computing?
"programming the complexity telescope for brain-like computing"
Links
Contact
admin@neuralensemble.orgFACETS 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?
Meeting Program
Tue. 22nd June | ||
| 8:30 | Welcome | |
| 8:45 | Gael Varoquaux (INRIA Saclay, Parietal) | Analyzing and modelling spontaneous brain activity in neuroimaging with Python [PDF] |
| 9:30 | David Koop (University of Utah and VisTrails, Inc.) | VisTrails: Using Provenance for Scientific Exploration through Workflows |
| 10:15 | Coffee Break | |
| 11:00 | Michele Mattioni (European Bioinformatics Institute, UK) | Sumatra and Neuronvisio. Run, Store, Search, Locate and Reload simulations' results [ODP] |
| 11:30 | Mike Hull (Edinburgh, UK) | Morphforge - Biophysical Simulation In Python [PDF] |
| 12:00 | Tom Schaul (IDSIA, Lugano) | PyBrain: a machine learning perspective on neural networks and learning tools |
| 12:30 | Lunch | |
| 14:00-18:00 | Code sprints, tutorials and discussions | |
| 20:00 | Banquet | |
Wed. 23rd June | ||
| 9:00 | Raphael Ritz (INCF, Stockholm) | INCF Digital Atlasing Infrastructure Initiative |
| 9:45 | Hugo Cornelis (Leuven University) | GENESIS 3/Neurospaces |
| 10:30 | Coffee Break | |
| 11:00 | Andrey Sobolev and Philipp Rautenberg (German Neuroinformatics Node, LMU Munich) | Development of tools for neurophysiology data management and sharing at the German Neuroinformatics Node |
| 11:30 | Lightning Talks | |
| 11:30 | Samuel Garcia (CNRS, Lyon) | NEO : base and integration in OpenElectrophy |
| 11:50 | John Kenyon (Blue Brain Project, EPFL, Lausanne, Switzerland) | PLY (Python Lex-Yacc) |
| 12:10 | Anthony Mouraud (UMR Mouvement et Perception, Marseille) | Spiking Neuron Networks Distributed Simulations with DAMNED |
| 12:30 | Lunch | |
| 14:00-18:00 | Code sprints, tutorials and discussions | |
Thurs. 24th June | ||
| 9:00 | Mihai Petrovici (KIP, Uni-Heidelberg) | Neuroscientific modeling with large-scale and highly accelerated neuromorphic hardware devices: methods, problems and perspectives [PDF] |
| 9:45 | Erik Anderson (University of Utah) | Using VisTrails to Analyze and Visualize MRI and EEG Data |
| 10:30 | Coffee Break | |
| 11:00 | Andrew Davison (UNIC, CNRS, France) | What's new with PyNN, what's new with Sumatra? |
| 11:30 | Lightning Talks | |
| 11:30 | Laurent Perrinet (INCM-CNRS, Marseille) | Hooking together the pieces to build a neuroscience demo |
| 11:50 | Sebastian Jeltsch (KIP, Uni-Heidelberg) | The WAF build system |
| 12:10 | Eilif Muller (Blue Brain Project, EPFL, Lausanne, Switzerland) | 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.
Organization
The meeting took place at the International Center for Mathematical Research (CIRM), in the beautiful natural site of the Calanques near Marseille. The meeting was organized by Andrew Davison, Abigail Morrison, Eilif Muller and Laurent Perrinet. Especially big thanks go to Laurent, who was juggling being the local organiser with his two-month-old baby.
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.