BrainScaleS CodeJam Workshop #5

14th-16th March 2012, Edinburgh, UK

Edinburgh Castle seen from Salisbury Crags

Edinburgh Castle seen from Salisbury Crags, copyright Kim Traynor, licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

The goal of the 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.

The 5th BrainScaleS/FACETS CodeJam took place as a joint meeting with the NeuroML Development Workshop, with the theme "Convergence in Computational Neuroscience".

The NeuroML workshop was on 12th and 13th March with 14th March as a joint NeuroML-CodeJam day, including a Mini-workshop on Convergence, Interoperability and Reuse in Neuroscience Modelling Software.


The meeting was held at the Informatics Forum, University of Edinburgh, located at 10 Crichton Street in Edinburgh, UK. The meeting was organised by Andrew Davison, Mike Hull, Abigail Morrison, Eilif Muller, Miha Pelko and Laurent Perrinet.


Group photo from the BrainScaleS CodeJam Workshop #5

Meeting Program

Wed. 14th March

08:00 Welcome
08:15 Describing networks I
08:15Birgit Kriener Description and testing of network connectivity [PDF]
08:45Mikael Djurfeldt Specifying connectivity using CSA [PDF]
09:15James Bednar Semi-declarative model specification in Python [PDF]
09:45 Break
10:15 Describing networks II
10:15Padraig Gleeson Integrating NeuroML 2 with PyNN, Brian & CSA [PDF]
10:40Jan Antolik Mozaik - a framework for large-scale spiking model development [PDF]
11:05Francesco Galluppi PyNN on SpiNNaker [link to slides]
11:30Stephan Gerhard Neural circuit reconstruction with CATMAID [link to slides]
12:00 Lunch
13:00 Code sprints, tutorials and discussions
13:00-16:40 Mini-workshop on Convergence, Interoperability and Reuse in Neuroscience Modelling Software
13:00Michael Vella Running multicompartment models on a grid [PDF]
13:30Marc de Kamps Modelling the population level and beyond [PDF]
14:00 Discussion

Thu. 15th March

08:00 Running an open-source scientific software project
08:00Michael Hanke The how and why of getting packaged [link to slides]
08:30Yury V. Zaytsev Continuous integration
09:00Valentin Hänel Open source project management [PDF]
09:20Pierre Yger Current status and future plans for NeuroTools [PDF]
09:45 Break
10:15 Compartmental neural modelling in Python
10:15Subhasis Ray Multi-compartmental and multi-scale modeling in MOOSE via Python [PDF]
10:45Armando Rodriguez GENESIS & Neurospaces in Python [link to slides]
11:15Michele Mattioni Neuronvisio: a Graphical User Interface with 3D capabilities for NEURON [link to slides]
11:35Mike Hull Morphforge: A Python library for modelling small networks of multicompartmental neurons
11:55 Lunch
13:00 Code sprints, tutorials and discussions
19:00- Banquet

Fri. 16th March

08:00 Code generation for neuronal simulation
08:00Damien Drix A domain-specific language for optimised GPU code generation
08:30Jochen Martin Eppler The NEST code generation roadmap: Rationale and methods [PDF]
09:00Andrew Davison Using NineML models in PyNN [PDF]
09:20 Break
09:50 Neuroscience data analysis with Python
09:50Stephan Gerhard NeuroHDF [link to slides]
10:15Samuel Garcia Neo [PDF]
10:45Raphael Ritz The INCF Cyberinfrastructure [PDF]
11:05Philipp Rautenberg Datajongleur - A pyToolkit for Dataobjects [PDF]
11:30 Lunch
13:00-17:00 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 BrainScaleS Project ("Brain-inspired multiscale computation in neuromorphic hybrid systems"; grant no. FP7-ICT-2009 269921) and of the INCF. We also wish to express our great appreciation to the School of Informatics at the University of Edinburgh for providing us with a great location and much assistance.