BrainScaleS CodeJam Workshop #5
14th-16th March 2012, Edinburgh, UK
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.
Organization
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.
Participants
- Jan Antolik14
- James Bednar
- Sandra Berger33
- Avrama Blackwell42
- Robert Cannon29
- Sharon Crook8
- Andrew Davison1
- Mikael Djurfeldt16
- Damien Drix32
- Jochen Martin Eppler26
- Matteo Farinella7
- Francesco Galluppi30
- Samuel Garcia28
- Stephan Gerhard
- Padraig Gleeson7
- Lyle Graham24
- Domenico Guarino22
- Michael Hanke21
- Moritz Helmstaedter40
- Sean Hill45
- Michael Hines44
- Mike Hull3
- Valentin Hänel2
- Giovanni Idili46
- Roshini Johri23
- Bernhard Kaplan35
- Sarah Keating12
- Christoph Koke25
- James Kozloski41
- Birgit Kriener20
- Stephen Larson15
- Yann Le Franc18
- Michele Mattioni10
- Abigail Morrison5,6
- Eilif Muller2
- Lyle Muller36
- Miha Pelko3
- Laurent Perrinet4
- Eugenio Piasini7
- Philipp Rautenberg37
- Subhasis Ray27
- Raphael Ritz17
- Armando Rodriguez13
- Malin Sandström17
- Thomas Sharp47
- Angus Silver7
- Sergio Solinas43
- Thomas Suslak39
- Balazs Szigeti38
- Richard Tomsett19
- Michael Vella34
- Dagmar Waltemath11
- Pierre Yger 9
- Yury V. Zaytsev5
- Marc de Kamps31
- Nicolas le Novere10
- 1UNIC, CNRS, Gif sur Yvette, France
- 2Blue Brain Project, EPFL, Switzerland
- 3Institute for Adaptive and Neural Computation, University of Edinburgh, Edinburgh, UK
- 4INCM, Marseille, France
- 5Bernstein Centre for Computational Neuroscience, Albert-Ludwigs-Universität, Freiburg, Germany
- 6Bernstein Center Freiburg, Freiburg, Germanz
- 7UCL, London, UK
- 8Arizona State University, Tempe, AZ, USA
- 9Imperial College, London, UK
- 10EBI, Cambridge, UK
- 11Systems Biology and Bioinformatics, Rostock University, Rostock, Germany
- 12EMBL_EBI, Hinxton, UK
- 13University of Texas Health Science Center at San Antonio, San Antonio, USA
- 14UNIC, CNRS, Gif sur Yvette, France
- 15UCSD, La Jolla, CA, USA
- 16KTH/INCF, Sweden
- 17INCF Secretariat, Stockholm, Sweden
- 18University of Antwerp, Wilrijk, Belgium
- 19Newcastle University, Newcastle upon Tyne, UK
- 20IMT UMB , Aas, Norway
- 21Otto-von-Guericke University, Magdeburg, Germany
- 22UNIC, Gif-sur-Yvette, France
- 23Pitney Bowes Software, United Kingdom
- 24CNRS, U. Paris Descartes, Paris, France
- 25Universität Heidelberg - Kirchhoff-Institut für Physik , Heidelberg, Germany
- 26Forschungszentrum Juelich GmbH, Juelich, Germany
- 27NCBS, Bangalore, India
- 28Université Claude Bernard Lyon 1, France
- 29Textensor Limited, Edinburgh, UK
- 30University of Manchester, Manchester, United Kingdom
- 31University of Leeds, Leeds, UK
- 32EPFL, Switzerland
- 33ASU, Tempe, USA
- 34University of Cambridge, Cambridge, UK
- 35Royal Institute of Technology, Stockholm, Sweden
- 36UNIC, CNRS, Gif-sur-Yvette, FRANCE
- 37German Neuroinformatics Node, Department Biologie II, Ludwig-Maximilians-Universität München, München, Germany
- 38University of Edinburgh Neuroinformatics Doctoral Training Centre, Edinburgh, United Kingdom
- 39University of Edinburgh, Edinburgh, UK
- 40Max Planck Institute of Neurobiology, Munich, Germany
- 41IBM, ., USA
- 42Krasnow Institute for Advanced Study, USA
- 43University of Pavia, Italy
- 44Yale University, New Haven, USA
- 45INCF, Stockholm, Sweden
- 46OpenWorm, US / Ireland / Italy / Russia
- 47The University of Manchester, Manchester, UK
Meeting Program
Wed. 14th March | ||
| 09:00 | Welcome | |
| 09:15 | Describing networks I | |
| 09:15 | Birgit Kriener | Description and testing of network connectivity [PDF] |
| 09:45 | Mikael Djurfeldt | Specifying connectivity using CSA [PDF] |
| 10:15 | James Bednar | Semi-declarative model specification in Python [PDF] |
| 10:45 | Break | |
| 11:15 | Describing networks II | |
| 11:15 | Padraig Gleeson | Integrating NeuroML 2 with PyNN, Brian & CSA [PDF] |
| 11:40 | Jan Antolik | Mozaik - a framework for large-scale spiking model development [PDF] |
| 12:05 | Francesco Galluppi | PyNN on SpiNNaker [link to slides] |
| 12:30 | Stephan Gerhard | Neural circuit reconstruction with CATMAID [link to slides] |
| 13:00 | Lunch | |
| 14:00 | Code sprints, tutorials and discussions | |
| 14:00-17:40 | Mini-workshop on Convergence, Interoperability and Reuse in Neuroscience Modelling Software | |
| 14:00 | Michael Vella | Running multicompartment models on a grid [PDF] |
| 14:30 | Marc de Kamps | Modelling the population level and beyond [PDF] |
| 15:00 | Discussion | |
Thu. 15th March | ||
| 09:00 | Running an open-source scientific software project | |
| 09:00 | Michael Hanke | The how and why of getting packaged [link to slides] |
| 09:30 | Yury V. Zaytsev | Continuous integration |
| 10:00 | Valentin Hänel | Open source project management [PDF] |
| 10:20 | Pierre Yger | Current status and future plans for NeuroTools [PDF] |
| 10:45 | Break | |
| 11:15 | Compartmental neural modelling in Python | |
| 11:15 | Subhasis Ray | Multi-compartmental and multi-scale modeling in MOOSE via Python [PDF] |
| 11:45 | Armando Rodriguez | GENESIS & Neurospaces in Python [link to slides] |
| 12:15 | Michele Mattioni | Neuronvisio: a Graphical User Interface with 3D capabilities for NEURON [link to slides] |
| 12:35 | Mike Hull | Morphforge: A Python library for modelling small networks of multicompartmental neurons |
| 12:55 | Lunch | |
| 14:00 | Code sprints, tutorials and discussions | |
| 20:00- | Banquet | |
Fri. 16th March | ||
| 09:00 | Code generation for neuronal simulation | |
| 09:00 | Damien Drix | A domain-specific language for optimised GPU code generation |
| 09:30 | Jochen Martin Eppler | The NEST code generation roadmap: Rationale and methods [PDF] |
| 10:00 | Andrew Davison | Using NineML models in PyNN [PDF] |
| 10:20 | Break | |
| 10:50 | Neuroscience data analysis with Python | |
| 10:50 | Stephan Gerhard | NeuroHDF [link to slides] |
| 11:15 | Samuel Garcia | Neo [PDF] |
| 11:45 | Raphael Ritz | The INCF Cyberinfrastructure [PDF] |
| 12:05 | Philipp Rautenberg | Datajongleur - A pyToolkit for Dataobjects [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 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.