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 Antolik1
- James Bednar
- Sandra Berger35
- Avrama Blackwell44
- Robert Cannon31
- Sharon Crook13
- Andrew Davison10
- Mikael Djurfeldt20
- Damien Drix34
- Jochen Martin Eppler30
- Matteo Farinella12
- Francesco Galluppi32
- Samuel Garcia4
- Stephan Gerhard
- Padraig Gleeson12
- Lyle Graham27
- Domenico Guarino25
- Michael Hanke24
- Moritz Helmstaedter42
- Sean Hill3
- Michael Hines5
- Mike Hull6
- Valentin Hänel11
- Giovanni Idili46
- Roshini Johri26
- Bernhard Kaplan37
- Sarah Keating17
- Christoph Koke29
- James Kozloski43
- Birgit Kriener23
- Stephen Larson19
- Yann Le Franc21
- Michele Mattioni15
- Abigail Morrison2,28
- Eilif Muller11
- Lyle Muller38
- Miha Pelko6
- Laurent Perrinet7
- Eugenio Piasini12
- Philipp Rautenberg39
- Subhasis Ray9
- Raphael Ritz8
- Armando Rodriguez18
- Malin Sandström8
- Thomas Sharp47
- Angus Silver12
- Sergio Solinas45
- Thomas Suslak41
- Balazs Szigeti40
- Richard Tomsett22
- Michael Vella36
- Dagmar Waltemath16
- Pierre Yger 14
- Yury V. Zaytsev2
- Marc de Kamps33
- Nicolas le Novere15
- 1UNIC, CNRS, Gif sur Yvette, France
- 2Bernstein Centre for Computational Neuroscience, Albert-Ludwigs-Universität, Freiburg, Germany
- 3INCF, Stockholm, Sweden
- 4Université Claude Bernard Lyon 1, France
- 5Yale University, New Haven, USA
- 6Institute for Adaptive and Neural Computation, University of Edinburgh, Edinburgh, UK
- 7INCM, Marseille, France
- 8INCF Secretariat, Stockholm, Sweden
- 9NCBS, Bangalore, India
- 10UNIC, CNRS, Gif sur Yvette, France
- 11Blue Brain Project, Lausanne, Switzerland
- 12UCL, London, UK
- 13Arizona State University, Tempe, AZ, USA
- 14Imperial College, London, UK
- 15EBI, Cambridge, UK
- 16Systems Biology and Bioinformatics, Rostock University, Rostock, Germany
- 17EMBL_EBI, Hinxton, UK
- 18University of Texas Health Science Center at San Antonio, San Antonio, USA
- 19UCSD, La Jolla, CA, USA
- 20KTH/INCF, Sweden
- 21University of Antwerp, Wilrijk, Belgium
- 22Newcastle University, Newcastle upon Tyne, UK
- 23IMT UMB , Aas, Norway
- 24Otto-von-Guericke University, Magdeburg, Germany
- 25UNIC, Gif-sur-Yvette, France
- 26Pitney Bowes Software, United Kingdom
- 27CNRS, U. Paris Descartes, Paris, France
- 28Bernstein Center Freiburg, Freiburg, Germanz
- 29Universität Heidelberg - Kirchhoff-Institut für Physik , Heidelberg, Germany
- 30Forschungszentrum Juelich GmbH, Juelich, Germany
- 31Textensor Limited, Edinburgh, UK
- 32University of Manchester, Manchester, United Kingdom
- 33University of Leeds, Leeds, UK
- 34EPFL, Switzerland
- 35ASU, Tempe, USA
- 36University of Cambridge, Cambridge, UK
- 37Royal Institute of Technology, Stockholm, Sweden
- 38UNIC, CNRS, Gif-sur-Yvette, FRANCE
- 39German Neuroinformatics Node, Department Biologie II, Ludwig-Maximilians-Universität München, München, Germany
- 40University of Edinburgh Neuroinformatics Doctoral Training Centre, Edinburgh, United Kingdom
- 41University of Edinburgh, Edinburgh, UK
- 42Max Planck Institute of Neurobiology, Munich, Germany
- 43IBM, ., USA
- 44Krasnow Institute for Advanced Study, USA
- 45University of Pavia, Italy
- 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.