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 Morrison^2,28
• 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

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.