FACETS CodeJam Workshop #3

7th-9th October 2009, Freiburg, Germany

Freiburger Rathaus - source: Luidger with permission under terms of GFDL

The first CodeJam focused on adding or improving Python support for different neuroscience simulators, and on the PyNN common simulator API.

The focus for the second CodeJam was expanded to include the next stages in the simulation workflow - analysis and visualisation of simulation results, and management of simulation projects to promote reproducibility and reliability.

The third CodeJam, aimed to catalyze development on a broad range of topics, including simulator interoperability, modeling langauge standardization, parallelizaion, Python tool-chain & abstraction development to further erode the complexity barrier facing computational neuroscientists, and much more ...

The general format of the workshop was to dedicate the mornings to invited and contributed talks on topics relating to simulation and collaborative software development in computational and systems neuroscience, leaving the afternoons free for discussions and code sprints.

Organization

The meeting was held at the Bernstein Center for Computational Neuroscience, located at Hansastr. 9A in Freiburg, Germany. The meeting was organised by Andrew Davison, Abigail Morrison, Eilif Muller and Bernd Wiebelt.

Participants

Larissa Albantakis¹
Ismail Ari²
Chris Ball
Stefan Behnel
David Colliaux³
Andrew Davison³
Moritz Deger⁴
Mikael Djurfeldt⁵
Jochen Martin Eppler^4,6
Luc Estebanez³
Christian Garbers⁴
Samuel Garcia⁷
Marc-Oliver Gewaltig⁶
Jose Guzman
Michael Hines⁸
Mike Hull⁹
Kay Inagaki
Sarah Jarvis
Bernhard Kaplan¹⁰
Andreas Klöckner¹¹
Jens Kremkow^4,12
Susanne Kunkel⁴
Stefan Lang
Abigail Morrison¹³
Eilif Muller¹⁴
Eric Müller¹⁰
Dejan Pecevski¹⁵
Mihai Petrovici¹⁰
Hans Ekkehard Plesser¹⁶
Philipp Rautenberg
Moritz Schilling¹⁰
Sven Schrader
Klaus Schuch¹⁵
Yuedong Song
Bartosz Telenczuk
Christian Tomm
Bernd Wiebelt⁴
Pierre Yger³
Yury V. Zaytsev^4,17

¹Computational Neuroscience Group, UPF, Barcelona, Spain
²Boğaziçi University, Computer Engineering Department, Istanbul, Turkey
³UNIC, CNRS, Gif sur Yvette, France
⁴Bernstein Centre for Computational Neuroscience, Albert-Ludwigs-Universität, Freiburg, Germany
⁵INCF, Stockholm, Sweden
⁶Honda Research Institute Europe GmbH, Germany
⁷Université Claude Bernard Lyon 1, France
⁸Yale University, New Haven, USA
⁹Institute for Adaptive and Neural Computation, University of Edinburgh, Edinburgh, UK
¹⁰Kirchoff-Institut für Physik, Ruprecht-Karls-Universität, Heidelberg, Germany
¹¹Divison of Applied Mathematics, Brown University, USA
¹²INCM, Marseille, France
¹³Diesmann Research Unit, RIKEN, Japan
¹⁴Laboratory of Computational Neuroscience, EPFL, Lausanne, Switzerland
¹⁵Institute for Theoretical Computer Science, Technische Universität Graz, Austria
¹⁶Dept. of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
¹⁷Institut für Mikrosystemtechnik, Freiburg, Germany

Group photo from the FACETS CodeJam Workshop #3

Meeting Program

Wed. 7th Oct.
09:00	Welcome
09:10	NeuroTools I
09:10	Andrew Davison	An overview of NeuroTools
09:15	Luc Estebanez and Pierre Yger	Data analysis with the "signals" and "analysis" modules
09:50	Luc Estebanez and Jens Kremkow	Importing data in text, NEX and Spike2 formats
10:05	Eilif Muller	Generating spike sequences with the "stgen" module
10:10	Andrew Davison	Managing model parameters with the "parameters" module
10:15	Andrew Davison	Caching intermediate results with the datastore module
10:20	Parallel Computation I
10:20	Mikael Djurfeldt	MUSIC [PDF]
11:10	Coffee break
11:40	Simulator updates I
11:40	Jochen Martin Eppler	NEST [PDF]
12:00	Michael Hines	NEURON [PDF]
12:20	Parallel Computation II
12:20	Eilif Muller	mpi4py tutorial I
12:50	Lunch
14:10-18:30	Code sprints and discussions

Thu. 8th Oct.
09:00	Parallel Computation III
09:00	Andreas Klöckner	PyOpenCl [PDF]
10:00	Eilif Muller	mpi4py tutorial II
10:30	Reproducible Research I
10:30	Marc-Oliver Gewaltig	Reproducible network descriptions
11:10	Coffee Break
11:40	Reproducible Research II
11:40	Andrew Davison	Sumatra, an electronic lab book for simulation projects [PDF]
12:10	Philipp Rautenberg	Python, Neuron and the SQLdatabase
12:25	Hans Ekkehard Plesser	Graphical network descriptions [PDF]
12:50	Lunch
14:10	Code sprints and discussions
14:10	Andreas Klöckner	PyOpenCl Hands-on Exercises [PDF]
16:00		code sprints and discussions
19:00-	Banquet

Fri. 9th Oct.
09:00	Faster and better Python
09:00	Stefan Behnel	Using the Cython compiler to write fast Python code [link to slides]
10:00	Chris Ball	Parameters and traits: extending Python attributes
10:20	NeuroTools II
10:20	Moritz Schilling	Development status of the "plotting" and "utilities" modules [PDF]
10:30	Samuel Garcia	The architecture of OpenElectrophy and coordination with NeuroTools [PDF]
10:45	Christian Garbers	FIND - A unified framework for neural data analysis
11:00	Coffee break
11:30	Simulator updates II
11:30	Dejan Pecevski	PCSIM [PDF]
11:45	Stefan Lang	NeuroDune
12:00	Andrew Davison	PyNN
12:10	Hardware
12:10	Eric Müller	The PyNN module for the FACETS wafer- scale neuromorphic hardware system [PDF]
12:30	Mihai Petrovici	The FACETS Demonstrator [PDF]
13:00	Lunch
14:20-18:30	Code sprints and discussions
16:50	Stefan Behnel	Cython Hands-on Exercises

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 FACETS Project (grant no. IST-2005-15879) and the INCF. We also wish to express our great appreciation to the Bernstein Center for Computational Neuroscience in Freiburg for providing us with a great location and much assistance.