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 which is located at Hansastr. 9A in Freiburg, Germany. The meeting was organised by Abigail Morrison and Bernd Wiebelt with Eilif Muller and Andrew Davison.

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 Hull
• Kay Inagaki
• Sarah Jarvis
• Bernhard Kaplan⁹
• Andreas Klöckner¹⁰
• Jens Kremkow
• Susanne Kunkel⁴
• Stefan Lang
• Abigail Morrison¹¹
• Eric Müller⁹
• Eilif Muller¹²
• Dejan Pecevski¹³
• Mihai Petrovici⁹
• Hans Ekkehard Plesser¹⁴
• Philipp Rautenberg
• Moritz Schilling⁹
• Sven Schrader
• Klaus Schuch¹³
• Yuedong Song
• Bartosz Telenczuk
• Christian Tomm
• Bernd Wiebelt⁴
• Pierre Yger³
• Yury V. Zaytsev^4,15

Meeting Program

Wed. 7th Oct.
9:00	Welcome
9:10	NeuroTools I
9:10	Andrew Davison (UNIC-CNRS)	An overview of NeuroTools
9:15	Pierre Yger and Luc Estabanez (UNIC-CNRS)	Data analysis with the "signals" and "analysis" modules
9:50	Luc Estabanez (UNIC-CNRS) and Jens Kremkow (BCCN-Freiburg)	Importing data in text, NEX and Spike2 formats
10:05	Eilif Muller (EPFL)	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 (KTH)	MUSIC [PDF]
11:10	Coffee Break
11:40	Simulator updates I
11:40	Jochen Eppler (Honda)	NEST [PDF]
12:00	Michael Hines (Yale)	NEURON [PDF]
12:20	Parallel Computation II
12:20	Eilif Muller (EPFL) and Lisandro Dalcin (CIMEC, Argentina)	mpi4py tutorial I
12:50	Lunch
14:10-18:30	Code sprints and discussions
Thur. 8th Oct.
9:00	Parallel Computation III
9:00	Andreas Klöckner (Brown)	PyOpenCl [PDF]
10:00	Eilif Muller (EPFL) and Lisandro Dalcin (CIMEC, Argentina)	mpi4py tutorial II
10:30	Reproducible Research I
10:30	Marc-Oliver Gewaltig (Honda)	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	Philip Rautenberg (BCCN-Munich)	Python, Neuron and the SQLdatabase
12:25	Hans Ekkehard Plesser (UMB, Norway)	Graphical network descriptions [PDF]
12:50	Lunch
14:10-18:30	Code sprints and discussions
14:10-16:00	Andreas Klöckner	PyOpenCl Hands-on Exercises [PDF]
19:00	Banquet
Fri. 9th Oct.
9:00	Faster and better Python
9:00	Stefan Behnel	Using the Cython compiler to write fast Python code [S5]
10:00	Chris Ball (U. Edinburgh)	Parameters and traits: extending Python attributes
10:20	NeuroTools II
10:20	Moritz Schilling (U. Heidelberg)	Development status of the "plotting" and "utilities" modules [PDF]
10:30	Samuel Garcia (CNRS-NSCC, Lyon)	The architecture of OpenElectrophy and coordination with NeuroTools [PDF]
10:45	Christian Garbers (BCCN-Freiburg)	FIND - A unified framework for neural data analysis
11:00	Coffee Break
11:30	Simulator updates II
11:30	Dejan Pecevski (TUGraz)	PCSIM [PDF]
11:45	Stefan Lang (U. Heidelberg)	NeuroDUNE
12:00	Andrew Davison	PyNN
12:10	Hardware
12:20	Eric Müller (U. Heidelberg)	The PyNN module for the FACETS wafer- scale neuromorphic hardware system [PDF]
12:40	Mihai Petrovici (U. Heidelberg)	The FACETS Demonstrator [PDF]
13:00	Lunch
14:20-18:30	Code sprints and discussions
14:20-16:00	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.

Discussions and code sprints

Some discussions took place on FriendFeed. A summary of some of the other discussions and code sprints that took place will be posted here soon.

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.