Python in Neuroscience satellite to Euroscipy

Paris, Ecole Normale Supérieure, August 29-30 2011 The “Python in Neuroscience” workshop aims at gathering researchers who develop software tools in different branches of neuroscience in order to share ideas, concepts, tools and to foster collaborative projects based on Python language.

29-30 Aug 2011 Paris (France)

Planning

Week Mon. 29 Tue. 30 List

	Mon. 29	Tue. 30
09:00 10:00 11:00 12:00 13:00 14:00 15:00 16:00 17:00	Welcome 9:15 - 9:30 (15min) Welcome Dussane neural simulation 9:30 - 11:00 (1h30) neural simulation Dussane Andrew Davison › What's new with Brian? - Romain Brette, Laboratoire de la Psychologie de la Perception, Département d'Etudes Cognitives 09:30-10:00 (30min) › PyNN: a unified interface for neuronal network simulators - Andrew Davison, Unité de Neuroscience, Information et Complexité 10:00-10:15 (15min) › Python Tools for Neuromorphic Systems Configuration - Emre Neftci, Institute of Neuroinformatics 10:15-10:30 (15min) › CLONES: A Closed-Loop Simulation Framework for Body, Muscles and Neurons - Thomas Voegtlin, Laboratoire Lorrain de Recherche en Informatique et Automatique 10:30-10:45 (15min) › DANA - Nicolas P. Rougier, INRIA Nancy Grand Est, Laboratoire Lorrain de Recherche en Informatique et Automatique 10:45-11:00 (15min) Coffee break 11:00 - 11:30 (30min) Coffee break electrophysiology 11:30 - 12:30 (1h) electrophysiology Dussane Romain Brette › Flexible spike sorting in Python - Bartosz Telenczuk, Institute for Theoretical Biology, Neurology - Belevtsoff Dmytro, Bernstein Center for Computational Neuroscience Berlin, Neurology 11:30-11:45 (15min) › NeurOnline: A software to perform online analysis and control of electrophysiological recordings - Ambard Maxime, Bernstein Center Freiburg 11:45-12:00 (15min) › Using Python tools for analysis of a mathematical model of after-depolarisation - Jakub Nowacki, Bristol Centre for Applied Nonlinear Mathematics 12:00-12:15 (15min) › Optimisation of stimulation patterns for specific questions in electrophysiology experiments: a Python framework - Damien Drix, Centre for Computational Neuroscience and Robotics 12:15-12:30 (15min) Lunch 12:30 - 14:00 (1h30) Lunch neuroimaging data processing Coffee break 14:00 - 15:30 (1h30) neuroimaging data processing Dussane Bertrand Thirion › The virtues and sins of PyMVPA - Yaroslav O. Halchenko, Dr. James V. Haxby Lab 14:00-14:30 (30min) › Classification, Induction and Brain Decoding - Emanuele Olivetti, NeuroInformatics Laboratory - Susanne Greiner, NeuroInformatics Laboratory 14:30-14:45 (15min) › BrainVISA: a complete software platform for neuroimaging - Dominique Geffroy, IFR 49 - Yann Cointepas, LNAO, NeuroSpin, CEA 14:45-15:00 (15min) › Pyhrf: a package to extract and study hemodynamics from fMRI data - Thomas VINCENT, Laboratoire de Neuro-imagerie Assistée par Ordinateur 15:00-15:15 (15min) 15:15 - 15:30 (15min) Coffee break Poster 15:30 - 17:00 (1h30) Poster › 3D Brain Atlas Reconstructor and Common Atlas Format, the infrastructure for constructing tree dimensional brain atlases - Piotr Majka, Departament of Neurophysiology, Nencki Institute of Experimental Biology 15:30-17:00 (1h30) › A Package for Kernel Smoothing via Diffusion: Rate Estimation of Spike Trains modeled as Non-homogeneous Poisson Processes. - Taskin Deniz, Bernstein Center Freiburg 15:30-17:00 (1h30) › Developing and evaluating a computerized tool for measuring perceived stress - Dalal Ben Loubir, Medical Informatics Laboratory - Mohamed Bennani Othmani, Medical Informatics Laboratory 15:30-17:00 (1h30) › Dynamical characterisation of neural networks and neurophysiological time series: Parallel approaches using Python - Thomas Greg Corcoran,, Centre for Computational Neuroscience and Robotics, University of Sussex 15:30-17:00 (1h30) › Gom2n: A toolchain to simulate and investigate selective stimulation strategies for FES - Laforet Jeremy, Biomecanique et BioIngenierie 15:30-17:00 (1h30) › Machine learning for fMRI in Python: inverse inference with scikit-learn - Bertrand Thirion, INRIA Saclay-Île-de-France 15:30-17:00 (1h30) › Random Subspace Methods for Neuroimaging - Diego Sona, NeuroInformatics Laboratory - Paolo Avesani, NeuroInformatics Laboratory 15:30-17:00 (1h30) › Simulating topographic distributions of event-related potentials using Brisk - Roman Goj, Psychological Imaging Laboratory 15:30-17:00 (1h30) › Waxholm Space - Raphael Ritz, Secretariat 15:30-17:00 (1h30)	workflows and pipelines for data processing 9:30 - 11:15 (1h45) workflows and pipelines for data processing Dussane Romain Brette › NiPyPE: A flexible, lightweight and extensible neuroimaging data processing framework - Satrajit Ghosh, Massachusetts Institute of Technology 09:30-10:15 (45min) › Nitime and IPython: tools for time-series analysis and high-level parallel computing - Fernando Perez, Henry H. Wheeler Brain Imaging Center, University of California, Berkeley 10:15-10:30 (15min) › More than batteries included: NeuroDebian - Michael Hanke, Department of Experimental Psychology, University of Magdeburg, Center for Cognitive Neuroscience, Dartmouth College, Department of Psychological and Brain Sciences, Dartmouth College 10:30-10:45 (15min) › Interoperability among Data Processing Frameworks: Reality or Wishful Thinking? - Tiziano Zito, Bernstein Center for Computational Neuroscience Berlin, Berlin Institute of Technology 10:45-11:00 (15min) › Soma-workflow: An unified and simple interface to parallel computing resources - Soizic Laguitton, LNAO, NeuroSpin, CEA 11:00-11:15 (15min) Coffee break 11:15 - 11:45 (30min) Coffee break data management and databasing 11:45 - 12:30 (45min) data management and databasing Dussane Andrew Davison › Neo: representing and manipulating electrophysiology data in Python - Andrew Davison, Unité de Neuroscience, Information et Complexité 11:45-12:00 (15min) › NiBabel: Conductor for a cacophony of neuro-imaging file formats - Michael Hanke, Department of Psychological and Brain Sciences, Dartmouth College, Center for Cognitive Neuroscience, Dartmouth College, Department of Experimental Psychology, University of Magdeburg 12:00-12:15 (15min) › Lessons learned from neuroimaging tool development in Python - Stephan Gerhard, EPFL Signal Processing Lab 5 12:15-12:30 (15min) Lunch 12:30 - 13:45 (1h15) Lunch IPython tools for time-series analysis and high-level parallel computing 13:45 - 14:30 (45min) IPython tools for time-series analysis and high-level parallel computing Fernando Perez visualization tools 14:30 - 15:15 (45min) visualization tools Dussane Gaël Varoquaux › Anatomist: a python framework for interactive 3D visualization of neuroimaging data - Yann Cointepas, LNAO, NeuroSpin, CEA 14:30-15:00 (30min) › 3D Brain Atlas Reconstructor and Common Atlas Format, the infrastructure for constructing tree dimensional brain atlases - Piotr Majka, Departament of Neurophysiology, Nencki Institute of Experimental Biology 15:00-15:15 (15min)

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