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Enabling sharing & collaborative development of models in computational neuroscience. Padraig Gleeson OSB Workshop 2014. Thanks to our sponsors. Overview. Open Source Brain NeuroML v2.0 & LEMS Collaborative Modelling. http://www.opensourcebrain.org. The Open Source Brain Repository. - PowerPoint PPT Presentation
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Padraig GleesonOSB Workshop 2014
Enabling sharing & collaborative development of models in computational neuroscience
Thanks to our sponsors
Overview
Open Source Brain
NeuroML v2.0 & LEMS
Collaborative Modelling
The Open Source Brain Repository
Wellcome Trust funded project
Open source model development repository for computational neuroscience
Structured database of well tested spiking neuron & network models in standardised formats
Allow anyone to comment on, extend, reuse models & run them across multiple simulators: a collaboration platform
Uses tools & best practices from Open Source software development
Models available on OSB
NeocortexMainen et al. (1995)
L5 Pyramidal cellRothman et al. (2010)
L5 Pyramidal cellHay et al (2011)
L5 Pyramidal cellTraub et al. (2005)
L2/3 Pyr (FRB/RS), L4SS, L5 Pyr (IB/RS), L6 Pyr,Deep & superficial basket, axo-axonic & LTS interneurons,Cortical column network model
CerebellumMaex and Schutter (1998)
Granule cell layerSteuber and Saviane, based on Berends et al. (2005)
Granule cellVervaeke et al. (2010)
Golgi cell networkSolinas et al. (2007a,b)
Granule cell, Golgi cellDe Schutter and Bower (1994)
Purkinje cellSteuber et al. (2011)
Cerebellar nucleus neuron
Basal GangliaBlackwell et al (in press)
Medium Spiny Neuron
ThalamusTraub et al. (2005)
Thalamocortical relay cell,Nucleus reticularis thalami cell
HippocampusMigliore et al. (2005)
CA1 Pyramidal cell
Abstract neuron modelsIzhikevich (2003)Morris & Lecar (1981)FitzHugh & Nagumo (1969)
C elegans
OpenWorm project302 cell connectome
Version control & GitHub
“Version control is as fundamental to programmingas accurate notes about lab procedures are toexperimental science”(G. Wilson, 2006. Where's the Real Bottleneck in Scientific Computing?)
CVS → SVN → Mercurial/Git
GitHub– Most popular open source code sharing website– “Social coding”
“Hub and Spoke” architecture
NeuroML
Standardised XML language for computational neuroscience
Version 1.x allowed specification of:– Detailed neuronal morphologies– Ion channels– Synapses– 3D network structure
30+ simulators/applications/databases/libraries support NeuroML
Cells
Channels/Synapses
Network
http://www.opensourcebrain.org
NEURON GENESIS MOOSE PSICS NeuroSpaces
PyNN neuroConstruct
Whole BrainCatalog
LFPy
NeurAnimNeuronvisio Moogli NeuronLand
TREES toolbox
NeuGenNeuroMorpho Channelpedia
OpenWorm TrakEM
CX3D
NeuroML v2.0 & LEMS
Example model: current through a passive channel
NeuroML v2.0 & LEMS
LEMS
http://www.opensourcebrain.org
OSBModel
Repository
Collaborative development
BioModels
OSBModel
Repository
Search
ModelDB
Projects
Modellers
Visualisation
Testing
Validation
Annotation
Conversion
PyNN
Simulators
Feedback from the Community
Simulators
Acknowledgements Silver Lab @ UCL
Angus Silver
Eugenio Piasini
Boris Marin
Adrian Quintana
Matteo Farinella
Yates Buckley
Matteo Cantarelli
Main Collaborators Robert Cannon
Sharon Crook
Mike Vella
Early Adopters Sergio Solinas
Egidio D'Angelo
Volker Steuber
Dieter Jaeger
Andrew Davison
Stephen Larson
Avrama Blackwell
Nicolas Le Novere
Funding source:
Members of the NeuroML community
OpenWorm project
UK INCF Node