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Padraig Gleeson OSB Workshop 2014

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.

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Padraig Gleeson OSB Workshop 2014

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  1. http://www.opensourcebrain.org Enabling sharing & collaborative development of models in computational neuroscience Padraig Gleeson OSB Workshop 2014

  2. Thanks to our sponsors

  3. Overview Open Source Brain NeuroML v2.0 & LEMS Collaborative Modelling http://www.opensourcebrain.org

  4. http://www.opensourcebrain.org 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

  5. Models available on OSB Basal Ganglia Blackwell et al (in press) Medium Spiny Neuron Cerebellum Maex and Schutter (1998) Granule cell layer Steuber and Saviane, based on Berends et al. (2005) Granule cell Vervaeke et al. (2010) Golgi cell network Solinas et al. (2007a,b) Granule cell, Golgi cell De Schutter and Bower (1994) Purkinje cell Steuber et al. (2011) Cerebellar nucleus neuron Neocortex Mainen et al. (1995) L5 Pyramidal cell Rothman et al. (2010) L5 Pyramidal cell Hay et al (2011) L5 Pyramidal cell Traub 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 Abstract neuron models Izhikevich (2003) Morris & Lecar (1981) FitzHugh & Nagumo (1969) Hippocampus Migliore et al. (2005) CA1 Pyramidal cell Thalamus Traub et al. (2005) Thalamocortical relay cell, Nucleus reticularis thalami cell C elegans OpenWorm project 302 cell connectome

  6. Version control & GitHub “Version control is as fundamental to programming as accurate notes about lab procedures are to experimental 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”

  7. “Hub and Spoke” architecture http://www.opensourcebrain.org

  8. http://www.opensourcebrain.org

  9. http://www.opensourcebrain.org

  10. http://www.opensourcebrain.org

  11. http://www.opensourcebrain.org

  12. http://www.opensourcebrain.org

  13. http://www.opensourcebrain.org 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

  14. Cells Channels/ Synapses Network

  15. http://www.opensourcebrain.org NEURON GENESIS MOOSE PSICS NeuroSpaces PyNN neuroConstruct OpenWorm LFPy TrakEM Whole Brain Catalog NeurAnim Neuronvisio NeuronLand Moogli TREES toolbox NeuGen NeuroMorpho Channelpedia CX3D

  16. NeuroML v2.0 & LEMS Example model: current through a passive channel

  17. NeuroML v2.0 & LEMS LEMS

  18. http://www.opensourcebrain.org

  19. http://www.opensourcebrain.org

  20. http://www.opensourcebrain.org

  21. Collaborative development OSB Model Repository

  22. BioModels Search ModelDB Annotation Visualisation Modellers OSB Model Repository Conversion PyNN Projects Testing Feedback from the Community Validation Simulators Simulators

  23. http://www.opensourcebrain.org 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 Members of the NeuroML community OpenWorm project UK INCF Node Funding source:

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