Padraig Gleeson OSB Workshop 2014

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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

Transcript of Padraig Gleeson OSB Workshop 2014

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    Version control & GitHubVersion 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

    GitHubMost popular open source code sharing websiteSocial coding

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    http://www.opensourcebrain.orgHub and Spoke architecture

  • http://www.opensourcebrain.org

  • http://www.opensourcebrain.org

  • http://www.opensourcebrain.org

  • http://www.opensourcebrain.org

  • http://www.opensourcebrain.org

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    NeuroMLStandardised XML language for computational neuroscience

    Version 1.x allowed specification of:Detailed neuronal morphologiesIon channelsSynapses3D network structure

    30+ simulators/applications/databases/libraries support NeuroML

    http://www.opensourcebrain.org

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    CellsChannels/SynapsesNetwork

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    NEURONGENESISMOOSEPSICSNeuroSpacesPyNNneuroConstructWhole BrainCatalogLFPyNeurAnimNeuronvisioMoogliNeuronLandTREES toolboxNeuGenNeuroMorphoChannelpediaOpenWormTrakEMCX3D

    http://www.opensourcebrain.org

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    NeuroML v2.0 & LEMSExample model: current through a passive channel

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    NeuroML v2.0 & LEMSLEMS

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    http://www.opensourcebrain.org

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    http://www.opensourcebrain.org

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    http://www.opensourcebrain.org

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  • OSBModelRepositoryCollaborative development

  • BioModels

    OSBModelRepositorySearchModelDB

    ProjectsModellersVisualisationTestingValidationAnnotationConversionPyNNSimulatorsFeedback from the CommunitySimulators

  • 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

    http://www.opensourcebrain.org

    ****04/20/12*******