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Padraig Gleeson CodeJam workshop, 28th January 2014
Enabling sharing & collaborative development of models in computational neuroscience Padraig Gleeson CodeJam workshop, 28th January 2014
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Current model development life-cycle
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Current model development life-cycle
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How can we make computational neuroscience more scientific?
Reproducibility: easy to rerun and validate simulation result reported in a scientific paper Accessibility: available to theoretical and experimental neuroscientists in an understandable format Portability: cross-simulator validation and exchange of models and components enabling reuse Transparency: exposure of internal properties and automated validation 4
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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
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OSB development scenario
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Models available on OSB
Basal Ganglia Blackwell et al (in press) Medium Spiny Neuron Neocortex Mainen et al. (1995) L5 Pyramidal cell Rothman et al. (2010) Hay et al (2011) 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 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 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 8
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“So why not just use GitHub?”
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“Hub and Spoke” architecture
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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
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04/20/12 Cells Channels/ Synapses Network 32
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NEURON GENESIS MOOSE PSICS NeuroSpaces PyNN neuroConstruct OpenWorm
LFPy TrakEM Whole Brain Catalog Neuronvisio NeuronLand NeurAnim Moogli TREES toolbox NeuroMorpho Channelpedia NeuGen CX3D
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NeuroML v2.0 & LEMS
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NeuroML v2.0 & LEMS
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Wider interoperability framework
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(most activity in development branches)
(most activity in development branches)
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Channel density distribution on Purkinje cell
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How can we make computational neuroscience more scientific?
Reproducibility: easy to rerun and validate simulation result reported in a scientific paper Accessibility: available to theoretical and experimental neuroscientists in an understandable format Portability: cross-simulator validation and exchange of models and components enabling reuse Transparency: exposure of internal properties and automated validation 48
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Acknowledgements Silver Lab @ UCL Members of the NeuroML community
Angus Silver Eugenio Piasini Boris Marin 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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