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WORKSHOP 4 Open collaboration in computational neuroscience

WORKSHOP 4 Open collaboration in computational neuroscience. Chair: Angus Silver University College London INCF - Neuroinformatics 2014. How can we scale up models of brain function and make models more accurate and reproducible?. Sensations. Input about the body and world.

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WORKSHOP 4 Open collaboration in computational neuroscience

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  1. WORKSHOP 4 Open collaboration in computational neuroscience Chair: Angus Silver University College London INCF - Neuroinformatics 2014 http://www.opensourcebrain.org

  2. How can we scale up models of brain function and make models more accurate and reproducible? Sensations Input about the body and world Electrical Actions Chemical Cognition 100 billion neurons 100 trillion synapses Neuronal classes Synaptic types Specialized networks

  3. Conventional model development Implement the model and tune it Experiment Clean up Publish 0.1 0.2 0.3 1.0 ...

  4. Requirements I: A culture change –collaborative development Publish Update Update Update Update Merge Merge t 1.0 1.1 1.2 ... 1.1.3 1.1.1 1.1.1.1 1.1.1.2 LAB A LAB B LAB C

  5. Requirements II: datasets, tools, standardization, and open scientific evaluation Datasets Standardized model descriptions NeuroMorpho SBML, CellML, NineML, SpineML Accessibility and critical evaluation Tools for collaborative model development Open source development tools- GitHub Simulators – e.g. Neuron, Brian Applications – e.g. neuroConstruct, Neurokernel, NeuronUnit Open Source Brain ModelDB, BioModels etc

  6. Pros and Cons of open development and collaboration in neuroinformatics Potential Benefits • Scaling up of modeled systems • Continuity of projects • Improved community resources • Development of integrated tool chain • Improved scientific value through improved : • Reproducibility, • Accessibility, • Portability • Transparency Difficulties/Issues • Neuroscience is a competitive system. • Vested interests - can we change the prevailing culture? • Big investment to develop the tool chain. • How will quality be ensured? • Will the efforts of the developers be adequately recognized? • Are computational neuroscientists ready to expose all the flaws of a model to public scrutiny?

  7. WORKSHOP 4 Open collaboration in computational neuroscience 10:20 Introduction : Angus Silver, UCL, UK 10:30OpenWorm - Stephen Larson, MetaCell, USA 10:50Open Source Brain - Padraig Gleeson, UCL, UK 11:10NeuronUnit & NeuroElectro - Rick Gerkin, Carnegie Mellon University, USA &Shreejoy Tripathy, University of British Columbia, Canada 11:35NeuroKernel - Aurel A. Lazar, Columbia University, USA 11:55Conclusions/Discussion

  8. Open collaboration in computational neuroscience Discussion – how to address the issues...? • Neuroscience is a competitive system. • Vested interests - can we change the prevailing culture? • Big investment to develop the tool chain. • How will quality be ensured? • Will the efforts of the developers be adequately recognized? • Are computational neuroscientists ready to expose all the flaws of a model to public scrutiny?

  9. Modelling brain function at different spatial scales Brain Network Neuron Biologically accurate multi-scale models of brain function. Synapse Molecular assemblies Genes

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