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

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

3. Conventional model development Experiment Implement the model and tune it Publish 0.10.20.31.0... Clean up

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

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

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

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