Neuronvisio codejam5
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Neuronvisio codejam5 Presentation Transcript

  • 1. Neuronvisio - A Graphical UserInterface for NEURON SimulatorenviromentMichele Mattionimattioni@ebi.ac.ukhttp://www.ebi.ac.uk/~mattioni@mattions CodeJam 5 -- Edinburgh EBI is an Outstation of the European Molecular Biology Laboratory.
  • 2. Every good work of software starts byscratching a developer’s personal itch. Eric S. Raymond - The Cathedral and the Bazaar
  • 3. Intro
  • 4. My Needs● Streamline a NEURON model investigation● Visualize in 3D a NEURON model● Save results of long running simulations in a format to allow post-simulation investigation● Take care of all the classic boilerplate actions: ● create HocVectors to record variable in sections ● make easier to plot variables Design
  • 5. Neuronvisio was born 0.1.0 - 30 Jun 2009 0.8.1 – 19 Mar 2012We still dont have a logo =)
  • 6. /Intro
  • 7. Get Started
  • 8. Run from an ipython session
  • 9. Adding Vectors to record the model
  • 10. /Get Started
  • 11. Visualization
  • 12. Matplotlib integration
  • 13. Mayavi magic =)
  • 14. Point and click
  • 15. http://www.youtube.com/watch?v=LOuptLKZ5rU
  • 16. http://www.youtube.com/watch?v=FWpBVxY6q7I
  • 17. /Visualization
  • 18. ModelDB
  • 19. ● Download the model● Unzip the model● Compiles the mod files● Load the model in the current session
  • 20. CreditsPull-Request by Uri Cohen
  • 21. /ModelDB
  • 22. STORAGE
  • 23. Technology● Data --> Numerical array● Data --> Geometry (NeuroML) HDF
  • 24. Current HDF designNeuroML Numerical ArrayNumerical Array: time
  • 25. Extending the class to store other vectors
  • 26. Reloading file
  • 27. /STORAGE
  • 28. Its on Githubrepo: http://github.com/mattions/neuronvisiodocs: http://mattions.github.com/neuronvisio/issues: https://github.com/mattions/neuronvisio/issuesML: http://groups.google.com/group/neuronvisioExamples:https://github.com/mattions/neuronvisio/tree/master/examples