Neuronvisio codejam5

749 views

Published on

Published in: Technology
  • Be the first to comment

  • Be the first to like this

Neuronvisio codejam5

  1. 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. 2. Every good work of software starts byscratching a developer’s personal itch. Eric S. Raymond - The Cathedral and the Bazaar
  3. 3. Intro
  4. 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. 5. Neuronvisio was born 0.1.0 - 30 Jun 2009 0.8.1 – 19 Mar 2012We still dont have a logo =)
  6. 6. /Intro
  7. 7. Get Started
  8. 8. Run from an ipython session
  9. 9. Adding Vectors to record the model
  10. 10. /Get Started
  11. 11. Visualization
  12. 12. Matplotlib integration
  13. 13. Mayavi magic =)
  14. 14. Point and click
  15. 15. http://www.youtube.com/watch?v=LOuptLKZ5rU
  16. 16. http://www.youtube.com/watch?v=FWpBVxY6q7I
  17. 17. /Visualization
  18. 18. ModelDB
  19. 19. ● Download the model● Unzip the model● Compiles the mod files● Load the model in the current session
  20. 20. CreditsPull-Request by Uri Cohen
  21. 21. /ModelDB
  22. 22. STORAGE
  23. 23. Technology● Data --> Numerical array● Data --> Geometry (NeuroML) HDF
  24. 24. Current HDF designNeuroML Numerical ArrayNumerical Array: time
  25. 25. Extending the class to store other vectors
  26. 26. Reloading file
  27. 27. /STORAGE
  28. 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

×