1. Neuronvisio - A Graphical User
Interface for NEURON Simulator
enviroment
Michele Mattioni
mattioni@ebi.ac.uk
http://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 by
scratching 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 2012
We still don't have a logo =)

6. /Intro

7. Get Started

8. Run from an ipython session

10. Adding Vectors to record the model

11. /Get Started

12. Visualization

13. Matplotlib integration

15. Mayavi magic =)

16. Point and click

17. http://www.youtube.com/watch?v=LOuptLKZ5rU

18. http://www.youtube.com/watch?v=FWpBVxY6q7I

19. /Visualization

20. ModelDB

22. ● Download the model
● Unzip the model
● Compiles the mod files
● Load the model in the current session

23. Credits
Pull-Request by Uri Cohen

24. /ModelDB

25. STORAGE

26. Technology
● Data --> Numerical array
● Data --> Geometry (NeuroML)
HDF

27. Current HDF design
NeuroML
Numerical Array
Numerical Array: time

28. Extending the class to store other
vectors

29. Reloading file

30. /STORAGE

31. It's on Github
repo: http://github.com/mattions/neuronvisio
docs: http://mattions.github.com/neuronvisio/
issues: https://github.com/mattions/neuronvisio/issues
ML: http://groups.google.com/group/neuronvisio
Examples:
https://github.com/mattions/neuronvisio/tree/master/examples