Neuronvisio is a graphical user interface for the NEURON simulator that allows users to: 1) Streamline investigation of NEURON models. 2) Visualize NEURON models in 3D. 3) Save results of long simulations for post-simulation analysis. It handles common tasks like creating vectors to record variables and plotting variables. Data is stored using HDF5 for numerical arrays and geometry. The software is open source and available on GitHub.

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