EBI is an Outstation of the European Molecular Biology Laboratory.

Neuronvisio - A Graphical User Interface for NEURON Simulator enviromentMichele Mattionimattioni@ebi.ac.ukhttp://www.ebi.ac.uk/~mattioni@mattions

CodeJam 5 -- Edinburgh

Every good work of software starts by scratching a developer’s personal itch.

Eric S. Raymond - The Cathedral and the Bazaar

Intro

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

Neuronvisio was born

0.1.0 - 30 Jun 20090.8.1 – 19 Mar 2012

We still don't have a logo =)

/Intro

Get Started

Run from an ipython session

Adding Vectors to record the model

/Get Started

Visualization

Matplotlib integration

Mayavi magic =)

Point and click

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

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

/Visualization

ModelDB

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

Credits

Pull-Request by Uri Cohen

/ModelDB

STORAGE

Technology

● Data --> Numerical array● Data --> Geometry (NeuroML)

HDF

Current HDF design

NeuroMLNumerical Array

Numerical Array: time

Extending the class to store other vectors

Reloading file

/STORAGE

It's on Github

repo: http://github.com/mattions/neuronvisiodocs: http://mattions.github.com/neuronvisio/issues: https://github.com/mattions/neuronvisio/issuesML: http://groups.google.com/group/neuronvisio

Examples:https://github.com/mattions/neuronvisio/tree/master/examples