This document is a tutorial for the Neuronvisio software. It provides an overview of the software, including how to visualize and interact with neuron models, plot simulation results, and integrate the software into other code. The tutorial describes how to save simulation results for later analysis and explores the software's website, documentation, and open source code availability. It concludes by offering a live demo of the Neuronvisio software.

1. Introduction
Software
Neuronvisio Tutorial
Michele Mattioni
mattioni@ebi.ac.uk
EMBL-EBI and University of Cambridge
06 March 2010
Michele Mattioni Neuronvisio Tutorial

2. Introduction
Software
Outline
1 Introduction
Background
2 Software
How to use it
Where to get it
Michele Mattioni Neuronvisio Tutorial

3. Introduction
Background
Software
Outline
1 Introduction
Background
2 Software
How to use it
Where to get it
Michele Mattioni Neuronvisio Tutorial

4. Introduction
Background
Software
Why I built it
Eric S. Raymond - The Cathedral and the Bazaar
Every good work of software starts by scratching a developer’s
personal itch.
Michele Mattioni Neuronvisio Tutorial

5. Introduction How to use it
Software Where to get it
Outline
1 Introduction
Background
2 Software
How to use it
Where to get it
Michele Mattioni Neuronvisio Tutorial

6. Introduction How to use it
Software Where to get it
At glance
Michele Mattioni Neuronvisio Tutorial

7. Introduction How to use it
Software Where to get it
Visualize a model
It is possible to zoom, rotate and move the model.
Michele Mattioni Neuronvisio Tutorial

8. Introduction How to use it
Software Where to get it
Plot the results
Michele Mattioni Neuronvisio Tutorial

9. Introduction How to use it
Software Where to get it
Explore the timecourse of a variable
Michele Mattioni Neuronvisio Tutorial

10. Introduction How to use it
Software Where to get it
How to integrate in your code
Figure: Python Model integration
Figure: Hoc Model integration
Michele Mattioni Neuronvisio Tutorial

11. Introduction How to use it
Software Where to get it
Controls window
Michele Mattioni Neuronvisio Tutorial

12. Introduction How to use it
Software Where to get it
Saving simulations results
Complex simulations can take ages
Store the results to analyze them later on
Manager class to create the data structure and to remap it
to neuronvisio.
Michele Mattioni Neuronvisio Tutorial

13. Introduction How to use it
Software Where to get it
Saving a simulation from the GUI
Michele Mattioni Neuronvisio Tutorial

14. Introduction How to use it
Software Where to get it
Integrating that with you cluster’ simulations
Michele Mattioni Neuronvisio Tutorial

15. Introduction How to use it
Software Where to get it
Website and Docs
http://mattions.github.com/neuronvisio/
Michele Mattioni Neuronvisio Tutorial

16. Introduction How to use it
Software Where to get it
Source code
Latest available
Version 0.4.3
Download http://pypi.python.org/pypi/neuronvisio/
Website http://mattions.github.com/neuronvisio/
The code is under GPL3.
On the website there are the instruction to install the
dependencies
Michele Mattioni Neuronvisio Tutorial

17. Introduction How to use it
Software Where to get it
Source code
Latest available
Version 0.4.3
Download http://pypi.python.org/pypi/neuronvisio/
Website http://mattions.github.com/neuronvisio/
The code is under GPL3.
On the website there are the instruction to install the
dependencies
Hacking
The current code in development is available from github
git clone git://github.com/mattions/neuronvisio.git
Michele Mattioni Neuronvisio Tutorial

18. Introduction How to use it
Software Where to get it
That’s all folks
The indecent proposal...
Do you want to see a live demo? :)
Michele Mattioni Neuronvisio Tutorial