NeuronVisio is a Graphical User Interface for NEURON simulator enviroment
Project description
NeuronVisio
===========
What is it
----------
NeuronVisio is a Graphical User Interface for `NEURON simulator enviroment
<http://www.neuron.yale.edu/neuron/>`_.
NeuronVisio connect with NEURON using the new python NEURON interface.
Features
--------
- 3D visualization of the model with the possibility to change it runtime
- Creation of vectors to record any variables present in the section
- Pylab integration to plot directly the result of the simulation
- Exploration of the timecourse of any variable among time using a color
coded scale
- the GUI runs in its own thread so it's possible to use the console (strongly suggested to run through ipython)
Installation
============
To install NeuronVisio you need to satisfy the following dependencies
- pygtk: http://www.pygtk.org/
- visual: http://vpython.org/
- matplotlib: http://matplotlib.sourceforge.net/
and of course NEURON_
.. _NEURON: http://www.neuron.yale.edu/neuron/
Easy Install
------------
The easiest way to get neuronvisio is if you have setuptools_ installed::
easy_install neuronvisio
Without setuptools, it's still pretty easy. Download the neuronvisio.tgz file from
`neuronvisio's Cheeseshop page`_, untar it and run::
python setup.py install
.. _neuronvisio's Cheeseshop page: http://pypi.python.org/pypi/neuronvisio/
.. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall
Documentation
=============
The documentation is available in the doc folder or online_ or in pdf format in the docs direcotry
.. _online: http://mattions.github.com/neuronvisio
Quickstart
==========
This code is just to give an idea in how to use nrnvisio module:
1. fire up an ipython console with pylab switch.::
ipython -pylab # If you don't use the switch you will not see any graph.
2. Import the module::
from neuronvisio.controls import Controls
controls = Controls()
When nrnvisio is started the thread is launched. In this thread all the process of
nrnvisio will happen without blocking the console.
As a quick example the following code:
1. Creates a single section called soma
2. Insert an Hodgkey-Huxley channel and a passive conductance
3. Insert an alphaSynapse to provide a stimul.
A quick example can be the following:::
from nrnvisio.controls import Controls
controls = Controls() # Starting the GUI
from neuron import h # Getting the HocInterpreter
soma = h.Section() # Creating a section
soma.insert('hh') # Inserting a HH channel
soma.insert('pas') # inserting a passive conductance
syn = h.AlphaSynapse(0.5, sec=soma) # synaptic input
syn.onset = 0.5 # when to fire
syn.gmax = 0.05 # the conductance of the synapse
syn.e = 0 # the reversal potential
More example in the example directory show how to use Neuronvisio with more
complex model.
Contacts
========
Homepage: http://mattions.github.com/neuronvisio/
Mailing List: http://groups.google.com/group/neuronvisio
Help and development
====================
If you'd like to help out, you can fork the project
at http://github.com/mattions/neuronvisio and report any bugs
at http://github.com/mattions/neuronvisio/issues.
===========
What is it
----------
NeuronVisio is a Graphical User Interface for `NEURON simulator enviroment
<http://www.neuron.yale.edu/neuron/>`_.
NeuronVisio connect with NEURON using the new python NEURON interface.
Features
--------
- 3D visualization of the model with the possibility to change it runtime
- Creation of vectors to record any variables present in the section
- Pylab integration to plot directly the result of the simulation
- Exploration of the timecourse of any variable among time using a color
coded scale
- the GUI runs in its own thread so it's possible to use the console (strongly suggested to run through ipython)
Installation
============
To install NeuronVisio you need to satisfy the following dependencies
- pygtk: http://www.pygtk.org/
- visual: http://vpython.org/
- matplotlib: http://matplotlib.sourceforge.net/
and of course NEURON_
.. _NEURON: http://www.neuron.yale.edu/neuron/
Easy Install
------------
The easiest way to get neuronvisio is if you have setuptools_ installed::
easy_install neuronvisio
Without setuptools, it's still pretty easy. Download the neuronvisio.tgz file from
`neuronvisio's Cheeseshop page`_, untar it and run::
python setup.py install
.. _neuronvisio's Cheeseshop page: http://pypi.python.org/pypi/neuronvisio/
.. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall
Documentation
=============
The documentation is available in the doc folder or online_ or in pdf format in the docs direcotry
.. _online: http://mattions.github.com/neuronvisio
Quickstart
==========
This code is just to give an idea in how to use nrnvisio module:
1. fire up an ipython console with pylab switch.::
ipython -pylab # If you don't use the switch you will not see any graph.
2. Import the module::
from neuronvisio.controls import Controls
controls = Controls()
When nrnvisio is started the thread is launched. In this thread all the process of
nrnvisio will happen without blocking the console.
As a quick example the following code:
1. Creates a single section called soma
2. Insert an Hodgkey-Huxley channel and a passive conductance
3. Insert an alphaSynapse to provide a stimul.
A quick example can be the following:::
from nrnvisio.controls import Controls
controls = Controls() # Starting the GUI
from neuron import h # Getting the HocInterpreter
soma = h.Section() # Creating a section
soma.insert('hh') # Inserting a HH channel
soma.insert('pas') # inserting a passive conductance
syn = h.AlphaSynapse(0.5, sec=soma) # synaptic input
syn.onset = 0.5 # when to fire
syn.gmax = 0.05 # the conductance of the synapse
syn.e = 0 # the reversal potential
More example in the example directory show how to use Neuronvisio with more
complex model.
Contacts
========
Homepage: http://mattions.github.com/neuronvisio/
Mailing List: http://groups.google.com/group/neuronvisio
Help and development
====================
If you'd like to help out, you can fork the project
at http://github.com/mattions/neuronvisio and report any bugs
at http://github.com/mattions/neuronvisio/issues.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
neuronvisio-0.4.1.tar.gz
(1.1 MB
view hashes)