#Optimizer Optimizer is a graphical tool for the optimization of Neuronal Models
Install git and type:
git clone https://github.com/pfriedrich/optimizer.git
More information on this here: http://rogerdudler.github.com/git-guide/
The following python libraries are required:
- python
- numpy
- scipy
- matplotlib
- wxPython
- inspyred
- pyelectro
The following libraries are recommended:
- neuron
You can get numpy, scipy and inspyred with easy_install or pip with the following command (for numpy):
pip install numpy
or
easy_install install numpy
You can get matplotlib with the following command:
apt-get install python-matplotlib
If you encounter any difficulties you can find a more detailed description at:
http://matplotlib.org/users/installing.html
You can get wxpython with the following command:
apt-get install python-wxgtk2.8 python-wxtools wx2.8-i18n
This command might not work if your OS has an earlier version in the standard software repository. If so, please follow the instructions at:
http://wiki.wxpython.org/InstallingOnUbuntuOrDebian
You can get pyelectro from:
https://github.com/vellamike/pyelectro.git
After cloning the repository you can install it by the standard installation method:
python setup.py install
Installing Neuron as a python package is optional since Optimizer can use any executable to run the simulations. WARNING: Optimizer was built around Neuron so we reccomend to install it! Installing Neuron as a python package is beyond the scope of this tutorial as it is somewhat complicated, but you can find a step-by-step guide at:
http://www.davison.webfactional.com/notes/accessing-hoc-python/
Use the standard install method for Python packages:
sudo python setup.py install
You can run optimizer directly from its installation folder with:
python optimizer.py -g
Or for the command line version (you must specify a configuration file as well):
python optimizer.py -c example.xml
To build a local copy of documentation you need a working install of Sphinx, then run the command:
sphinx-build ./doc <local build directory>
from the top-level optimizer directory where should be replaced with a custom filepath.
The package was tested on the following systems:
1. Mandriva 2010.2 (kernel 2.6.33, glibc 2.11)
- python 2.6.5
- numpy 1.6.2
- scipy 0.7.2
- matplotlib 1.1.1
- wxPython 2.8.10.1
- inspyred 1.0
- pyelectro
- neuron 7.3
2. CentOS 6.4 (kernel 2.6.32, glibc 2.12)
- python 2.6.6
- numpy 1.6.1
- scipy 0.10.1
- matplotlib 1.3.1
- wxPython 2.8.12.0
- inspyred 1.0
- pyelectro
- neuron 7.2
3. Ubuntu 12.04.3 LTS (kernel 3.2.0-54-generic, glibc 2.15)
- Python 2.7.3
- numpy 1.7.0
- scipy 0.11.0
- matplotlib 1.1.1rc
- wxPython 2.8.12.1
- inspyred 1.0
- pyelectro
- neuron 7.2
Notes
- Since Neuron with the python interpreter is not working perfectly on Windows, we recommend to use Ubuntu (installing and setting up a virtual os is not hard).
- inspyred requires a feature which is only included in python 2.7, but ther is a workaround for this problem: https://groups.google.com/forum/#!topic/inspyred/YwJb3ABVtL8
Project Leader:
- Szabolcs Káli:
kali@koki.hu
Lead Developer:
- Peter Friedrich:
p.friedrich.m@gmail.com
Contributors:
- Mike Vella