#Optimizer Optimizer is a graphical tool for the optimization of Neuronal Models

Installation

Get a read only copy of optimizer

Install git and type:

git clone https://github.com/pfriedrich/optimizer.git

More information on this here: http://rogerdudler.github.com/git-guide/

Dependencies

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/

Install optimizer

Use the standard install method for Python packages:

sudo python setup.py install

Run optimizer

To start optimizer, please run the provided neuraloptimizer script, which will start the GUI. Alternatively 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

Build documentation

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.

Test Platforms

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