#Optimizer

A recent fork of Optimizer (an optimization package) by vellamike, which is no longer in active development.

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/russelljjarvis/optimizer.git

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

Dependencies

The following python libraries are required:

• python
• numpy
• scipy
• matplotlib, to be replaced with plotly.
• wxPython
• inspyred
• pyelectro, to be factored out.
• neuroelectro, to be factored in then out.

The following libraries are recommended:

• neuron-7.4 to be factored out

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

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 7.2 (desirable NEURON-7.4)

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 (desirable NEURON-7.4)

3. Ubuntu 14.04.3 LTS 
  - 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 (desirable NEURON-7.4)

  4. Ubuntu 16.04
   - 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-7.4

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 there is a workaround for this problem: https://groups.google.com/forum/#!topic/inspyred/YwJb3ABVtL8

Developers

Contributors:

- Mike Vella