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#Optimizer Optimizer is a graphical tool for fitting the parameters of neuronal models

Installation

Get a read only copy of optimizer

Install git and type:

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

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

Dependencies

The following python libraries are required:

  • python
  • numpy
  • scipy
  • matplotlib
  • PyQt5
  • inspyred
  • pyelectro
  • eFEL
  • Pygmo
  • bluepyopt

The following libraries are recommended:

  • neuron

You can get numpy, scipy, Pygmo, bluepyopt and inspyred with easy_install or pip with the following command (for numpy):

pip install numpy

or

easy_install install numpy

You can get eFEL with pip:

pip install efel

You can get matplotlib with the following command:

Debian / Ubuntu : sudo apt-get install python-matplotlib

Fedora / Redhat : sudo yum install python-matplotlib

or:

pip install matplotlib

If you encounter any difficulties you can find a more detailed description at:

http://matplotlib.org/users/installing.html

You can get pyelectro from:

https://github.com/vellamike/pyelectro.git

or:

pip install pyelectro

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: Many features of Optimizer are designed to work with Neuron, so we recommend that you 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://andrewdavison.info/notes/installation-neuron-python/

Install optimizer

Use the standard install method for Python packages:

sudo python setup.py install

Run optimizer

You can run Optimizer (with a GUI) 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

If you should require a local copy of the Optimizer 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. Ubuntu 14.04.4 LTS 
2. Fedora release 32 (Thirty Two) (neurofedora)

Notes

- Since Neuron with the python interpreter is not working perfectly on Windows, we recommend to use Ubuntu, Mint, or another common Linux distribution (installing and setting up a virtual os is not hard).

Developers

Project Leader:

- Szabolcs Káli:
    kali@koki.hu

Lead Developer:

- Máté Mohácsi
mohacsi.mate@koki.mta.hu

- Sára Sáray
saray.sara@koki.mta.hu

- Márk Török Patrik
torok.mark.patrik@gmail.com

- Peter Friedrich:
    p.friedrich.m@gmail.com

Contributors:

- Mike Vella