#Optimizer Optimizer is a graphical tool for fitting the parameters of neuronal models
Install git and type:
git clone https://github.com/KaliLab/optimizer.git
More information on this here: http://rogerdudler.github.com/git-guide/
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/
Use the standard install method for Python packages:
sudo python setup.py install
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
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.
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).
Project Leader:
- Szabolcs Káli:
[email protected]
Lead Developer:
- Máté Mohácsi
[email protected]
- Sára Sáray
[email protected]
- Márk Török Patrik
[email protected]
- Peter Friedrich:
[email protected]
Contributors:
- Mike Vella