#Neuroptimus Neuroptimus is a graphical tool for fitting the parameters of neuronal models
Install git and type:
git clone https://github.com/KaliLab/neuroptimus.git
The following python libraries are required:
- python
- numpy
- eFEL
- matplotlib
The following libraries are recommended:
- neuron
- scipy
- PyQt5
- inspyred (install from github, see below)
- pyelectro
- Pygmo
- bluepyopt
- ipyparallel
- nest
You can get required or recommended libraries with the following command:
pip install -r requirements_minimal.txt
or
pip install -r requirements_full.txt
You can get individual package with pip:
pip install neuron
For the latest inspyred version:
pip install git+https://github.com/aarongarrett/inspyred
You can run Neuroptimus (with a GUI) directly from its installation folder with:
python neuroptimus.py -g
Or for the command line version (you must specify a configuration file as well):
python neuroptimus.py -c example.xml
If you should require a local copy of the Neuroptimus documentation, you need a working install of Sphinx, then run the command:
sphinx-build ./doc <local build directory>
from the top-level neuroptimus 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)
Project Leader:
- Szabolcs Káli:
[email protected]
Lead Developer:
- Máté Mohácsi
[email protected]
- Sára Sáray
[email protected]
- Márk Török Patrik
[email protected]