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

Installation

Get a read only copy of Neuroptimus

Install git and type:

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

Dependencies

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

Run Neuroptimus

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

Build documentation

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.

Test Platforms

The package was tested on the following systems:

1. Ubuntu 14.04.4 LTS 
2. Fedora release 32 (Thirty Two) (neurofedora)

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