CLSI Widgets

Description

clsi-widgets is a collection of reusable interactive widgets developed for CLSI scientific workflows.

The first workflow included in this package is the Synaptic Events Fitting widget. It supports fitting synaptic events using experimental data and computational models.

Additional CLSI widgets and workflows will be added to this repository in future releases.

Installation

To install clsi-widgets from a local clone of the repository in development mode, run:

pip install -e ".[test]"

To install the optional dependency required for local best-fit analysis with NEURON, run:

pip install -e .[neuron]

Please note that installation of neuron from PyPI may not work on all operating systems. For Windows, NEURON should be installed separately using the official Windows installer.

JupyterLab

To use the widgets in JupyterLab, make sure JupyterLab is installed in the same Python environment:

pip install jupyterlab

Then start JupyterLab:

jupyter lab

The maintained Synaptic Events Fitting notebook is: notebooks/SynapticEventsFitting.ipynb

EBRAINS authentication

Some features require authentication with EBRAINS services. If you are running locally, set the CLB_AUTH environment variable before launching JupyterLab:

export CLB_AUTH="{Your TokenString copied from EBRAINS Collab}"

To retrieve the token string, run the following command in the EBRAINS JupyterLab environment (https://lab.ebrains.eu/):

clb_oauth.get_token()

Contributors

• Carmen Alina Lupascu, carmen.lupascu@ibf.cnr.it
• Roberto Smiriglia, roberto.smiriglia@ibf.cnr.it
• Luca Leonardo Bologna, lucaleonardo.bologna@cnr.it
• Dario Curreri, dario.curreri@ibf.cnr.it