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.
For an overview of the workflow and its main concepts, see the previous Synaptic Events Fitting documentation. Please note that some implementation details may differ from the current widget.
Additional CLSI widgets and workflows will be added to this repository in future releases.
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.
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
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()
- 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