opensourcebrain/HodgkinHuxleyTutorial

1## Jupyter notebook for the Hodgkin Huxley model2 3This is an interactive web notebook using [Jupyter technologies](https://jupyter.org/) which can be used to run the HH model, change the parameters of the model and display the dynamical properties of variables.4 5<p align="center" ><kbd><a href="#running-the-notebook"><img src="../../Tutorial/_media/HH_Jupyter.png" width="600"/></a></kbd></p>6 7This notebook was developed as part of [Google Summer of Code 2022 by Rahul Sonkar](notebooks/GSoC_2022_Submission/GSoC_Documentation.md).8 9## Running the notebook10 11### Option 1) Using Open Source Brain version 212 13*Advantage: you can save any changes you make to the notebook in your [OSBv2 workspace](https://docs.opensourcebrain.org/OSBv2/Overview.html), and view/edit other files associated with the model including the [Python implementation of the HH model](https://github.com/openworm/hodgkin_huxley_tutorial/blob/master/Tutorial/Source/HodgkinHuxley.py).*14 15- Go to [Open Source Brain v2](https://v2.opensourcebrain.org) and [register for a new account](https://docs.opensourcebrain.org/OSBv2/Guided_tour.html#register-sign-in-to-osbv2) and log in.16- Go to the Hodgkin Huxley model repository page at https://v2.opensourcebrain.org/repositories/33.17- Click on **New workspace from selection** (blue button).18- When this has been created, go to the new workspace page and click on **Open with JupyterLab**.19- This opens a copy of all the files in the repository in [JupyterLab](https://docs.opensourcebrain.org/OSBv2/JupyterLab.html#osbv2-applications-jupyterlab).20- In the left had file browser navigate to the folder `Hodgkin Huxley Tutorials/master/notebooks/Python_HH_version` and double click on `Python_Notebook_HH.ipynb` to open the notebook.21- You should be able to run the interactive widget by click the double arrow (&#9654;&#9654;) in the JupyterLab toolbar at the top of the notebook.22- Note: the lighter version of the JupyterLab interface shown above can be accessed in the menu: `Settings -> Theme -> JupyterLab Light`.23 24 25### Option 2) Using Binder26 27*Advantage: quick to start & run, no login required*28 29- The notebook can also be opened using [Binder](https://mybinder.org/). Click here to open the HH notebook: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openworm/hodgkin_huxley_tutorial/master?labpath=notebooks%2FPython_HH_version%2FPython_Notebook_HH.ipynb)30- You should be able to run the interactive widget by click the double arrow (▶▶) in the JupyterLab toolbar at the top of the notebook.31