Merge branch 'development' into experimental

* development: (45 commits)
  Fix typo
  feat: use values from text boxes for simulation
  Add note that current is in pA also...
  Tweak main readme
  Update README.md
  Image updates & text clarifications
  New circuit image & updated text
  Changing reversal potentials of Na and K to match NEURON tutorial
  Renamed I_inj_amplitude etc. to use delay/duration/amplitude
  Restructure notebook, more info in readme
  Fix image link
  Improved vclamp memory handling
  Reduce size of arrays (increase dt) for vclamp
  Move main python code from notebook to method launch_interactive_widget()
  Adding plot for conductance densities of Na and K
  Adding test on python hh example, by saving results to file
  Notebook updates
  Adding readmes and an image of the interactive notebook
  Extra requirement
  Add requirements file, initial update notebook
  ...

Author: pgleeson

.github/workflows/non-omv.yml

@@ -26,4 +26,5 @@ jobs:
       run: |
         pip install scipy matplotlib
         cd Tutorial/Source
-        python HodgkinHuxley.py
+        python HodgkinHuxley.py # test in current clamp mode
+        python HodgkinHuxley.py -vclamp # test in voltrage clamp mode

.github/workflows/omv-ci.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [ 3.7, 3.9 ]
-        engine: [ jNeuroML_Brian2, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate, jNeuroML_PyNN_NEURON ]
+        engine: [ jNeuroML_Brian2, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate, jNeuroML_PyNN_NEURON, Brian2 ]
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -36,3 +36,5 @@ Tutorial/Source/*json
 *code.gen.*
 *_eden.py
 **/.ipynb_checkpoints/
+/Tutorial/Source/HHCellNetwork.net.nml__flattened.xml
+/notebooks/Python_HH_version/hh_py_v.dat

README.md

@@ -1,8 +1,8 @@
 ## Hodgkin Huxley Tutorials
 
-This repository contains the code for 2 related tutorials on the Hodgkin Huxley model
+This repository contains the code for a number of related tutorials on the Hodgkin Huxley model
 
-### Tutorial 1: HH model in Python and NeuroML
+### Tutorial 1A: HH model in Python and NeuroML
 
 *Target audience: those who want to learn how to implement the HH model*
 
@@ -12,13 +12,23 @@ This was originally created by [@joebowen](https://github.com/joebowen) on behal
 
 The latest version of the tutorial is visible [online at ReadTheDocs](http://hodgkin-huxley-tutorial.readthedocs.org/en/latest/).
 
+### Tutorial 1B: Interactive introduction to the HH model in a Jupyter notebook
+
+*Target audience: those who want to simulate the HH model using an interactive Python based web notebook*
+
+This interactive [Jupyter notebook](https://jupyter.org/) can be used to run the Python version of the HH model from above, change the parameters of the model and display the dynamical properties of variables, without the need to write any code.
+
+<p align="center"><kbd><a href="notebooks/Python_HH_version/README.md"><img src="https://raw.githubusercontent.com/openworm/hodgkin_huxley_tutorial/master/notebooks/HH_Jupyter.png" width="600"/></kbd></p>
+
+Full details can be found [here](notebooks/Python_HH_version/README.md). This work was carried out as part of [Google Summer of Code 2022 by Rahul Sonkar](notebooks/GSoC_2022_Submission/GSoC_Documentation.md).
+
 ### Tutorial 2: Interactive introduction to the HH model on Open Source Brain
 
 *Target audience: those who want to learn the basics of the HH model through running in-browser simulations*
 
-This tutorial also uses the NeuroML model from above, but provides a high level introduction to the concepts of the model (as well as computational modelling in neuroscience). 
+This tutorial also uses the NeuroML model from above, but provides a high level introduction to the concepts of the model (as well as computational modelling in neuroscience).
 
-It can be accessed on the Open Source Brain site at this location: http://www.opensourcebrain.org/tutorials. It is built on the [Geppetto platform](http://www.geppetto.org/), which was also initially developed in the OpenWorm project. 
+It can be accessed on the Open Source Brain site at this location: http://www.opensourcebrain.org/tutorials. It is built on the [Geppetto platform](http://www.geppetto.org/), which was also initially developed in the OpenWorm project.
 
 ![HH](https://raw.githubusercontent.com/openworm/hodgkin_huxley_tutorial/master/Tutorial2/NeuroML2/images/HH_OSB.png)
 
@@ -29,10 +39,7 @@ See also http://www.opensourcebrain.org/projects/hodgkin-huxley-tutorial.
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1493456.svg)](https://doi.org/10.5281/zenodo.1493456)
 
 
+
 ### Reusing this model
 
 The code in this repository is provided under the terms of the [software license](LICENSE) included with it. If you use this model in your research, we respectfully ask you to cite the references outlined in the [CITATION](CITATION.md) file.
-
-
-
-