opensourcebrain/HodgkinHuxleyTutorial

1.. Hodgkin Huxley LEMS Tutorial documentation master file, created by
2   sphinx-quickstart on Sat Dec 20 13:20:26 2014.
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5
6Welcome to the Hodgkin Huxley Tutorial
7===============================================
8
9This tutorial gives an introduction to the `Hodgkin-Huxley model <https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model>`_ through the use of executable example implementations in Python and `NeuroML <http://www.neuroml.org>`_.
10
11
12**The aims of this tutorial are:**
13
141) Provide `a guide <_static/Tutorial.html>`_ to implementing the Hodgkin-Huxley model using both `Python <https://www.python.org/>`_ and a `NeuroML2 implementation <http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract>`_ of the same equations.
152) Give some background information on the `electrophysiology <_static/Electrophysiology.html>`_ underlying the Hodgkin-Huxley model.
16
17The original HH tutorial was created by `@joebowen <https://github.com/joebowen>`_ on behalf of the `OpenWorm project <http://www.openworm.org>`_.
18
19New interactive introduction to the HH model in a Jupyter notebook
20==================================================================
21
22A new interactive `Jupyter notebook <https://jupyter.org>`_ can be used to run the HH model, change the parameters of the model and display the dynamical properties of variables, without the need to write any code.
23
24.. image:: _media/HH_Jupyter.png
25   :target: https://github.com/openworm/hodgkin_huxley_tutorial/blob/master/notebooks/Python_HH_version/README.md
26
27
28Full details can be found `here <https://github.com/openworm/hodgkin_huxley_tutorial/blob/master/notebooks/Python_HH_version/README.md>`_ with a link to execute the model in your browser. This work was carried out as part of `Google Summer of Code 2022 by Rahul Sonkar <https://github.com/openworm/hodgkin_huxley_tutorial/blob/master/notebooks/GSoC_2022_Submission/GSoC_Documentation.md>`_.
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30
31What is the Hodgkin-Huxley model?
32=================================
33
34`From Wikipedia <https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model>`_:
35The Hodgkin–Huxley model is a mathematical model that describes how action potentials in neurons
36are initiated and propagated.
37
38The model describes represents the electrical properties of
39excitable membranes as typical electrical circuit components. For instance,
40the cell's membrane is modeled as a capacitor, and voltage-dependent
41conductances stand in for what are now known to be voltage-gated ion
42channels.
43
44For a detailed run through of the Hodgkin-Huxley model's electronics, math and
45biology, take a look at the `Electrophysiology page <_static/Electrophysiology.html>`_.
46
47After you understand the electronic model there, check out the
48`code walkthrough <_static/Tutorial.html>`_ to see an example
49implementation of the Hodgkin-Huxley model in Python, using a cell
50modeled in `NeuroML2 <https://www.neuroml.org/neuromlv2>`_.
51
52You can look at the `current-voltage characteristic page <_static/iv_curve.html>`_
53to get an understanding of another biological-electronic equivalence
54that is useful in describing ion channel and cell models.
55
56There are also some `exercises <_static/Exercises.html>`_ you can complete to get a feel for the model. These
57can be completed using either the Python or NeuroML versions.
58
59Table of Contents:
60
61.. toctree::
62   :maxdepth: 4
63
64   _toc/Tutorial
65   _toc/Electrophysiology
66   _toc/iv_curve
67   _toc/Exercises
68   _toc/Source
69