From db83265c34c3ab768daf16ce01bebf5f4058949d Mon Sep 17 00:00:00 2001
From: Dhruva Gowda Storz <dhruvastorz@gmail.com>
Date: Thu, 18 Jan 2018 17:05:15 +0530
Subject: [PATCH] Added squid demo to tutorials. Removed squid demo from
quickstart. Wrote a bit of theory and history about squid demo. removed
redundant modules.rst file.
---
docs/source/docs/source/modules.rst | 2 --
docs/source/user/py/quickstart/demos.rst | 18 -----------
docs/source/user/py/tutorials/Squid.rst | 35 +++++++++++++++++++++
docs/source/user/py/tutorials/index_tut.rst | 3 +-
4 files changed, 37 insertions(+), 21 deletions(-)
delete mode 100644 docs/source/docs/source/modules.rst
create mode 100644 docs/source/user/py/tutorials/Squid.rst
diff --git a/docs/source/docs/source/modules.rst b/docs/source/docs/source/modules.rst
deleted file mode 100644
index bf86f144..00000000
--- a/docs/source/docs/source/modules.rst
+++ /dev/null
@@ -1,2 +0,0 @@
-projectdir
-==========
diff --git a/docs/source/user/py/quickstart/demos.rst b/docs/source/user/py/quickstart/demos.rst
index 6614ac95..7fe408f1 100644
--- a/docs/source/user/py/quickstart/demos.rst
+++ b/docs/source/user/py/quickstart/demos.rst
@@ -21,24 +21,6 @@ Start, Stop, and setting clocks
.. automodule:: stimtable
:members:
-The Hodgkin-Huxley demo
------------------------
-
-This is a self-contained graphical demo implemented by Subhasis Ray,
-closely based on the 'Squid' demo by Mark Nelson which ran in GENESIS.
-
-.. figure:: ../../../images/squid_demo.png
- :alt: Hodgkin-Huxley's squid giant axon experiment
-
-Simulation of Hodgkin-Huxley's experiment on squid giant axon
-showing action potentials generated by a step current injection.
-
-
-The demo has built-in documentation and may be run from the
-``moose-examples/squid`` subdirectory of MOOSE.
-
-.. _quickstart-python_from_moose:
-
Run Python from MOOSE
---------------------
diff --git a/docs/source/user/py/tutorials/Squid.rst b/docs/source/user/py/tutorials/Squid.rst
new file mode 100644
index 00000000..60657e5c
--- /dev/null
+++ b/docs/source/user/py/tutorials/Squid.rst
@@ -0,0 +1,35 @@
+****************
+Squid giant axon
+****************
+
+This tutorial is an interactive graphical simulation of a squid giant axon,
+closely based on the 'Squid' demo by Mark Nelson which ran in GENESIS.
+
+The `squid giant axon <https://en.wikipedia.org/wiksi/Squid_giant_axon>`_ is a very large axon that plays a role in the water jet propulsion systems of squid.
+
+Alan Hodgkin, Andrew Huxley, and John Eccles won the nobel prize in physiology or medicine for their pioneering work on the squid axon. Hodgin and Huxley were the first to qualitatively describe action potentials within neurons. The large diameter of the squid giant axon (0.5 mm to 1 mm) allowed them to affix electrodes and voltage clamps to precisely measure the action potential as it travelled through the axon. They later went on to mathematically describe this in an equation that paved the road for mathematical and computational biology's development.
+
+This tutorial models the Hodglin-Huxley equation within a neat graphical interface that allows one to change different parameters and see how it affects the resulting action potential.
+
+.. figure:: ../../../images/squid_demo.png
+ :alt: Hodgkin-Huxley's squid giant axon experiment
+
+ The GUI of the simulation.
+
+The tutorial can be run from within the ``.../moose/moose-examples/squid`` directory by running
+::
+
+ python squid_demo.py
+
+in command line from within the directory.
+
+Once the model loads, you can access the inbuilt documentation by clicking on ``Help running`` in the top right of the window as shown below
+
+.. figure:: ../../../images/Help.png
+ :alt: Help running
+
+ The "Help running" tab is highlighted in red
+
+The page that pops up will take you through using the GUI, changing the parameters and understanding the model.
+
+For more details on the biophysics behind the model, you can click on ``Help biophysics`` tab to the immediate right of the ``Help running`` tab (note that for smaller default window sizes, the tab might not be visible and can be accessed by clicking the ``>>`` on the top right corner of the GUI).
diff --git a/docs/source/user/py/tutorials/index_tut.rst b/docs/source/user/py/tutorials/index_tut.rst
index 13c82837..9bcc8a87 100644
--- a/docs/source/user/py/tutorials/index_tut.rst
+++ b/docs/source/user/py/tutorials/index_tut.rst
@@ -1,11 +1,12 @@
Teaching Tutorials
==================
-These tutorials use the moose simulation environment to illustrate various aspects of chemical bistables and oscillators. As such the materials in this section are useful for both teaching and learning about these topics.
+These tutorials use the moose simulation environment to illustrate various scientific concepts, phenomena, and research. As such the materials in this section are useful for both teaching and learning about these topics.
.. toctree::
:maxdepth: 2
ChemicalBistables
ChemicalOscillators
+ Squid
--
GitLab