diff --git a/docs/source/user/py/cookbook/chem_load_save.rst b/docs/source/user/py/cookbook/chem_load_save.rst
index b278dffd4bfb94f9d51a7e65eb77aae382e344b7..d5dc9814d4fed255ac5371d5825cebb78be48206 100644
--- a/docs/source/user/py/cookbook/chem_load_save.rst
+++ b/docs/source/user/py/cookbook/chem_load_save.rst
@@ -2,6 +2,35 @@
Load - Run - Save models
************************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
+
Load a Kinetic Model
--------------------
diff --git a/docs/source/user/py/cookbook/chem_sim_eg.rst b/docs/source/user/py/cookbook/chem_sim_eg.rst
index 5eac01de87afc208e0aa2d65d4d60b9357c13fbb..c06304a8f33fb6d0e1fb32eef1cf98d199518d1c 100644
--- a/docs/source/user/py/cookbook/chem_sim_eg.rst
+++ b/docs/source/user/py/cookbook/chem_sim_eg.rst
@@ -1,6 +1,33 @@
***************
Simple Examples
***************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
Set-up a kinetic solver and model
---------------------------------
diff --git a/docs/source/user/py/cookbook/chem_tut.rst b/docs/source/user/py/cookbook/chem_tut.rst
index 439b75420013d7707602e03e8c6d70866d0d8cd4..d9e336f9a26d664e94fb5421a0121f4c625f408a 100644
--- a/docs/source/user/py/cookbook/chem_tut.rst
+++ b/docs/source/user/py/cookbook/chem_tut.rst
@@ -2,6 +2,34 @@
Tutorials
*********
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Finding Steady State (CSpace)
-----------------------------
diff --git a/docs/source/user/py/cookbook/elec_load_run.rst b/docs/source/user/py/cookbook/elec_load_run.rst
index 14879a7fbf181184659557ff3653d019a1aa3ed1..f3503c1b088eb0313aabd0522c78be3d86ed7c17 100644
--- a/docs/source/user/py/cookbook/elec_load_run.rst
+++ b/docs/source/user/py/cookbook/elec_load_run.rst
@@ -2,6 +2,34 @@
Load and Run simple models
**************************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Single Cubicle Compartmental Neuron
-----------------------------------
diff --git a/docs/source/user/py/cookbook/elec_sim_eg.rst b/docs/source/user/py/cookbook/elec_sim_eg.rst
index 224cf913e7c5429701ef78692b5a0fd31ab08862..9f01aa650a67587ef8cce85b4c45c965f6a2bcd4 100644
--- a/docs/source/user/py/cookbook/elec_sim_eg.rst
+++ b/docs/source/user/py/cookbook/elec_sim_eg.rst
@@ -2,6 +2,34 @@
Simple Examples
***************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Create a Leaky Neuron
---------------------
diff --git a/docs/source/user/py/cookbook/multi_rdes.rst b/docs/source/user/py/cookbook/multi_rdes.rst
index baf5719bd85b42dec18aac48e1e1a8d7fb06f091..2015743a75e5e827cd0b40b1a46f40c9a4024f9b 100644
--- a/docs/source/user/py/cookbook/multi_rdes.rst
+++ b/docs/source/user/py/cookbook/multi_rdes.rst
@@ -2,6 +2,34 @@
More Rdesigneur Examples
************************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Building Chemical-Electrical Signalling Models
----------------------------------------------
diff --git a/docs/source/user/py/cookbook/multi_sim_eg.rst b/docs/source/user/py/cookbook/multi_sim_eg.rst
index 529ee4c3911a9729ba3db76dfe404330b6823cec..104868c2fa17d1b3cb23ac755105a4ce1173f3bf 100644
--- a/docs/source/user/py/cookbook/multi_sim_eg.rst
+++ b/docs/source/user/py/cookbook/multi_sim_eg.rst
@@ -2,6 +2,34 @@
Simple Examples
***************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Single-compartment multiscale model
-----------------------------------
diff --git a/docs/source/user/py/cookbook/net_sim_eg.rst b/docs/source/user/py/cookbook/net_sim_eg.rst
index ef9f46e5be1f225cfaeed05787c6ffd3d15997e9..6b15acdb7d0c7dc8d554693ad05343774110b17a 100644
--- a/docs/source/user/py/cookbook/net_sim_eg.rst
+++ b/docs/source/user/py/cookbook/net_sim_eg.rst
@@ -2,6 +2,34 @@
Simple Examples
***************
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Connecting two cells via a synapse
----------------------------------
diff --git a/docs/source/user/py/cookbook/net_tut.rst b/docs/source/user/py/cookbook/net_tut.rst
index ea98c2f96f799938a8cf1630ea853e7a4ae0040d..b784105698ee7f02fac4e823f2aa8d9cd4caaf9b 100644
--- a/docs/source/user/py/cookbook/net_tut.rst
+++ b/docs/source/user/py/cookbook/net_tut.rst
@@ -2,6 +2,34 @@
Tutorials
*********
+.. hidden-code-block:: reStructuredText
+ :label: How to run these examples
+
+ Each of the following examples can be run by clicking on the green source button
+ on the right side of each example, and running from within a ``.py`` python file
+ on a computer where moose is installed.
+
+ Alternatively, all the files mentioned on this page can be found in the main
+ moose directory. They can be found under
+
+ (...)/moose/moose-examples/snippets
+
+ They can be run by typing
+
+ $ python filename.py
+
+ in your command line, where filename.py is the python file you want to run.
+
+ All of the following examples show one or more methods within each python file.
+ For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
+ describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
+ methods.
+
+ The filename is the bit that comes before the ``.`` in the blue boxes, with
+ ``.py`` added at the end of it. In this case, the file name would be
+ ``cubeMeshSigNeur.py``.
+|
+
Network with Ca-based plasticity
--------------------------------
diff --git a/docs/source/user/py/tutorials/ChemicalBistables.rst b/docs/source/user/py/tutorials/ChemicalBistables.rst
index 6ac360cb3b67e38a77ed7c33bd017e23615951c2..b4a449ab9595cd052c2443472d3de1857b2ab32a 100644
--- a/docs/source/user/py/tutorials/ChemicalBistables.rst
+++ b/docs/source/user/py/tutorials/ChemicalBistables.rst
@@ -21,9 +21,18 @@ In chemical bistable models that use solvers, there are optional arguments that
python filename.py [gsl | gssa | ee]
-Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm.
+Where:
-All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
+ - gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
+ - gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
+ - Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
+
+All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome.
+
+Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
+
+|
+|
Simple Bistables
================
diff --git a/docs/source/user/py/tutorials/ChemicalOscillators.rst b/docs/source/user/py/tutorials/ChemicalOscillators.rst
index c356ab6aabcd389356d929c5db7c9d2e1af0f290..2fb8c5abeb5a6a679bc3f54d39ea73e94ed025d8 100644
--- a/docs/source/user/py/tutorials/ChemicalOscillators.rst
+++ b/docs/source/user/py/tutorials/ChemicalOscillators.rst
@@ -23,9 +23,15 @@ In chemical models that use solvers, there are optional arguments that allow you
python filename.py [gsl | gssa | ee]
-Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm.
+Where:
-All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
+ - gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
+ - gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
+ - Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
+
+All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome.
+
+Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
|
|
diff --git a/docs/source/user/py/tutorials/Squid.rst b/docs/source/user/py/tutorials/Squid.rst
index 60657e5c4b6f2a486a7a9822e9616c29907a0eb6..c249b4f2579e9c9b382ba0433e0701f8acf5d0a5 100644
--- a/docs/source/user/py/tutorials/Squid.rst
+++ b/docs/source/user/py/tutorials/Squid.rst
@@ -5,7 +5,7 @@ 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.
+The `squid giant axon <https://en.wikipedia.org/wiki/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.