Merge pull request #233 from Dhruva-Storz/master

Documentation update 2

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
 --------------------
 

docs/source/user/py/cookbook/chem_sim_eg.rst

 ***************
 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
 ---------------------------------

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)
 -----------------------------
 

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
 -----------------------------------
 

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
 ---------------------
 

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
 ----------------------------------------------
 

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
 -----------------------------------
 

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
 ----------------------------------
 

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
 --------------------------------
 

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
 ================

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. 
 
 |
 |

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.