diff --git a/docs/README.txt b/docs/README.txt
index 5145c53c40ebc60f1a709a52feab53d0c457c068..a4295711aed5263973ecebcc1972c6b857669390 100644
--- a/docs/README.txt
+++ b/docs/README.txt
@@ -1 +1,15 @@
-The source code of documentation is ./source directory.
+The source code of documentation is /source directory.
+
+This directory contains MOOSE user documentation in reST format that can be
+compiled into various formats by sphinx. To build the documentation in HTML,
+format enter the command:
+
+ make html
+
+in this directory. Then you can open build/html/index.html in browser to
+browse the generated documentation.
+
+Other files in /source folder
+ - conf.py: the Sphinx configuration file.
+ - index.rst: This is the index file for use when building the Python
+ docs using sphinx.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 92521adc5c93de779b7978b25ed0039a52b9ee96..f3d787c8d8f668d52c5df341e587151d8e9eeb0e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -15,6 +15,7 @@ import subprocess
import os
import sys
import sphinx_rtd_theme
+import mock
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
@@ -261,13 +262,13 @@ numpydoc_show_class_members = False
# autodoc options to mock MOOSE module
autodoc_mock_imports = [ 'numpy' , 'moose.sbml' , 'moose.genesis' , 'moose.LIF'
- , 'moogli.extensions.moose' , 'extensions.moose', 'moose' , 'moose.SBML'
- , 'pylab' , 'moose.genesis' , 'datetime' , 'getpass' , 'h5py'
- , 'matplotlib' , 'squid' , 'PyQt4' , 'moogli' , 'moose.utils'
- , 'math' , 'SquidAxon' , '_moogli' , 'XRRRates' , 'neuroml.NeuroML'
+ , 'moogli.extensions.moose' , 'extensions.moose', 'moose' , 'moose.SBML'
+ , 'pylab' , 'moose.genesis' , 'datetime' , 'getpass' , 'h5py'
+ , 'matplotlib' , 'squid' , 'PyQt4' , 'moogli' , 'moose.utils'
+ , 'math' , 'SquidAxon' , '_moogli' , 'XRRRates' , 'neuroml.NeuroML'
,'neuroml' , 'rdesigneur' , 'pyplot' , 'gnuplot' , 'cm'
- , 'matplotlib.pyplot' , 'matplotlib.image' , 'matplotlib.cm' , 'shapes'
- , 'chemUtil.add_Delete_ChemicalSolver'
+ , 'matplotlib.pyplot' , 'matplotlib.image' , 'matplotlib.cm' , 'shapes'
+ , 'chemUtil.add_Delete_ChemicalSolver'
]
#include reference files
diff --git a/docs/source/known_issues/index.rst b/docs/source/known_issues/index.rst
index 0ad5cdd653f187c374b75e0d605f748d2e3c8ea9..74f66887abe966ee27f2786d2f573496fe0d6f4b 100644
--- a/docs/source/known_issues/index.rst
+++ b/docs/source/known_issues/index.rst
@@ -3,7 +3,7 @@ Known issues
Full report can be found at the following places
-- Related to build, packages and documentation `https://github.com/BhallaLab/moose/issues`
-- Related to python interface of MOOSE `https://github.com/BhallaLab/moose-core/issues`
-- Related to MOOSE GUI `https://github.com/BhallaLab/moose-gui/issues`
-- Related to ``moogli`` `https://github.com/BhallaLab/moogli/issues`
+- Related to `build, packages and documentation <https://github.com/BhallaLab/moose/issues>`_
+- Related to `moose-core <https://github.com/BhallaLab/moose-core/issues>`_
+- Related to `MOOSE-GUI <https://github.com/BhallaLab/moose-gui/issues>`_
+- Related to `moogli <https://github.com/BhallaLab/moogli/issues>`_
diff --git a/docs/source/user/py/cookbook/chem_GUI.rst b/docs/source/user/py/cookbook/chem_GUI.rst
index f7d1136c03c13fc3f4cada1b316e8c872bf0b42b..390b56ee104ab200ada187c945987ffc3959d8a5 100644
--- a/docs/source/user/py/cookbook/chem_GUI.rst
+++ b/docs/source/user/py/cookbook/chem_GUI.rst
@@ -49,7 +49,7 @@ into the synapse, followed by calcium binding to calmodulin, and then
calmodulin activation of numerous enzymes. These events can be
represented in chemical terms:
- 4 Ca2+ + CaM <===> Ca4.CaM
+ 4 Ca\ :sup:`2+`\ + CaM <===> Ca\ :sub:`4`\.CaM
Such chemical equations can be modeled through standard Ordinary
Differential Equations, if we ignore space::
@@ -82,7 +82,7 @@ chemical calculations.
`Overview <#TOC>`__
^^^^^^^^^^^^^^^^^^^
-- Load models using **'File -> Load model'**. A reaction schematic for the chemical system appears in the **'Editor view'** tab.
+- Load models using **'File -> Load model'**. A reaction schematic for the chemical system appears in the **'Editor view'** tab.
- From **'Editor view'** tab
- View parameters by clicking on icons, and looking at entries in **'Properties'** table to the right.
@@ -91,7 +91,7 @@ chemical calculations.
- From **'Run View'**
- Pools can be plotted by clicking on their icons and dragging the icons onto the plot Window. Presently only concentration v/s time is plottable.
- - Select simulation, diffusin dt's along updateInterval for plot and Gui with numerical method using options under **'Preferences'** button in simulation control.
+ - Select simulation, diffusion dt's along updateInterval for plot and Gui with numerical method using options under **'Preferences'** button in simulation control.
- Run model using **'Run'** button.
- Save plots image using the icons at the top of the **'Plot Window'** or right click on plot to Export to csv.
@@ -112,11 +112,11 @@ and change the layout of the model.
Resizing the model layout and icons:
-- **Zoom**:Â Â Comma and period keys. Alternatively, the mouse scroll wheel or vertical scroll line on the track pad will cause the display to zoom in and out.
-- **Pan**:Â Â The arrow keys move the display left, right, up, and down.
-- **Entire Model View**:Â Â Pressing the **'a'** key will fit the entire model into the entire field of view.
-- **Resize Icons**:Â Â Angle bracket keys, that is, **'<'** and **'>'** or **'+'** and **'-'**. This resizes the icons while leaving their positions on the screen layout more or less the same.
-- **Original Model View**:Â Â Pressing the **'A'** key (capital 'A') will revert to the original model view including the original icon scaling.
+- **Zoom**: Comma and period keys. Alternatively, the mouse scroll wheel or vertical scroll line on the track pad will cause the display to zoom in and out.
+- **Pan**: The arrow keys move the display left, right, up, and down.
+- **Entire Model View**: Pressing the **'a'** key will fit the entire model into the entire field of view.
+- **Resize Icons**: Angle bracket keys, that is, **'<'** and **'>'** or **'+'** and **'-'**. This resizes the icons while leaving their positions on the screen layout more or less the same.
+- **Original Model View**: Pressing the **'A'** key (capital 'A') will revert to the original model view including the original icon scaling.
`Compartment <#TOC>`__
^^^^^^^^^^^^^^^^^^^^^^
@@ -155,11 +155,11 @@ Different chemical states of the same molecule are in different pools.
- **nInit**: Initial number of molecules in the pool. 'n' gets set
to this value when the 'reinit' operation is done.
- **conc**: Concentration of the molecules in the pool.
- ``conc = n * unit_scale_factor / (N<sub>A</sub> * vol)``
+ ``conc = n * unit_scale_factor / (N_A * vol)``
- **concInit**: Initial concentration of the molecules in the pool.
'conc' is set to this value when the 'reinit' operation is done.
- ``concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)``
+ ``concInit = nInit * unit_scale_factor / (N_A * vol)``
- **Pool fixed parameters**
@@ -184,7 +184,7 @@ buffered pools.
- **concInit**: Fixed concentration of the molecules in the pool.
'conc' is set to this value throughout the run.
- ``concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)``
+ ``concInit = nInit * unit_scale_factor / (N_A * vol)``
- **Pool fixed parameters**:
@@ -212,17 +212,17 @@ indicated by the direction of the green arrow.
- **Reaction editable parameters**:
- **Name** : Name of reaction
- - **K\ :sub:`f`** : 'Forward rate' of reaction, in
+ - **K**\ :sub:`f`\ : 'Forward rate' of reaction, in
'concentration/time' units. This is the normal way to express and
manipulate the reaction rate.
- - **k\ :sub:`f`** : Forward rate of reaction, in 'number/time'
+ - **k**\ :sub:`f`\ : Forward rate of reaction, in 'number/time'
units. This is used internally for computations, but is
volume-dependent and should not be used to manipulate the reaction
rate unless you really know what you are doing.
- - **K\ :sub:`b`** : Backward rate' of reaction, in
+ - **K**\ :sub:`b`\ : Backward rate' of reaction, in
'concentration/time' units. This is the normal way to express and
manipulate the reaction rate.
- - **k\ :sub:`b`** : Backward rate of reaction, in 'number/time'
+ - **k**\ :sub:`b`\ : Backward rate of reaction, in 'number/time'
units. This is used internally for computations, but is
volume-dependent and should not be used to manipulate the reaction
rate unless you really know what you are doing.
@@ -261,21 +261,21 @@ arrows.
- **Enzyme editable parameters**
- **name** : Name of enzyme.
- - **K\ :sub:`m`** : Michaelis-Menten value for enzyme, in
+ - **K**\ :sub:`m` \ : Michaelis-Menten value for enzyme, in
'concentration' units.
- - **k\ :sub:`cat`** : Production rate of enzyme, in '1/time' units.
- Equal to k\ :sub:`3`, the rate of the second, irreversible
+ - **k**\ :sub:`cat` \ : Production rate of enzyme, in '1/time' units.
+ Equal to k\ :sub:`3`\, the rate of the second, irreversible
reaction.
- - **k1** : Forward rate of the **E+S** reaction, in number and
+ - **k**\ :sub:`1` \ : Forward rate of the **E+S** reaction, in number and
'1/time' units. This is what is used in the internal calculations.
- - **k2** : Backward rate of the **E+S** reaction, in '1/time' units.
+ - **k**\ :sub:`2` \ : Backward rate of the **E+S** reaction, in '1/time' units.
Used in internal calculations.
- - **k3** : Forward rate of the **E.S -> E + P** reaction, in
- '1/time' units. Equivalent to k\ :sub:`cat`. Used in internal
+ - **k**\ :sub:`3` \ : Forward rate of the **E.S -> E + P** reaction, in
+ '1/time' units. Equivalent to k\ :sub:`cat`\. Used in internal
calculations.
- - **ratio** : This is equal to k\ :sub:`2`/k:sub:`3`. Needed to
+ - **ratio** : This is equal to k\ :sub:`2`\/k\ :sub:`3`\. Needed to
define the internal rates in terms of K\ :sub:`m` and
- k\ :sub:`cat`. I usually use a value of 4.
+ k\ :sub:`cat`\. I usually use a value of 4.
- **Enzyme-substrate-complex editable parameters**: These are identica'l to those of any other pool.
@@ -284,10 +284,10 @@ arrows.
- **nInit**: Initial number of molecules in the complex. 'n' gets set to this value when the 'reinit' operation is done.
- **conc**: Concentration of the molecules in the pool.
- ``conc = n * unit_scale_factor / (N<sub>A</sub> * vol)``
+ ``conc = n * unit_scale_factor / (N_A * vol)``
- **concInit**: Initial concentration of the molecules in the pool.
'conc' is set to this value when the 'reinit' operation is done.
- ``concI'nit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)``
+ ``concI'nit = nInit * unit_scale_factor / (N_A * vol)``
- **Enzyme-substrate-complex fixed parameters**:
@@ -301,7 +301,7 @@ arrows.
These are enzymes that obey the Michaelis-Menten equation
-``V = V<sub>max</sub> * [S] / ( K<sub>m</sub> + [S] ) = k<sub>cat</sub> * [Etot] * [S] / ( K<sub>m</sub> + [S] )``
+``V = V_max * [S] / ( K_m + [S] ) = k_cat * [Etot] * [S] / ( K_m + [S] )``
where
- V\ :sub:`max` is the maximum rate of the enzyme
- [Etot] is the total amount of the enzyme
@@ -333,9 +333,9 @@ enzyme reaction is indicated by the red arrows.
- **Enzyme editable parameters**:
- **name**: Name of enzyme.
- - K\ :sub:`m`: Michaelis-Menten value for enzyme, in 'concentration'
+ - **K**\ :sub:`m`\: Michaelis-Menten value for enzyme, in 'concentration'
units.
- - k\ :sub:`cat`: Production rate of enzyme, in '1/time' units. Equal to k\ :sub:`3`, the rate of the second, irreversible reaction.
+ - **k**\ :sub:`cat`\: Production rate of enzyme, in '1/time' units. Equal to k\ :sub:`3`, the rate of the second, irreversible reaction.
`Summation <#TOC>`__
^^^^^^^^^^^^^^^^^^^^
@@ -355,13 +355,9 @@ variables can be input from pool object.
- **New**: **File -> New -> Model name**. This opens a empty widget for model building
- **Saving models**: **File -> Save Model -> select from dialog**.
- **Changing numerical methods**: **Preference->Chemical tab** item from Simulation Control. Currently supports:
-- Runge Kutta: 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.
-- Gillespie: 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.
+1. Runge Kutta: 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.
+2. Gillespie: 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.
+3. Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
`Model building <#TOC>`__
-------------------------
@@ -369,7 +365,7 @@ variables can be input from pool object.
- The **Edit Widget** includes various menu options and model icons on
the top. Use the mouse buttton to click and drag icons from toolbar
to Edit Widget, two things will happen, **icon** will appear in the
- editor widget and a **object editor** will pop up with lots of
+ editor widget and an **object editor** will pop up with lots of
parameters with respect to moose object.
.. figure:: ../../../images/chemical_CS.png
@@ -385,7 +381,7 @@ variables can be input from pool object.
**Note**:
::
- * Drag in pool's and reaction on to the editor widget, now one can set up a reaction.
+ * Drag in pool and reaction on to the editor widget, now one can set up a reaction.
* Click on mooseObject one can find a little arrow on the top right corner of the object, drag from this little arrow to any object for connection. e.g pool to reaction and reaction to pool. Specific connection type gets specific colored arrow. e.g. Green color arrow for specifying connection between reactant and product for reaction.
* Clicking on the object one can rearrange object for clean layout.
* Second order reaction can also be done by repeating the connection over again
diff --git a/docs/source/user/py/cookbook/chem_sim_eg.rst b/docs/source/user/py/cookbook/chem_sim_eg.rst
index 63c87e0785d2d3a77efdc2811f2f3ae226d20b6c..96b19eafd6c7ec1f14c44ffc69e2035f739fea56 100644
--- a/docs/source/user/py/cookbook/chem_sim_eg.rst
+++ b/docs/source/user/py/cookbook/chem_sim_eg.rst
@@ -51,11 +51,11 @@ typically:
into voxels.
* **Pool** s have one key parameter, the initial
concentration **concInit**.
- * **Reac** tions have two parameters: **Kf** and **Kb**.
- * **Enz** ymes have two primary parameters **kcat** and **Km**.
+ * **Reac** tions have two parameters: **K**\ :sub:`f`\ and **K**\ :sub:`b`\.
+ * **Enz** ymes have two primary parameters **k**\ :sub:`cat`\ and **K**\ :sub:`m`\.
That is enough for **MMenz** ymes. Regular **Enz** ymes have
- an additional parameter **k2** which by default is set to 4.0
- times **kcat**, but you may also wish to explicitly assign it
+ an additional parameter **k**\ :sub:`2`\ which by default is set to 4.0
+ times **k**\ :sub:`cat`\, but you may also wish to explicitly assign it
if you know its value.
#. Connect up the reaction system using moose messaging.
diff --git a/docs/source/user/py/cookbook/chem_tut.rst b/docs/source/user/py/cookbook/chem_tut.rst
index 1a3a5a9e55cf825710067db67191a7ba4e53c5e1..439b75420013d7707602e03e8c6d70866d0d8cd4 100644
--- a/docs/source/user/py/cookbook/chem_tut.rst
+++ b/docs/source/user/py/cookbook/chem_tut.rst
@@ -8,9 +8,6 @@ Finding Steady State (CSpace)
.. automodule:: cspaceSteadyState
:members:
-Building Simple Reaction Model
-------------------------------
-
Define a kinetic model using the scripting
------------------------------------------
diff --git a/docs/source/user/py/cookbook/elec_GUI.rst b/docs/source/user/py/cookbook/elec_GUI.rst
index 695619661a7942e625809ee8ec721ed94014a53b..3b98e1c8adea2deaedf46a2e82321b0d79feec0f 100644
--- a/docs/source/user/py/cookbook/elec_GUI.rst
+++ b/docs/source/user/py/cookbook/elec_GUI.rst
@@ -5,8 +5,8 @@ Neuronal simulations in MOOSEGUI
Neuronal models in various formats can be loaded and simulated in the
**MOOSE Graphical User Interface**. The GUI displays the neurons in 3D,
and allows visual selection and editing of neuronal properties. Plotting
-and visualization of activity proceeds concurrently with the simulation.
-Support for creating and editing channels, morphology and networks is
+and visualization of activity proceed concurrently with the simulation.
+Support for creating and editing channels, morphology, and networks is
planned for the future. MOOSEGUI uses SI units throughout.
moose-examples
diff --git a/docs/source/user/py/cookbook/elec_mod.rst b/docs/source/user/py/cookbook/elec_mod.rst
index 2a6d5755e336f257c000ab167be80bad6d05dbd1..765a015141433daa76691073311a71589cb61c2c 100644
--- a/docs/source/user/py/cookbook/elec_mod.rst
+++ b/docs/source/user/py/cookbook/elec_mod.rst
@@ -52,14 +52,14 @@ format which is mostly supported across simulators. Channels, neuronal
morphology (compartments), and networks can be specified using various
levels of NeuroML, namely ChannelML, MorphML and NetworkML. Importing of
cell models in the `GENESIS <http://www.genesis-sim.org/GENESIS>`_
-.p format is supported for backwards compatibitility.
+.p format is supported for backward compatibitility.
Modeling details
================
Some salient properties of neuronal building blocks in MOOSE are
described below. Variables that are updated at every simulation time
-step are are listed **dynamical**. Rest are parameters.
+step are listed **dynamically**. Rest are parameters.
- **Compartment**
When you select a compartment, you can view and edit its properties
diff --git a/docs/source/user/py/cookbook/elec_sim_eg.rst b/docs/source/user/py/cookbook/elec_sim_eg.rst
index 68077b54c8244fc64546bd364c77c7776cafcd34..0506b94c093caaf775b3a3fc0e0399c931718772 100644
--- a/docs/source/user/py/cookbook/elec_sim_eg.rst
+++ b/docs/source/user/py/cookbook/elec_sim_eg.rst
@@ -18,7 +18,7 @@ Voltage Clamping
----------------
.. automodule:: vclamp
- :members:
+ :members:
Generate Pulse
----------------
@@ -33,7 +33,7 @@ Synapse
-------
.. automodule:: synapse
- :members:
+ :members:
Message transmission via synapse
--------------------------------
diff --git a/docs/source/user/py/cookbook/multi_rdes.rst b/docs/source/user/py/cookbook/multi_rdes.rst
index 8725b916346fa583589fe546ea8b44e217a904e9..dce3f35878901693b3f6a530a84c6b310e2ecd44 100644
--- a/docs/source/user/py/cookbook/multi_rdes.rst
+++ b/docs/source/user/py/cookbook/multi_rdes.rst
@@ -2,8 +2,8 @@
RDesigneur
**********
-Building Chemical-Electrical Signalling Models using Rdesigneur
----------------------------------------------------------------
+Building Chemical-Electrical Signalling Models
+----------------------------------------------
Building a compartment
^^^^^^^^^^^^^^^^^^^^^^
diff --git a/docs/source/user/py/cookbook/multi_sim_eg.rst b/docs/source/user/py/cookbook/multi_sim_eg.rst
index e80193c5bbb0d03ebed2215e84eb123b53076f8d..564bdb7fab6c5ae715e87a6e84405dc0fc36ca57 100644
--- a/docs/source/user/py/cookbook/multi_sim_eg.rst
+++ b/docs/source/user/py/cookbook/multi_sim_eg.rst
@@ -14,9 +14,6 @@ Multi compartment Single Neuron Model
.. automodule:: multiComptSigNeur
:members:
-Multi-compartment multiscale model
-----------------------------------
-
Modeling chemical reactions in neurons
--------------------------------------
diff --git a/docs/source/user/py/introduction/changes/index.rst b/docs/source/user/py/introduction/changes/index.rst
deleted file mode 100644
index 9a167f14daf7633c581babd2cd82e2b452ad0900..0000000000000000000000000000000000000000
--- a/docs/source/user/py/introduction/changes/index.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Changes
-=======
-
-.. todo:: collect changes from OBS.
diff --git a/docs/source/user/py/introduction/index.rst b/docs/source/user/py/introduction/index.rst
deleted file mode 100644
index b55005ae6f816a5f00fdf23c1bad96f77bd1f681..0000000000000000000000000000000000000000
--- a/docs/source/user/py/introduction/index.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-Introduction
-============
-
-.. toctree::
-
- install/index
- release_notes/index
- changes/index
- known_issues/index
diff --git a/docs/source/user/py/introduction/install/index.rst b/docs/source/user/py/introduction/install/index.rst
deleted file mode 100644
index 888aede83b0df0716bc7b784444ac2f5e914d210..0000000000000000000000000000000000000000
--- a/docs/source/user/py/introduction/install/index.rst
+++ /dev/null
@@ -1,208 +0,0 @@
-Installation
-============
-
-Use pre-built packages
-----------------------
-
-Linux
-^^^^^
-
-We recommend that you use our repositories hosted at `Open Build Service
-<http://build.opensuse.org>`_. We have packages for the following distributions
-
-- Debian 7.0, 8.0
-- Ubuntu 12.04, 14.04, 15.04, 15.10, 16.04
-- CentOS 6, 7
-- Fedora 20, 21, 22, 23
-- OpenSUSE 13.1, 13.2, Factory ARM, Leap 42.1, Tumbleweed
-- SLE 12, 12 SP1
-- RHEL 7
-- Scientific Linux 7
-
-Visit `this page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-pick you distribution and follow instructions.
-
-.. note::
- ``moogli`` (tool to visualize network activity) is not available for CentOS-6.
-
-.. raw:: html
- <iframe
- src="http://software.opensuse.org/download/package.iframe?project=moose&package=moose"></iframe>
-
-.. todo:: Packages for gentoo, Arch Linux
-
-
-Mac OSX
-^^^^^^
-
-:strike:`Download the ``dmg`` file from `here <https://github.com/BhallaLab/moose/releases/download/ghevar_3.0.2/Moose_3.0.2_OSX.dmg>`_.` We no longer build `dmg` files.
-
-
-On MacOSX, `MOOSE` is available via `homebrew <https://brew.sh>`_.
-::
- $ brew install homebrew/science/moose
-
-
-Windows/Cygwin
-^^^^^^^^^^^^^^
-
-Building MOOSE
---------------
-
-In case your distribution is not listed on `our repository page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-, or if you want to build the lastest development code, read on.
-
-First, you need to get the source code. You can use ``git`` (clone the
-repository) or download snapshot of github repo by clicking on `this link
-<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
- $ git clone https://github.com/BhallaLab/moose
-
-Or,
-::
- $ wget https://github.com/BhallaLab/moose/archive/master.zip
- $ unzip master.zip
-
-If you don't want lasest snapshot of ``MOOSE``, you can download other released
-versions from here `https://github.com/BhallaLab/moose/releases`.
-
-Install dependencies
-~~~~~~~~~~~~~~~~~~~
-
-Next, you need to install required dependencies. Depending on your OS, names of
-following packages may vary.
-
-- cmake (version 2.8 or higher)
-- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
-- libhdf5 development package e.g. `libhdf5-serial-dev` or `libhdf5-devel`
-- python development package e.g. `python-dev` or `python-devel`
-- numpy e.g. `python-numpy` or `numpy`
-
-Most of the dependencies can be installed using package manager.
-
-On ``Debian/Ubuntu``
-::
- $ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
-
-.. note::
- Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
- higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
-
-On ``CentOS/Fedora/RHEL/Scientific Linux``
-::
- $ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-On ``OpenSUSE``
-::
- $ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-Now use `cmake` to build moose
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. codeblock:: bash
- $ cd /to/moose/source/code
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ ctest --output-on-failure # optional
-
-This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
-check if build process was successful.
-
-.. note::
- To install MOOSE into non-standard directory, pass additional argument
- `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
- ::
- $ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..
-
- To use different version of python
- ::
- $ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..
-
-After that installation is pretty easy
-::
- $ sudo make install
-
-If everything went fine, you should be able to import moose in python shell.
-
-.. code-block:: python
- import moose
-
-
-Graphical User Interface (GUI)
-------------------------------
-
-You can get the source of ``moose-gui`` from `here
-<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
-clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
-or by using ``git`` ::
- $ git clone https://github.com/BhallaLab/moose-gui
-
-To be able to launch ``moose-gui``, you need to install some more packages
-
-- matplotlib
-- python-qt4
-
-On ``Ubuntu/Debian``, these can be installed with
-::
- $ sudo apt-get install python-matplotlib python-qt4
-
-On ``CentOS/Fedora/RHEL``
-::
- $ sudo yum install python-matplotlib python-qt4
-
-Now you can fire up the GUI
-::
- $ cd /to/moose-gui
- $ python mgui.py
-
-.. note::
- If you have installed ``moose`` package, then GUI is launched by
- running following commnad::
- $ moose
-
-Building moogli
----------------
-
-``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here <http://moose.ncbs.res.in/moogli>`_.
-
-`Moogli` is part of `moose` package. Building moogli can be tricky because of
-multiple depednecies it has.
-
-
-To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
-
-Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
-be easily available for your operating system.
-For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
-source code.
-
-Depending on distribution of your operating system, you would need following
-packages to be installed.
-
-On ``Ubuntu/Debian``
-::
- $ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev
-
-On ``Fedora/CentOS/RHEL``
-::
- $ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4
-
-On ``openSUSE``
-::
- $ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4
-
-After this, building and installing ``moogli`` should be as simple as
-::
- $ cd /path/to/moogli
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ sudo make install
-
-If you run into troubles, please report it on our `github repository
-<https://github.com/BhallaLab/moose/issues>`_.
diff --git a/docs/source/user/py/introduction/known_issues/index.rst b/docs/source/user/py/introduction/known_issues/index.rst
deleted file mode 100644
index 0ad5cdd653f187c374b75e0d605f748d2e3c8ea9..0000000000000000000000000000000000000000
--- a/docs/source/user/py/introduction/known_issues/index.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-Known issues
-============
-
-Full report can be found at the following places
-
-- Related to build, packages and documentation `https://github.com/BhallaLab/moose/issues`
-- Related to python interface of MOOSE `https://github.com/BhallaLab/moose-core/issues`
-- Related to MOOSE GUI `https://github.com/BhallaLab/moose-gui/issues`
-- Related to ``moogli`` `https://github.com/BhallaLab/moogli/issues`
diff --git a/docs/source/user/py/introduction/release_notes/index.rst b/docs/source/user/py/introduction/release_notes/index.rst
deleted file mode 100644
index 862216e95c1d42e9c53d4f176e75ffdfe2987165..0000000000000000000000000000000000000000
--- a/docs/source/user/py/introduction/release_notes/index.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Release Notes
-============
-
-.. todo:: Collect release notes from github.
diff --git a/docs/source/user/py/quickstart/moose_quickstart.rst b/docs/source/user/py/quickstart/moose_quickstart.rst
index b1604e7f91963bab52655f57a31804096f7956d3..094a82b78e6ff9fcbaa0a82ee670cdc73d724a32 100644
--- a/docs/source/user/py/quickstart/moose_quickstart.rst
+++ b/docs/source/user/py/quickstart/moose_quickstart.rst
@@ -54,7 +54,7 @@ MOOSE has built-in documentation in the C++-source-code independent of
Python. The ``moose`` module has a separate ``doc`` function to extract
this documentation. ::
- >>> moose.doc(moose.Compartment)
+ >>> moose.doc('moose.Compartment')
The class level documentation will show whatever the author/maintainer
of the class wrote for documentation followed by a list of various kinds
@@ -332,7 +332,7 @@ the pulse generator output to the soma input ::
``connect(source, source_field, dest, dest_field)`` creates a
``message`` from ``source`` element's ``source_field`` field to ``dest``
-elements ``dest_field`` field and returns that message. Messages are
+element's ``dest_field`` field and returns that message. Messages are
also elements. You can print them to see their identity ::
>>> print m
diff --git a/docs/source/user/py/quickstart/qs_GUI.rst b/docs/source/user/py/quickstart/qs_GUI.rst
index b0b58c50c15c8cd6f8767b8fea936acd645876ba..c8bd99cb804b3bfcec7e840dd79816b84fb8afe7 100644
--- a/docs/source/user/py/quickstart/qs_GUI.rst
+++ b/docs/source/user/py/quickstart/qs_GUI.rst
@@ -55,8 +55,8 @@ Introduction
------------
The Moose GUI currently allow you work on
-`chemical <Kkit12Documentation.html>`_ models using a interface. This
-document describes the salient features of the GUI
+:doc:`chemical <../cookbook/chem_GUI>` and :doc:`electrical <../cookbook/elec_GUI>` models using a interface. This
+document describes the salient features of the GUI.
Interface
---------
diff --git a/docs/user/py/builtins_classes/README.txt b/docs/user/py/builtins_classes/README.txt
deleted file mode 100644
index d3aa45730c237fbb7eb5515f93dd34c73510b1b1..0000000000000000000000000000000000000000
--- a/docs/user/py/builtins_classes/README.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-This directory contains MOOSE user documentation in reST format that can be
-compiled into various formats by sphinx. To build the documentation in HTML,
-format enter the command:
-
-make html
-
-in this directory. Then you can open _build/html/index.html in browser to
-browse the generated documentation.
-
-Every MOOSE class has builtin documentation. This can be extracted into a
-reST file by running the script:
-
- python create_all_rst_doc.py
-
-This process must be carried out before making the docs after any
-change in the built-in documentation is compiled into MOOSE.
-
-Other files
- - conf.py: the Sphinx configuration file.
- - index.rst: This is the index file for use when building the Python
- docs using sphinx.
- - moose_builtins.rst: This is for sphinx to process the pymoose builtin
- doc strings (using autodoc extension).
- - moose_classes.rst: The Python docs extracted above using
- create_all_rst_doc.py
-
-
diff --git a/docs/user/py/cookbook/README.txt b/docs/user/py/cookbook/README.txt
deleted file mode 100644
index 3a690338605432ef90a6cad168318af60ddfe03e..0000000000000000000000000000000000000000
--- a/docs/user/py/cookbook/README.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-This directory contains MOOSE user documentation in reST format that can be
-compiled into various formats by sphinx. To build the documentation in HTML,
-format enter the command:
-
-make html
-
-in this directory. Then you can open _build/html/index.html in browser to
-browse the generated documentation.
-
-files
- - conf.py: the Sphinx configuration file.
- - index.rst: This is the index file for use when building the Python
- docs using sphinx.
- - moose_cookbook.rst: Recipes for specific tasks in moose.
-
-
diff --git a/docs/user/py/quickstart/README.txt b/docs/user/py/quickstart/README.txt
deleted file mode 100644
index 30d946d6a241e15e928a78bdfd7b20a74561035a..0000000000000000000000000000000000000000
--- a/docs/user/py/quickstart/README.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-This directory contains MOOSE user documentation in reST format that can be
-compiled into various formats by sphinx. To build the documentation in HTML,
-format enter the command:
-
-make html
-
-in this directory. Then you can open _build/html/index.html in browser to
-browse the generated documentation.
-
-files
- - conf.py: the Sphinx configuration file.
- - index.rst: This is the index file for use when building the Python
- docs using sphinx.
- - moose_quickstart.rst: Recipes for specific tasks in moose.
-
-
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