diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..b043515251fc96310c062a3c065b6bf6d9acc2ab
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,258 @@
+# -*- coding: utf-8 -*-
+#
+# MOOSE documentation build configuration file, created by
+# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
+# updated on Thr Jan 21 00:30:10 2016
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+import subprocess
+
+# 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
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('../python'))
+sys.path.append(os.path.abspath('../../moose-examples/snippets'))
+sys.path.append(os.path.abspath('../../moose-examples/tutorials/ChemicalOscillators'))
+sys.path.append(os.path.abspath('../../moose-examples/tutorials/ChemicalBistables'))
+sys.path.append(os.path.abspath('../../moose-examples/tutorials/ExcInhNet'))
+sys.path.append(os.path.abspath('../../moose-examples/neuroml/lobster_pyloric'))
+sys.path.append(os.path.abspath('../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.autosummary',
+ 'sphinx.ext.viewcode',
+ 'numpydoc'
+ ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'MOOSE'
+copyright = u'2016, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray, Harsha Rani and Dilawar Singh'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '3.2'
+# The full version, including alpha/beta/rc tags.
+release = '3.2'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'sphinx_rtd_theme'
+#html_theme = 'default'
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+# html_theme_options = {'stickysidebar': 'true',
+# 'sidebarwidth': '300'}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = 'images/moose_logo.png'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'MOOSEdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'MOOSE.tex', u'MOOSE Documentation',
+ u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = 'images/moose_logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+latex_show_pagerefs = True
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'moose', u'MOOSE Documentation',
+ [u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'MOOSE', u'MOOSE Documentation',
+ u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
+ 'Science'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+#numpydoc option
+numpydoc_show_class_members = True
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6eaf405ade8709b64fa26258a6fcc614849ec667
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,39 @@
+.. MOOSE documentation master file, created by
+ sphinx-quickstart on Tue Jul 1 19:05:47 2014.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+the Multiscale Object-Oriented Simulation Environment
+=====================================================
+What is MOOSE and what is it good for?
+--------------------------------------
+MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
+
+.. figure:: ../../images/Gallery_Moose_Multiscale.png
+ :alt: **multiple scales in moose**
+ :scale: 50%
+
+ *Multiple scales can be modelled and simulated in MOOSE*
+
+MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
+
+MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
+
+MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+ :numbered:
+
+ introduction/index
+ user/py/index
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/docs/introduction/index.rst b/docs/introduction/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7644a78a5efd195a4a63388ea3ca25c1e81a13b2
--- /dev/null
+++ b/docs/introduction/index.rst
@@ -0,0 +1,11 @@
+Introduction
+============
+
+.. toctree::
+ :maxdepth: 1
+
+ install
+ release_notes
+ changes
+ known_issues
+
diff --git a/docs/user/py/index.rst b/docs/user/py/index.rst
index fc48c70ff8707d6c5f7f563f8a0eaf9b1410f26a..20b8a4830f8a0225174b88b80c038068f0fa94d7 100644
--- a/docs/user/py/index.rst
+++ b/docs/user/py/index.rst
@@ -1,42 +1,10 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jul 1 19:05:47 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-the Multiscale Object-Oriented Simulation Environment
-=====================================================
-What is MOOSE and what is it good for?
---------------------------------------
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
-
-.. figure:: ../../images/Gallery_Moose_Multiscale.png
- :alt: **multiple scales in moose**
- :scale: 50%
-
- *Multiple scales can be modelled and simulated in MOOSE*
-
-MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
-
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
-
-MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
-
Contents:
.. toctree::
:maxdepth: 2
:numbered:
- moose_build
moose_quickstart
moose_cookbook
moose_builtins
moose_classes
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/docs/user/py/moose_build.rst b/docs/user/py/moose_build.rst
deleted file mode 100644
index 548d8c57efa7d2824679d88aa760b76f113f7891..0000000000000000000000000000000000000000
--- a/docs/user/py/moose_build.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Building and installing MOOSE
-=============================
-
-todo
diff --git a/docs/user/py/moose_quickstart.rst b/docs/user/py/moose_quickstart.rst
index d5468d2c6478216831dacf21c1d64b62e6a3ad6d..f4f01bce2dad1112a4777a97e5497454a0b085e5 100644
--- a/docs/user/py/moose_quickstart.rst
+++ b/docs/user/py/moose_quickstart.rst
@@ -1,6 +1,5 @@
-***********************************************
Getting started with python scripting for MOOSE
-***********************************************
+==============================================
.. :Author: Subhasis Ray
.. :Date: December 12, 2012,