diff --git a/docs/conf.py b/docs/conf.py
index ee2c2dfff8190e50c5a61e63a5fd8bf8aada1c54..87d43a57cda8a8225ff7f30ce707b741a9776c2c 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -63,19 +63,19 @@ copyright = u'2016, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Sub
# built documents.
#
# The short X.Y version.
-version = '3.2'
+version = '3.1'
# The full version, including alpha/beta/rc tags.
-release = '3.2'
+release = 'chamcham (3.1.1)'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
-#language = None
+language = 'English'
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
-#today = ''
+today = ''
# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
diff --git a/docs/generate-documentation b/docs/generate-documentation
index c50795126136755153b1c7f2b00e1101820166fc..94b6de2e89929da5c89a7e6b78f381ca41d202cc 100755
--- a/docs/generate-documentation
+++ b/docs/generate-documentation
@@ -15,4 +15,3 @@ echo "##############################################################"
#Files will be created in _build/html
mkdir -p _build
sphinx-build . _build
-
diff --git a/docs/index.rst b/docs/index.rst
index 9ba3f9d9d0786209ed6c0831229bad670a7f516a..f89b5d9bd5cdf67c69cd153ae2d3bb5acf0582c6 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -48,8 +48,7 @@ Contents:
user/py/quickstart/index
user/py/rdesigneur/index
user/py/cookbook/index
- user/py/builtins/index
- user/py/classes/index
+ user/py/builtins_classes/index
Indices and tables
==================
diff --git a/docs/introduction/index.rst b/docs/introduction/index.rst
index 88ba2bdae746ec62908fd7cf40a715af3e909b8a..b55005ae6f816a5f00fdf23c1bad96f77bd1f681 100644
--- a/docs/introduction/index.rst
+++ b/docs/introduction/index.rst
@@ -7,4 +7,3 @@ Introduction
release_notes/index
changes/index
known_issues/index
-
diff --git a/docs/user/py/builtins_classes/index.rst b/docs/user/py/builtins_classes/index.rst
index 7f1f6a66fb206cd17ef7e8ba7b77944736df4c20..e7d70b16f7ab35d39d9a4da3115f7a91fa9eab26 100644
--- a/docs/user/py/builtins_classes/index.rst
+++ b/docs/user/py/builtins_classes/index.rst
@@ -1,25 +1,7 @@
-.. 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
-=====================================================
-Automatically generated documentation for MOOSE built-in functions and MOOSE classes, as accessed through Python.
-
Contents:
.. toctree::
:maxdepth: 2
- :numbered:
moose_builtins
moose_classes
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/docs/user/py/cookbook/conf.py b/docs/user/py/cookbook/conf.py
deleted file mode 100644
index e842dbff1a9196773097e74faf5a5411d84eba90..0000000000000000000000000000000000000000
--- a/docs/user/py/cookbook/conf.py
+++ /dev/null
@@ -1,258 +0,0 @@
-# -*- 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
-
-# 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('../../../../moose-core/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 = False
diff --git a/docs/user/py/cookbook/index.rst b/docs/user/py/cookbook/index.rst
index a5d9d198700da2e36627baf988bbe945275fd997..ea6f3dde1e2fefe6844283606d069d8e4e03208c 100644
--- a/docs/user/py/cookbook/index.rst
+++ b/docs/user/py/cookbook/index.rst
@@ -1,24 +1,4 @@
-.. 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
-=====================================================
-The MOOSE Cookbook contains recipes showing you, how to do specific tasks in MOOSE
-
-Contents:
-
.. toctree::
:maxdepth: 2
- :numbered:
moose_cookbook
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/docs/user/py/cookbook/moose_cookbook.rst b/docs/user/py/cookbook/moose_cookbook.rst
index 193d3eee706a21084b1b8293a949fd0afa329fec..a0c40aa0c98693eed101fb493b8497ea076b7fed 100644
--- a/docs/user/py/cookbook/moose_cookbook.rst
+++ b/docs/user/py/cookbook/moose_cookbook.rst
@@ -683,6 +683,3 @@ Animation of values along an axis
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Using MOOGLI widgets to display a neuron
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-
diff --git a/docs/user/py/quickstart/conf.py b/docs/user/py/quickstart/conf.py
deleted file mode 100644
index e842dbff1a9196773097e74faf5a5411d84eba90..0000000000000000000000000000000000000000
--- a/docs/user/py/quickstart/conf.py
+++ /dev/null
@@ -1,258 +0,0 @@
-# -*- 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
-
-# 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('../../../../moose-core/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 = False
diff --git a/docs/user/py/quickstart/index.rst b/docs/user/py/quickstart/index.rst
index 959d1342c3b35524013047f7fa9a82c7e5812558..42f6f093187d65092fdb1d3136928f2433388b61 100644
--- a/docs/user/py/quickstart/index.rst
+++ b/docs/user/py/quickstart/index.rst
@@ -1,38 +1,4 @@
-.. 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_quickstart
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-