<commit_before>.. include:: readme_sphinx.rst

------------
Tutorials
------------

.. toctree::
   :maxdepth: 1

   Quickstart guide <tutorials/quickstart>

Introductory
#############

.. toctree::
   :maxdepth: 1

   An introduction to WESTPA (video tutorial) <https://www.youtube.com/watch?v=YpltPzpcmLY>
   Analysis Tools (video tutorial) <https://www.youtube.com/watch?v=rMFvcHOOxZc>
   Spatially-resolved Systems Biology (MCell) Models (video tutorial) <https://www.youtube.com/watch?v=rY-IJcLFiaM>
   Chignolin tutorial <tutorials/chignolin>
   AMBER   <tutorials/amber>
   GROMACS <tutorials/gromacs>
   NAMD    <tutorials/namd>

Advanced
#############

.. toctree::
   :maxdepth: 1

   Molecular Scale Systems <tutorials/p53>
   OpenMM <tutorials/openmm>
   Weighted ensemble-based string method <http://stringmethodexamples.readthedocs.org/>

------------
Advanced Reference
------------

.. toctree::
   :maxdepth: 1

    WEST                      <users_guide/west>
    WEST tools                <users_guide/west_tools>
    WEST work manager         <users_guide/wwmgr>
    WEST extensions           <users_guide/westext>
    Command line tool index   <users_guide/command_line_tools>
    HDF5 file schema          <users_guide/hdf5>


------------
Development
------------

.. toctree::
   :maxdepth: 1

    Overview                           <development/overview>
    Code and documentation style guide <development/style_guide>
    Source code management             <development/source_code>
    Building the documentation         <development/documentation>
    API                                <development/api><commit_msg>Fixed header markup<commit_after>.. include:: readme_sphinx.rst

------------
Tutorials
------------

.. toctree::
   :maxdepth: 1

   Quickstart guide <tutorials/quickstart>

Introductory
#############

.. toctree::
   :maxdepth: 1

   An introduction to WESTPA (video tutorial) <https://www.youtube.com/watch?v=YpltPzpcmLY>
   Analysis Tools (video tutorial) <https://www.youtube.com/watch?v=rMFvcHOOxZc>
   Spatially-resolved Systems Biology (MCell) Models (video tutorial) <https://www.youtube.com/watch?v=rY-IJcLFiaM>
   Chignolin tutorial <tutorials/chignolin>
   AMBER   <tutorials/amber>
   GROMACS <tutorials/gromacs>
   NAMD    <tutorials/namd>

Advanced
#############

.. toctree::
   :maxdepth: 1

   Molecular Scale Systems <tutorials/p53>
   OpenMM <tutorials/openmm>
   Weighted ensemble-based string method <http://stringmethodexamples.readthedocs.org/>

-------------------
Advanced Reference
-------------------

.. toctree::
   :maxdepth: 1

    WEST                      <users_guide/west>
    WEST tools                <users_guide/west_tools>
    WEST work manager         <users_guide/wwmgr>
    WEST extensions           <users_guide/westext>
    Command line tool index   <users_guide/command_line_tools>
    HDF5 file schema          <users_guide/hdf5>


------------
Development
------------

.. toctree::
   :maxdepth: 1

    Overview                           <development/overview>
    Code and documentation style guide <development/style_guide>
    Source code management             <development/source_code>
    Building the documentation         <development/documentation>
    API                                <development/api>
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