.. Opal documentation master file, created by
   sphinx-quickstart on Mon Apr  9 11:43:58 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

OBiBa Opal Documentation
=========================

Targeted at individual studies and study consortia, `OBiBa <http://obiba.org/>`_ software stack (Opal, Mica etc.) provides a software solution for epidemiological data management, analysis and publication. `Opal <http://www.obiba.org/pages/products/opal/>`_ is the core data warehouse application that provides all the necessary tools to import, transform and describe data. Opal can be used with `Agate <http://www.obiba.org/pages/products/agate/>`_, the `OBiBa <http://obiba.org/>`_'s central authentication server.

.. toctree::
   :maxdepth: 2

   introduction

.. toctree::
   :maxdepth: 1
   :caption: Administrator Guide

   admin/installation
   admin/configuration
   admin/plugins
   admin/rserver

.. toctree::
   :maxdepth: 1
   :caption: Cookbook

   cookbook/index
   cookbook/import-data
   cookbook/r-datashield

.. toctree::
   :maxdepth: 1
   :caption: Web User Guide

   web-user-guide/index
   web-user-guide/projects
   web-user-guide/search
   web-user-guide/administration
   web-user-guide/my-profile
   web-user-guide/permissions

.. toctree::
   :maxdepth: 1
   :caption: R DataSHIELD User Guide

   r-user-guide/index
   r-user-guide/r
   r-user-guide/datashield

.. toctree::
   :maxdepth: 1
   :caption: Python User Guide

   python-user-guide/index
   python-user-guide/api
   python-user-guide/commands

.. toctree::
  :maxdepth: 1
  :caption: Magma Javascript API

  magma-user-guide/index
  magma-user-guide/methods

Partners and Funders
====================

The development of this application was made possible thanks to the support of our partners and funders:

.. |mr-logo| image:: https://www.obiba.org/assets/themes/bootstrap/img/logo-maelstrom.png
  :height: 60px
  :target: https://www.maelstrom-research.org/

.. |ep-logo| image:: https://www.obiba.org/assets/themes/bootstrap/img/epigeny.png
  :height: 40px
  :target: https://www.epigeny.io/

.. |can-logo| image:: https://www.obiba.org/assets/themes/bootstrap/img/canarie.png
  :height: 60px
  :target: https://www.canarie.ca/

.. |ecc-logo| image:: https://www.obiba.org/assets/themes/bootstrap/img/eucanconnect.png
  :height: 50px
  :target: https://www.eucanconnect.eu/

+------------+------------+------------+------------+
| |mr-logo|  + |ep-logo|  + |can-logo| + |ecc-logo| +
+------------+------------+------------+------------+

Support
=======

Please visit `OBiBa support <https://www.obiba.org/pages/support/>`_ page.