index.rst

This documentation is deprecated

The documentation here is no longer up to date. Functionality within django-misa and django-mbrowse were combined into django-mogi and functionality was developed specifically for the creation of DMAdb.

See dmadb-docs for most up to date documentation

MOGI suite

Django applications & projects

The MOGI suite is a collection of Django applications to manage and organise metabolomic studies using Galaxy, ISA and Django frameworks.

The suite consists of the following reusable applications:

• :ref:`django-mogi`
• :ref:`django-misa`
• :ref:`django-galaxy`
• :ref:`django-mbrowse`
• :ref:`django-gfiles`

The django-mogi application inherits all of the detailed applications below to create ready to go framework for organising metabolomics studies with Galaxy and ISA. The full suite of applications can be used in either a docker container or directly as Django package run. See :ref:`user-docs` for details about how to get up and running with the full suite of applications.

Additionally, each application has been developed to be reusable. This allows the more general functionality to be used in other Django projects and applications. See the individual package documentation for more details.

The figure below shows how the applications fit within Django project website

What the MOGI suite can do

• Organise metabolomics studies following ISA framework
• Interface with Galaxy (initiate workflows, manage history, inport/export data)
• Search metabolomics spectra across multiple projects (spectral matching, mass search)
• Summarise compound annotations (e.g. from different annotation approaches like MetFrag, CSI:FingerID, spectral matching)

User Documentation

.. toctree::
   :maxdepth: 2

   User docs <user-docs/index.rst>

django-mogi

Metabolome Organisation with Galaxy and ISA (imports all of the django-applications within the Django MOGI application suite)

.. toctree::
   :maxdepth: 2

   django-mogi <django-mogi/index.rst>

django-galaxy

Django interfacing with Galaxy. Backend using the bioblend API.

.. toctree::
   :maxdepth: 2

   django-galaxy  <django-galaxy/index.rst>

django-misa

ISA organisation for metabolomic studies with Django

.. toctree::
   :maxdepth: 2

   django-misa <django-misa/index.rst>

django-mbrowse

Browse, view and search metabolomic datasets

.. toctree::
   :maxdepth: 2

   django-mbrowse <django-mbrowse/index.rst>

django-gfiles

Simple file management for generic files in Django

.. toctree::
   :maxdepth: 2

   django-gfiles <django-gfiles/index.rst>

About

.. toctree::

   Contacts  <contacts.rst>