About ``CMPB``
==============

The *CarveMe + ModelPolisher based (CMPB)* workflow curates a model using ``refineGEMs`` and ``ModelPolisher``.
The starting point is either the input files for ``CarveMe`` (future update) or an already built model.

This workflow aims at minimising the user's workload by concatenating steps that could be done individually with the 
integrated tools.

.. _cmpb-overview:

Overview of the ``CMPB`` worfklow
---------------------------------

The following image shows an overview of the steps of the worfklow:

.. _cmpb_workflow:

.. figure:: ../images/cmpb_pipeline-overview.png
  :alt: Workflow from CaveMe to close-to-final model

  Workflow from ``CaveMe`` to close-to-final model

The following steps are executed in the workflow:

.. hint::
  All steps can also be performed individually.

  Many of the steps of the worfklow can be fine tuned and turned off/on. 
  Check the :doc:`configuration file <cmpb-config>` for a full list of all parameters.

- Step 0: Possible inputs

  - Model (e.g. created with CarveMe)
  - Data to create a model with CarveMe

- Step 1.A: If the model is/was built with ``CarveMe`` a correction is performed as ``CarveMe`` adds valuable information for example in the notes and not the corresponding fields of the SBML document. 
- Step 1.B: The model is gap filled. The gap fill step includes all available algorithmns from the ``refineGEMs`` gapfill module. 
- Step 2: ``ModelPolisher`` is used to enhance the annotation content (future update). 
- Step 3: Annotations

  - Adding pathways as Groups from KEGG
  - Using ``SBOannotator`` to get more specific SBO term annotations

- Step 4: Model cleanup

  - Using MassChargeCuration
  - Optionally: Using ``BOFdat``
  - Optionally: Removing duplicates

- Step 5: Model analyses

  - Model statistics
  - Analysing growth
  - Testing for amino acid auxotrophies
  - Optionally: Analysing with ``FROG`` (future update)
  - Optionally: Analysing with ``MEMOTE``

| For each step the model version and, optionally, the according ``MEMOTE`` report can be saved.
| All tools are accessed via ``refineGEMs`` unless stated otherwise. 
| Steps or tools marked as future update will be added in a later version of the workflow.

.. note::

    All accessible functions are listed in the :ref:`Contents of SPECIMEN` section.