diff --git a/docs/source/cmpb/about-pipeline.rst b/docs/source/cmpb/about-pipeline.rst index a4f7295..279c7be 100644 --- a/docs/source/cmpb/about-pipeline.rst +++ b/docs/source/cmpb/about-pipeline.rst @@ -2,18 +2,15 @@ About ``CMPB`` ============== The CarveMe + ModelPolisher based (CMPB) pipeline curates a model using refineGEMs and ModelPolisher. -The starting point is either the input files for CarveMe (future update) or an already built model. If the model is/was -built with CarveMe a correction is performed. After that the model is gap filled. The gap fill step can be either done -with a manually created file or automatically. Afterwards ModelPolisher is used to enhance the annotation content -(future update). Further annotation enhancement is done by adding Pathways as Groups from KEGG and using the SBOannotator -via the refineGEMs connection to get more specific SBO term annotations. Afterwards the model is cleaned up with -MassChargeCuration and, optionally, with BOFdat. Both tools are accessed via refineGEMs. A further option for the clean -up is the removal of duplicates. There are optional steps to analyse the model with FROG (future update) or MEMOTE. The -default analysis steps include model statistics, growth analysis and auxotrophy tests. For each step the model version and, -optionally, the according MEMOTE report can be saved. - -Overview of the CMPB Pipeline ------------------------------ +The starting point is either the input files for CarveMe (future update) or an already built model. + +This pipeline 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`` Pipeline +--------------------------------- The following image shows an overrview of the steps of the pipeline: @@ -23,3 +20,45 @@ The following image shows an overrview of the steps of the pipeline: :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 pipeline can be fine tuned and turned off/on. + Check the :doc:`configuration file ` for a full list of all parameters. + +- Step 0: Possible inputs + + - Model (e.g. created with CarveMe) + - Data to create a model with CarveMe (future update) + +- 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 can be either done with a manually created file or automatically. +- 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 soon. + +.. note:: + + All accessible functions are listed in the :ref:`Contents of SPECIMEN` section. diff --git a/docs/source/cmpb/run-pipeline.rst b/docs/source/cmpb/run-pipeline.rst index b2166a4..092de98 100644 --- a/docs/source/cmpb/run-pipeline.rst +++ b/docs/source/cmpb/run-pipeline.rst @@ -5,7 +5,7 @@ This page explains how to run the complete ``CMPB`` (CarveMe + ModelPolisher bas and how to collect the neccessary data. For more information about the steps of the pipeline, -see :ref:`Overview of the CMPB Pipeline`. +see :ref:`cmpb-overview`. ``CMPB``: Quickstart -------------------- @@ -16,7 +16,7 @@ see :ref:`Overview of the CMPB Pipeline`. The CarveMe connection will be added in a future update. The pipeline can either be run directly from the command line or its functions can be called from inside a Python script. -The input in both cases is a `configuration file `__ that contains all information needed (data file paths and parameters) to run it. +The input in both cases is a :doc:`configuration file ` that contains all information needed (data file paths and parameters) to run it. The configuration can be downloaded using the command line: