Finalised intro, index & installation #120 #121

draeger-lab · Jul 15, 2024 · 1f5b026 · 1f5b026
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diff --git a/docs/source/database/intro.rst b/docs/source/database/intro.rst
@@ -33,11 +33,11 @@ Working with the Data
 
 For understanding the database and the data it contains, it is vital to understand the meaning of
 an *in silico* medium and how to transform a medium e.g. from the labratory (*in vivo* medium)
-into an *in silico* medium. 
+into an *in silico* medium. Our standardised aproach is described in :doc:`in_silico_media_generation`.
 
-Afterwards, you can find a detailed explaination of the database architecture.
+You can find a detailed explanation of the database architecture under :doc:`db_architecture`.
 
-Additionally, the last point refers to more information about accessing the database.
+Additionally, the last point refers to more information about accessing the database. ``TODO`` Worauf bezieht sich das hier genau?
 
 .. toctree::
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -56,7 +56,7 @@ Connections to other tools
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 ``refineGEMs`` also provides access points for other tools:
 
-* Reporting the `Memote <https://memote.readthedocs.io/en/latest/index.html>`__ score or generating a complete `Memote <https://memote.readthedocs.io/en/latest/index.html>`__ report
+* Reporting the `MEMOTE <https://memote.readthedocs.io/en/latest/index.html>`__ score or generating a complete MEMOTE report
 * Updating the SBO-Term annotations based on `SBOannotator <https://github.com/draeger-lab/SBOannotator>`__\ :footcite:p:`Leonidou2023_sboann`
 * Balancing the masses and charges with `MassChargeCuration (MCC) <https://github.com/Biomathsys/MassChargeCuration>`__\ :footcite:p:`Finnem2023_mcc`
 * Correcting a biomass objective function with `BOFdat <https://github.com/jclachance/BOFdat>`__

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -20,7 +20,3 @@ To install refineGEMs as Python package from `PyPI <https://pypi.org/project/ref
    pip install refineGEMs
 
 The corresponding project site can be found `here <https://pypi.org/project/refineGEMs/>`__.
-
-.. note::
-
-   TODO: Add content about how to install BOFdat and MCC!