Production ready[3] fixes: improvements: touchup and cleanup

docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md

@@ -1,7 +1,7 @@
 Developer Guidelines For Adding New Dependent Libraries
 ======================================================
 
-# Our dependency library philosophy
+## Our dependency library philosophy
 
 In short, requirements for adding a new library are:
 - indispensable functionality

docs/additional-resources/external-code-using-openms.md

@@ -11,7 +11,7 @@ ways to do this:
 Once you've finished your new tool, and it only needs to run on the development machine. To ship it to a new client machine,
 see, read further in this document.
 
-# Compiling external code
+## Compiling external code
 
 It is very easy to set up an environment to write your own programs using OpenMS. Make sure to downloaded and installed
 the source package of OpenMS/TOPP properly.
@@ -93,7 +93,7 @@ For more information visit the website of cmake at cmake.org and consult the doc
 Have fun coding with OpenMS!
 ```
 
-# Shipping external code to a new machine
+## Shipping external code to a new machine
 
 If you've modified OpenMS itself and not used an external project use our installer scripts, to build your own OpenMS
 installer for your platform (see our internal FAQ which is built using "make doc_internal") and ship that to a client

docs/glossary.md

@@ -4,6 +4,46 @@ OpenMS Glossary
 A glossary of common terms used throughout OpenMS documentation.
 
 ```{glossary}
+
+OpenMS API
+  [OpenMS API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html).
+  The object-oriented OpenMS core library contains over 1,300 classes and is built on modern C++ infrastructure
+  with native compiler support on Windows, Linux and macOS. The classes are representing core concepts in mass
+  spectrometry as well as the corresponding ontologies defined by the Human Proteome Organization Proteomics
+  Standard Initiative (HUPO-PSI).
+
+Workflow
+  A set of over 185 different tools for common mass spectrometric tasks can be accessed by routine users through
+  the KNIME, and Galaxy workflow systems.
+
+SILAC
+  **S**table **I**sotope **L**abeling by/with **A**mino acids in **C**ell culture is a technique based on mass
+  spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling.
+
+iTRAQ
+  **I**sobaric **T**ags for **R**elative and **A**bsolute **A**uantitation (iTRAQ) is an isobaric labeling method
+  used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different
+  sources in a single experiment.
+
+TMT
+  A **T**andem **M**ass **T**ag (TMT) is a chemical label that facilitates sample multiplexing in mass spectrometry
+  ({term}`MS`)-based quantification and identification of biological macromolecules such as proteins, {term}`peptides`
+  and nucleic acids.
+
+SRM
+  **S**elected **R**eaction **M**onitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used
+  in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass
+  spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass
+  spectrometer stage for detection.
+
+SWATH
+  SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims
+  to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted
+  proteomics at large scale.
+
+KNIME
+  **K**onstanz **I**nformation **M**iner, is a free and open-source data analytics, reporting and integration platform.
+
 LC-MS
   [Liquid Chromatography(LC)](introduction.md#liquid-chromatography-lc) and [Mass Spectrometry(MS)](introduction.md#mass-spectrometry).
 

docs/index.rst

@@ -2,25 +2,25 @@ About OpenMS
 ============
 
 `OpenMS <http://www.openms.org/>`_
-is an open-source software C++ library for LC-MS data management and
+is an open-source software C++ library for {term}`LC-MS` data management and
 analyses. It offers an infrastructure for rapid development of mass
 spectrometry related software. OpenMS is free software available under the
 three clause BSD license and runs under Windows, macOS, and Linux.
 
 It comes with a vast variety of pre-built and ready-to-use tools for proteomics
-and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D
-visualization (TOPPView).
+and metabolomics data analysis ({term}`TOPP Tools`) as well as powerful 1D, 2D and 3D
+visualization ({term}`TOPPView`).
 
 OpenMS offers analyses for various quantitation protocols, including label-free
-quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc.
+quantitation, {term}`SILAC`, {term}`iTRAQ`, {term}`TMT`, {term}`SRM`, {term}`SWATH`, etc.
 
 It provides built-in algorithms for de-novo identification and database search,
-as well as adapters to other state-of-the art tools like X!Tandem, Mascot,
+as well as adapters to other state-of-the art tools like X!Tandem, {term}`Mascot`,
 OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
-engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and
+engines like {term}`KNIME`, Galaxy, WS-Pgrade, and {term}`TOPPAS` via the TOPPtools concept and
 a unified parameter handling via a 'common tool description' (CTD) scheme.
 
-With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API
+With {term}`pyOpenMS`, OpenMS offers Python bindings to a large part of the {term}`OpenMS API`
 to enable rapid algorithm development. OpenMS supports the Proteomics Standard
 Initiative (PSI) formats for MS data. The main contributors of OpenMS are
 currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität
@@ -67,29 +67,30 @@ Contents
 
 .. toctree::
    :maxdepth: 2
-   :caption: Frequently Asked Questions
-
-   faqs/developer-faq.md
-   faqs/contributor-faq.md
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Advanced Resources
+   :caption: Developer Resources
 
+   additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md
+   additional-resources/external-code-using-openms.md
    advanced-resources/custom-compilation.md
    advanced-resources/build-custom-openms-knime-package.md
 
 .. toctree::
    :maxdepth: 2
-   :caption: Additional Resources
+   :caption: OpenMS GitHub Workflow
 
-   additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md
-   additional-resources/external-code-using-openms.md
    additional-resources/openms-git-workflow.md
    additional-resources/reporting-bugs-and-issues.md
    additional-resources/write-and-label-github-issues.md
    additional-resources/pull-request-checklist.md
 
+.. toctree::
+   :maxdepth: 2
+   :caption: Frequently Asked Questions
+
+   faqs/developer-faq.md
+   faqs/contributor-faq.md
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Downloads

docs/introduction.md

@@ -101,6 +101,6 @@ wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstall
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe
 ```
 
-```{tab} MacOS
+```{tab} macOS
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg
 ```