OpenMS · tapaswenipathak · Jun 8, 2022 · Jun 7, 2022
diff --git a/docs/glossary.md b/docs/glossary.md
@@ -185,6 +185,6 @@ De novo peptide sequencing
   ({term}`MS/MS` or {term}`MS^3`) fragment ions, without comparison to a reference proteome.
 
 TOPPAS
-  An assistant for GUI-driven TOPP workflow design.
+  An assistant for GUI-driven TOPP workflow design. It is recommended to use OpenMS through the KNIME plugins.
 ```
 
diff --git a/docs/images/tutorials/knime/KNIME_Install.png b/docs/images/tutorials/knime/KNIME_Install.png
diff --git a/docs/images/tutorials/knime/KNIME_screenshot.png b/docs/images/tutorials/knime/KNIME_screenshot.png
diff --git a/docs/images/tutorials/knime/KNIME_update_site.jpeg b/docs/images/tutorials/knime/KNIME_update_site.jpeg
diff --git a/docs/index.rst b/docs/index.rst
@@ -20,6 +20,14 @@ OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
 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.
 
+.. important::
+As part of the **Center for Integrative Bioinformatics** (CiBi) in the **German Network for Bioinformatics**
+`deNBI <https://www.denbi.de/>`_,
+OpenMS is currently focusing the development efforts on the integration of OpenMS into KNIME. KNIME is a well-established
+data analysis framework that supports the generation of workflows for data analysis. Using a Common Tool Description
+(CTD) file which is writeable by every TOPP tool and a node generator program (`Generic KNIME Nodes <https://github.com/genericworkflownodes/GenericKnimeNodes>`_), all :term:`TOPP tools` can be made available to run in KNIME.
+
+
 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
@@ -57,6 +65,7 @@ Contents
 
    tutorials/TOPP/TOPP-tutorial
    tutorials/TOPPAS/TOPPAS-tutorial
+   tutorials/KNIME/KNIME-tutorial
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/tutorials/KNIME/KNIME-tutorial.md b/docs/tutorials/KNIME/KNIME-tutorial.md
@@ -0,0 +1,67 @@
+KNIME Tutorial
+==============
+
+Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future.
+
+The below image shows an example workflow in {term}`KNIME`.
+
+![](../../images/tutorials/knime/KNIME_screenshot.png)
+
+
+## Installing OpenMS in KNIME
+
+Installation of OpenMS in {term}`KNIME` is platform-independent across Windows, MacOSX, and Linux.
+
+1. Download the latest {term}`KNIME` release from the [KNIME website](https://www.knime.com/).
+2. In the full install of {term}`KNIME` skip the following installation routine since all required plugins should be
+   installed by default. For the standard (core) installation, follow the instructions here or in the extended [user-tutorial]().
+
+   ![](../../images/tutorials/knime/KNIME_Install.png)
+
+3. In KNIME click on **Help** > **Install new Software**.
+4. Install the required KNIME File Handling nodes from the official KNIME Update Site (a standard entry in the update
+   sites). Choose the update site from the **Work with:** dropdown menu.
+
+
+   **Name**: KNIME Analytics Platform ${YOUR_KNIME_VERSION} Update Site.
+
+   **Location**: http://update.knime.org/analytics-platform/${YOUR_KNIME_VERSION}
+
+5. Filter the results for **File handling** and select the {term}`KNIME` File Handling Nodes. Click **Next** and install.
+
+   ![](../../images/tutorials/knime/KNIME_update_site.jpeg)
+
+6. Now, install the actual OpenMS pluging. Next to the **Work with:** dropdown menu, click on **Add...**. In the opening
+   dialog fill in at least one of the following additional Update Sites (if not already present):
+
+   **Recommened**:
+
+   **Name**: KNIME Community Contributions (Stable)
+
+   **Location**: http://update.knime.org/community-contributions/trusted/${YOUR_KNIME_VERSION}
+
+   **Unstable**:
+
+   **Name**: KNIME Nightly Community Contributions (trunk)
+
+   **Location**:  http://update.knime.org/community-contributions/trunk
+
+7. Use the search or navigate to **KNIME Community Contributions – Bioinformatics & NGS** and select **OpenMS**. Then
+   click **Next** and follow the installation instructions. A restart of KNIME might be necessary afterward. On Windows,
+   if prompted to install additional requirements like the Microsoft Visual Studio Redistributable for the conversion
+   software ProteoWizard that is packaged with our plugin.
+8. After a restart of KNIME the OpenMS nodes will be available in your Node Repository (panel on the lower left) under
+   **Community Nodes**.
+
+## Creating workflows with KNIME
+
+Download Introduction to OpenMS in KNIME [user tutorial]() containing hands-on training material covering also basic
+usage of KNIME. See the official [KNIME Getting Started Guide](https://tech.knime.org/knime) for a more in-depth view of
+the KNIME functionality besides OpenMS.
+
+If you face any issues, please [contact us](../../contact-us.md) and specifically for the usage of OpenMS in KNIME, the
+KNIME community contribution [forum](https://tech.knime.org/forum/openms).
+
+## Creating your own Generic KNIME Nodes
+
+See the more advanced instructions on our [Getting Started]() page for developers in OpenMS API reference.
diff --git a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md
@@ -5,6 +5,11 @@ TOPPAS Tutorial
 The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition
  in the `.toppas` file.
 
+```{important}
+Active development of TOPPAS is stopped. In near future, TOPPAS will be completely deprecated. Please migrate to using
+OpenMS KNIME integration.
+```
+
 ```{toctree}
 :maxdepth: 1