OpenMS · matteopilz · Dec 8, 2022 · Dec 8, 2022 · Dec 8, 2022 · Dec 8, 2022
diff --git a/docs/contribute-to-openms/pull-request-checklist.md b/docs/contribute-to-openms/pull-request-checklist.md
@@ -8,7 +8,7 @@ Before opening a pull request, check the following:
  Windows).
 2. **Do all tests pass?**
  To check if all tests have passed, execute `ctest`.
- If a test that is unrelated to your changes fails, check the [nightly builds](http://cdash.openms.de/index.php?project=OpenMS)
+ If a test that is unrelated to your changes fails, check the [nightly builds](https://cdash.openms.de/index.php?project=OpenMS)
  to see if the error is also in `develop`. If the error is in develop, [create a github issue](write-and-label-github-issues.md).
 3. **Is the code documented?**
  Document all new classes, including their methods and parameters.

diff --git a/docs/introduction/entry-points-to-openms.md b/docs/introduction/entry-points-to-openms.md
@@ -36,7 +36,7 @@ The following entry points for OpenMS and its TOPP tools are available for users
 :::
 
 :::{grid-item-card} {fab}`python;sd-text-info fa-xl` **pyOpenMS** <br/> Use the pyOpenMS python library to rapidly prototype methods and scripts
- :link: https://pyopenms.readthedocs.io/en/latest/installation.html
+ :link: https://pyopenms.readthedocs.io/en/latest/user_guide/installation.html
  :link-type: url
  :class-title: flex
 

diff --git a/docs/openms-applications-and-tools/openms-applications/swathwizard.md b/docs/openms-applications-and-tools/openms-applications/swathwizard.md
@@ -7,7 +7,7 @@ SwathWizard
 SwathWizard is an assistant for Swath analysis.
 
 The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the
-[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
+[TOPP Documentation: OpenSwathWorkflow](https://openms.readthedocs.io/en/latest/tutorials-and-quickstart-guides/openms-user-tutorial.html#id44) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
 
 Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation
 status and warn the user if a component is missing.

diff --git a/docs/run-workflows-with-openms-tools/knime/installation.md b/docs/run-workflows-with-openms-tools/knime/installation.md
@@ -51,10 +51,10 @@ Installation of OpenMS in {term}`KNIME` is platform-independent across Windows,
 ## Creating workflows with KNIME
 
 Download Introduction to OpenMS in KNIME [user tutorial](../../tutorials-and-quickstart-guides/openms-user-tutorial.md) 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
+usage of KNIME. See the official [KNIME Getting Started Guide](https://www.knime.com/getting-started-guide) for a more in-depth view of
 the KNIME functionality besides OpenMS.
 
-If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/c/community-extensions/openms/40).
+If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tag/openms).
 
 ## Creating your own Generic KNIME Nodes
 

diff --git a/docs/run-workflows-with-openms-tools/knime/tutorial.md b/docs/run-workflows-with-openms-tools/knime/tutorial.md
@@ -2493,7 +2493,7 @@ Now launch ”Spyder” (python IDE) in the home menu.
 
 ### Build instructions
 
-Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/build_from_source.html).
+Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/community/build_from_source.html).
 
 ### Scripting with pyOpenMS
 
@@ -3062,7 +3062,7 @@ Human Metabolome Database in 2013, Nucleic Acids Res 41(Database issue),D801–7
 
 [^17]: J. Griss, A. R. Jones, T. Sachsenberg, M. Walzer, L. Gatto, J. Hartler, G. G.
 Thallinger, R. M. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan,
-F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), <a href="https://www.mcponline.org/article/S1535-9476(20)32821-8/fulltext">doi:10.1074/mcp.O113.036681</a>. 69
+F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), <a href="https://pyopenms.readthedocs.io/en/latest/user_guide/ms_data.html">doi:10.1074/mcp.O113.036681</a>. 69
 
 [^18]: S. Böcker, M. C. Letzel, Z. Lipták, and A. Pervukhin, SIRIUS: Decomposing isotope
 patterns for metabolite identification, Bioinformatics 25(2), 218–224 (2009), <a href="https://academic.oup.com/bioinformatics/article/25/2/218/218950">doi:10.1093/bioinformatics/btn603</a>. 75

diff --git a/docs/topp-and-utils/swathwizard.md b/docs/topp-and-utils/swathwizard.md
@@ -7,7 +7,7 @@ SwathWizard
 An assistant for Swath analysis.
 
 The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the
-[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
+[TOPP Documentation: OpenSwathWorkflow](https://openms.readthedocs.io/en/latest/tutorials-and-quickstart-guides/openms-user-tutorial.html#id44) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
 
 Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation
 status and warn the user if a component is missing.

diff --git a/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md b/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md
@@ -5,7 +5,7 @@ To contribute to OpenMS:
 
 - Familiarise yourself with the [OpenMS online documentation](../../index.rst).
 - Learn how to [build OpenMS](../../develop-with-openms/build-openms-from-source.md).
-- Check out the [OpenMS tutorial for developers](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/OpenMS_tutorial.html).
+- Check out the [OpenMS tutorial for developers](https://openms.readthedocs.io/en/latest/develop-with-openms/developer-tutorial.html).
 
 For any questions, please [contact us](/quick-reference/contact-us.md).
 
@@ -61,7 +61,7 @@ Nightly tests run on different platforms. It is recommended to test on different
 This saves time and increases productivity during continuous integration tests.
 ```
 
-Nightly tests: [CDASH](http://cdash.openms.de/index.php?project=OpenMS).
+Nightly tests: [CDASH](https://cdash.openms.de/index.php?project=OpenMS).
 
 ## Further contributor resources
 

diff --git a/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md b/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md
@@ -2492,7 +2492,7 @@ Now launch ”Spyder” (python IDE) in the home menu.
 
 ### Build instructions
 
-Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/build_from_source.html).
+Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/community/build_from_source.html).
 
 ### Scripting with pyOpenMS
 
@@ -3061,7 +3061,7 @@ Human Metabolome Database in 2013, Nucleic Acids Res 41(Database issue),D801–7
 
 [^17]: J. Griss, A. R. Jones, T. Sachsenberg, M. Walzer, L. Gatto, J. Hartler, G. G.
 Thallinger, R. M. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan,
-F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), <a href="https://www.mcponline.org/article/S1535-9476(20)32821-8/fulltext">doi:10.1074/mcp.O113.036681</a>. 69
+F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), <a href="https://pyopenms.readthedocs.io/en/latest/user_guide/ms_data.html">doi:10.1074/mcp.O113.036681</a>. 69
 
 [^18]: S. Böcker, M. C. Letzel, Z. Lipták, and A. Pervukhin, SIRIUS: Decomposing isotope
 patterns for metabolite identification, Bioinformatics 25(2), 218–224 (2009), <a href="https://academic.oup.com/bioinformatics/article/25/2/218/218950">doi:10.1093/bioinformatics/btn603</a>. 75

diff --git a/docs/tutorials/KNIME/KNIME-tutorial.md b/docs/tutorials/KNIME/KNIME-tutorial.md
@@ -58,10 +58,10 @@ Installation of OpenMS in {term}`KNIME` is platform-independent across Windows,
 ## Creating workflows with KNIME
 
 Download Introduction to OpenMS in KNIME [user tutorial](../../tutorials-and-quickstart-guides/openms-user-tutorial.md) 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
+usage of KNIME. See the official [KNIME Getting Started Guide](https://www.knime.com/getting-started-guide) for a more in-depth view of
 the KNIME functionality besides OpenMS.
 
-If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/c/community-extensions/openms/40).
+If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tag/openms).
 
 ## Creating your own Generic KNIME Nodes