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Update to webapps page #236

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9adc917
fix broken links
matteopilz Aug 15, 2023
f627c6b
fix broken links
matteopilz Aug 15, 2023
7bebec4
relink developer quickstart guide
matteopilz Oct 2, 2023
6a458d0
Merge remote-tracking branch 'origin/develop' into develop
matteopilz Oct 2, 2023
5fdc275
Merge remote-tracking branch 'matteo/develop' into develop
matteopilz Feb 17, 2024
a5c332f
update TOPPView intensity mode description
matteopilz Feb 17, 2024
5d9874c
update tutorials
matteopilz Feb 17, 2024
c0c6ca9
Merge remote-tracking branch 'matteo/develop' into develop
matteopilz Feb 20, 2024
69f527d
remove duplicated tutorial
matteopilz Feb 20, 2024
34656b7
reordered sections
matteopilz Feb 21, 2024
a9b513f
Merge branch 'develop' into develop
matteopilz Feb 21, 2024
f18009d
Merge branch 'develop' into develop
poshul Feb 21, 2024
e72aefe
download fix
matteopilz Feb 21, 2024
dcf8ddb
Merge remote-tracking branch 'matteo/develop' into develop
matteopilz Feb 21, 2024
654665a
Merge remote-tracking branch 'matteo/develop' into develop
matteopilz Apr 3, 2024
34b565f
major restructure
matteopilz Apr 8, 2024
8cfba0f
fixed installation cross ref
matteopilz Apr 9, 2024
89e6ccf
updated knime tutorial references
matteopilz Apr 11, 2024
08f3b43
fixed warnings
matteopilz Apr 12, 2024
35f9400
fixed download link
matteopilz Apr 15, 2024
346079a
fixed links
matteopilz Apr 15, 2024
e2aea33
fixed links
matteopilz Apr 15, 2024
f0fd9d5
Merge remote-tracking branch 'matteo/develop' into develop
matteopilz Nov 11, 2024
dc8e042
added new webapps
matteopilz Nov 11, 2024
d48b158
added SagePTMScanner
matteopilz Nov 14, 2024
4e5202f
removed outdated pages
matteopilz Nov 20, 2024
b5b2ac6
fixed outdated url
matteopilz Nov 20, 2024
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2 changes: 1 addition & 1 deletion docs/about/learning/background.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Proteomics and metabolomics focus on complex interactions within biological syst
OpenMS is an open-source, C++ framework for analyzing large volumes of mass spectrometry data. It has been specially designed for analyzing high performance LC-MS data but over recent times, has been extended to analyze data generated by other techniques.

```{note}
OpenMS in recent times has been expanded to support a wide variety of mass spectrometry experiments. To design your analysis solution, [contact the OpenMS team](https://openms.github.io/community/) today.
OpenMS in recent times has been expanded to support a wide variety of mass spectrometry experiments. To design your analysis solution, [contact the OpenMS team](https://openms.de/communication/) today.
```

To use OpenMS effectively, an understanding of chromatography and mass spectrometry is required as many of the algorithms are based on these techniques.
Expand Down
10 changes: 3 additions & 7 deletions docs/getting-started/knime-get-started.md
Original file line number Diff line number Diff line change
@@ -1,9 +1,6 @@
KNIME
=====

## Installation
Click [here](knime/knime-installation.md) to install KNIME, the OpenMS plugin and its required packages.

## Ready-made KNIME workflows

You can get ready-made KNIME workflows and workflow components with OpenMS nodes from our
Expand All @@ -13,10 +10,10 @@ For more, e.g., thirdparty OpenMS workflows use the search bar on the hub and se
["openms"](https://hub.knime.com/search?q=openms).


## Creating workflows with KNIME
## Installing KNIME and creating workflows

Download Introduction to OpenMS in KNIME [user tutorial](/tutorials/knime-user-tutorial.md) containing hands-on training material covering also basic
usage of KNIME. See the official [KNIME Getting Started Guide](https://www.knime.com/getting-started-guide) for a more in-depth view of
Read through a introduction to OpenMS in KNIME [user tutorial](/tutorials/knime-user-tutorial.md) containing hands-on training material covering also basic
usage of KNIME and how to install it. 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](/about/communication.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tag/openms).
Expand All @@ -29,6 +26,5 @@ maxdepth: 1
hidden: True
---

Install <knime/knime-installation.md>
knime/minimal-workflow.md
```
50 changes: 0 additions & 50 deletions docs/getting-started/knime/knime-installation.md

This file was deleted.

35 changes: 26 additions & 9 deletions docs/getting-started/webapps.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,27 +5,44 @@ WebApps
:gutter: 2

.. grid-item-card:: FLASHTaggerViewer
:img-top: /_images/webapps/flashtaggerviewer.png
:img-top: /_images/webapps/FLASH_TnT.png
:link: https://abi-services.cs.uni-tuebingen.de/flashtaggerviewer/
:link-type: url
:columns: 12
:columns: 6

Visualizes outputs from FLASH* tools
FLASHTaggerviewer visualizes output from FLASH* tools.

.. grid-item-card:: NASEWEIS
:img-top: /_images/webapps/naseweis.png
:link: https://abi-services.cs.uni-tuebingen.de/naseweis/
:link-type: url
:columns: 6

NASEWEIS is webapp version of the NucleicAcidSearchEngine (NASE), a tool for library searching of Oligonucleotides

.. grid-item-card:: NuXL
:img-top: /_images/webapps/nuxl.jpg
:img-top: /_images/webapps/NuXL_logo.png
:link: https://abi-services.cs.uni-tuebingen.de/nuxl/
:link-type: url
:columns: 12
:columns: 6

A specialized protein nucleic-acid crosslink search engine
NuXL is a dedicated software package designed for the analysis of XL-MS (cross-linking mass spectrometry).

.. grid-item-card:: SagePTMScanner
:img-top: /_images/webapps/SagePTMScannerlogo.png
:link: https://abi-services.cs.uni-tuebingen.de/SagePTMScanner/
:link-type: url
:columns: 6

Sage search engine is a fast and reliable proteomics search engine for the anaylsis of MS data.

.. grid-item-card:: UmetaFlow
:img-top: /_images/webapps/umetaflow.png
:img-top: /_images/webapps/umetaflow-logo.png
:link: https://abi-services.cs.uni-tuebingen.de/umetaflow/
:link-type: url
:columns: 12
:columns: 6

The UmetaFlow webapp is a pipeline for untargeted metabolomics in an accessible user interface.



A universal metabolomics tool
3 changes: 1 addition & 2 deletions docs/manual/additional/swathwizard.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@ 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://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.
The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, 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.
Expand Down
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