diff --git a/docs/glossary.md b/docs/glossary.md index c8622c9a..e3f2eb48 100644 --- 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 new file mode 100644 index 00000000..1bf43c83 Binary files /dev/null and b/docs/images/tutorials/knime/KNIME_Install.png differ diff --git a/docs/images/tutorials/knime/KNIME_screenshot.png b/docs/images/tutorials/knime/KNIME_screenshot.png new file mode 100644 index 00000000..f98895ca Binary files /dev/null and b/docs/images/tutorials/knime/KNIME_screenshot.png differ diff --git a/docs/images/tutorials/knime/KNIME_update_site.jpeg b/docs/images/tutorials/knime/KNIME_update_site.jpeg new file mode 100644 index 00000000..cb3abbfc Binary files /dev/null and b/docs/images/tutorials/knime/KNIME_update_site.jpeg differ diff --git a/docs/index.rst b/docs/index.rst index 740ae7a8..d317f99b 100644 --- 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 `_, +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 `_), 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 new file mode 100644 index 00000000..179f4184 --- /dev/null +++ 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 index f44f47a7..03cb9501 100644 --- 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