From e293b624249c91d966b701bc7fa2f1fa83234a43 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:00:30 +0530 Subject: [PATCH 01/10] fix: follow Sentence case for h2 or less --- docs/installations/installation-on-gnu-linux.md | 6 +++--- docs/installations/installation-on-windows.md | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index c6908aa7..f81dbfd3 100644 --- a/docs/installations/installation-on-gnu-linux.md +++ b/docs/installations/installation-on-gnu-linux.md @@ -25,7 +25,7 @@ conda install -c bioconda libopenms conda install -c bioconda openms-thirdparty ``` -## Install via Debian Package +## Install via Debian package For Debian-based Linux users, it is suggested to use the [deb-package](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) provided. It is most easily installed with **[gdebi](https://launchpad.net/gdebi)** which automatically resolves the dependencies available in the PPA Repositories. @@ -59,7 +59,7 @@ If you encounter errors with unavailable packages, troubleshoot using the follow `/usr/share/OpenMS/THIRDPARTY` 5. Add the folders in your `PATH` for a convenient use of the adapters. -## Install via Package Managers +## Install via package managers Packaged versions of **OpenMS** are provided for Fedora, OpenSUSE, Debian, and Ubuntu. You can find them to download [here](https://pkgs.org/download/openms). For other GNU/Linux distributions or to obtain the most recent version of the @@ -81,7 +81,7 @@ The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM. ``` -## Run via a (Bio)Docker Image +## Run via a (Bio)Docker image Make sure you have [Docker installed](https://docs.docker.com/engine/install/). diff --git a/docs/installations/installation-on-windows.md b/docs/installations/installation-on-windows.md index 6cf2b24b..2e3fdcb2 100644 --- a/docs/installations/installation-on-windows.md +++ b/docs/installations/installation-on-windows.md @@ -1,7 +1,7 @@ Installation on Windows ======================= -## Install via Windows Installer +## Install via Windows installer To Install the binary package of OpenMS & TOPP: @@ -14,7 +14,7 @@ The windows binary version works with most versions of windows from Win7 to Win1 still work but are untested). ``` -## Known Issues +## Known issues 1. During installation, an error message pops up, saying "The installation of the Microsoft .NET 3.5 SP1' package failed! From a4b4a3c585c3029c2f3dee344d2dc52ae26deb82 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:06:56 +0530 Subject: [PATCH 02/10] fix: glossary terms in introduction page --- docs/introduction.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/introduction.md b/docs/introduction.md index 4aa8e696..f1e110a0 100644 --- a/docs/introduction.md +++ b/docs/introduction.md @@ -82,12 +82,12 @@ The measurement of one sample is called an MS run and the set of spectra called The left image displays spectrum with peaks (m/z and intensity values) and the right image shows spectra stacked in retention time yielding a peak map. -In proteomics and metabolomics, the MS(1) intensity is often used for the quantification of an analyte. Identification -based on the MS(1) mass-to-charge and the isotope pattern is highly ambiguous. To improve identification, tandem mass -spectrometry (MS/MS) can be applied to assess the analyte substructure. To this end, the precursor ion is isolated and +In proteomics and metabolomics, the {term}`MS(1)` intensity is often used for the quantification of an analyte. Identification +based on the {term}`MS(1)` mass-to-charge and the isotope pattern is highly ambiguous. To improve identification, tandem mass +spectrometry {term}`(MS/MS)` can be applied to assess the analyte substructure. To this end, the precursor ion is isolated and kinetically fragmented using an inert gas (e.g., Argon). Fragments produced by {term}`collision-induced dissociation (CID)` -are stored in an MS^2^ (or MS/MS) spectrum and provide information that helps to resolve the ambiguities in identification. -Alternatively, MS/MS spectra can be used for quantification. +are stored in an {term}`MS^2` (or {term}`MS/MS`) spectrum and provide information that helps to resolve the ambiguities in identification. +Alternatively, {term}`MS/MS` spectra can be used for quantification. Get started with installing OpenMS using the installers available for different operating systems! From d4fa6bd6b4e193c2641e59bcb158a57df820bf66 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:09:24 +0530 Subject: [PATCH 03/10] add tabs: ux --- docs/advanced-resources/custom-compilation.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/advanced-resources/custom-compilation.md b/docs/advanced-resources/custom-compilation.md index a8487430..0cba8b7e 100644 --- a/docs/advanced-resources/custom-compilation.md +++ b/docs/advanced-resources/custom-compilation.md @@ -5,15 +5,14 @@ To compile with self built compilers and non default standard libraries, follow To choose any specific compiler, instead of the system default, add the whole path to these options for the cmake call: -- GCC: - ```bash - cmake -DCMAKE_C_COMPILER=/path/to/c-compiler/binary/gcc -DCMAKE_CXX_COMPILER=/path/to/c++-compiler/binary/g++ - ``` +```{tab} GCC -- Clang: - ```bash - cmake -DCMAKE_C_COMPILER=/path/to/c-compiler/binary/clang -DCMAKE_CXX_COMPILER=/path/to/c++-compiler/binary/clang++ +`cmake -DCMAKE_C_COMPILER=/path/to/c-compiler/binary/gcc -DCMAKE_CXX_COMPILER=/path/to/c++-compiler/binary/g++` ``` +```{tab} Clang + +`cmake -DCMAKE_C_COMPILER=/path/to/c-compiler/binary/clang -DCMAKE_CXX_COMPILER=/path/to/c++-compiler/binary/clang++` +``` To compile OpenMS with clang and a specific GCC stdlib, instead of the system default one: From 8df1608385151837924c3dec2a4df6830214d454 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:10:32 +0530 Subject: [PATCH 04/10] fix: follow Title Case and reword --- docs/topp/adding-new-tool-to-topp.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/topp/adding-new-tool-to-topp.md b/docs/topp/adding-new-tool-to-topp.md index dbd431c5..36b9082c 100644 --- a/docs/topp/adding-new-tool-to-topp.md +++ b/docs/topp/adding-new-tool-to-topp.md @@ -1,8 +1,6 @@ -Adding your own tool to the TOPP suite +Adding New Tool to The TOPP suite ===================================== -# What is TOPP/UTILS? - ## The OpenMS pipeline (TOPP) Any tool that is written with the OpenMS library can easily be made into a TOPP tool by simply using the OpenMS command From 396e0a28d153ac3ec80865eaa2f10c67894f31a4 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:11:50 +0530 Subject: [PATCH 05/10] add: description plus file name --- docs/topp/topp.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/topp/topp.md b/docs/topp/topp.md index edfb7fe8..7f3c3881 100644 --- a/docs/topp/topp.md +++ b/docs/topp/topp.md @@ -13,10 +13,10 @@ Few of the graphical tools are explained below: ```{toctree} :maxdepth: 1 -toppview: A viewer for mass spectrometry data. -toppas: An assistant for GUI-driven TOPP workflow design. -ini-file-editor: An editor for OpenMS configuration files. -swathwizard: A user-friendly step-by-step wizard for SWATH data analysis. +: A viewer for mass spectrometry data. +: An assistant for GUI-driven TOPP workflow design. +: An editor for OpenMS configuration files. +: A user-friendly step-by-step wizard for SWATH data analysis. ``` For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html). From 77a61b3bcc42a126c6943e4615b2b7ce20801026 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:12:45 +0530 Subject: [PATCH 06/10] fix: dropdown menu sidebar toppas tut --- docs/tutorials/TOPPAS/TOPPAS-tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md index 10e721d4..f44f47a7 100644 --- a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md +++ b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md @@ -8,7 +8,7 @@ The parameters of all involved tools can be edited within TOPPAS and are also sa ```{toctree} :maxdepth: 1 - general-introduction - user-interface - examples - ``` +general-introduction +user-interface +examples +``` From ed0ae1c229fc4e85f3d03e7f4af386345deb5636 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:25:09 +0530 Subject: [PATCH 07/10] add: +reword .github templates --- .github/CONTRIBUTING.md | 17 ++++++++++++++++- .github/ISSUE_TEMPLATE/feature-request.md | 8 ++++---- 2 files changed, 20 insertions(+), 5 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 5acbdaa7..9c192a88 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,7 +27,22 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op 2. Restrict the line length to 120 characters, including space(s). 3. Title and H1 heading should be in `Title Case`. Follow `Sentence case`, until otherwise stated. 4. Write as OpenMS is writing for itself as an object and subject. -5. Be nice, polite, and respectful. +5. Use American English. +6. Use `backtick`(s) for formatting code, library name, files, and path. +7. Use **bold** for product name, object name, an independent entity. +8. Use **bold** for menu title in an application. +9. Link to glossary terms using {term}`this is a glossary term`. +10. OpenMS documentation uses following Admonitions + - Hint + - Important + - Note + - Warning + - Tip + - See Also + Example of these are present in documentation, please follow them. +11. Always specify lexers for code blocks. +12. Format keyboard strokes using `qwerty-keyboard-button`. +13. Be nice, polite, and respectful. ### Naming files diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md index 6a4ad6b0..ebdb28fd 100644 --- a/.github/ISSUE_TEMPLATE/feature-request.md +++ b/.github/ISSUE_TEMPLATE/feature-request.md @@ -13,14 +13,14 @@ Thanks for suggesting a new feature for the OpenMS Documentation! Please delete this text and anything that's not relevant from the template below: --> -## Is your feature request related to a OpenMS Documentation problem? Please describe +## Is your feature request related to a OpenMS API Reference Documentation? Please describe. - -- [ ] I have attached screenshot describing the problem, if applicable +- [ ] I have attached screenshot describing the problem, if applicable. ## Describe the documentation enhancement you'd like From d931ac694be2692acedc76e1a0d757470e116f1a Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:52:11 +0530 Subject: [PATCH 08/10] add: more glossary --- docs/glossary.md | 31 ++++++++++++++++++- docs/guides/contributors-quickstart-guide.md | 4 +-- .../user-guides/user-quickstart-guide.md | 23 +++++++------- .../installations/build-openms-from-source.md | 2 +- docs/installations/installation-on-macos.md | 8 ++--- docs/installations/installation-on-windows.md | 2 +- 6 files changed, 50 insertions(+), 20 deletions(-) diff --git a/docs/glossary.md b/docs/glossary.md index 3756aea2..2bf63216 100644 --- a/docs/glossary.md +++ b/docs/glossary.md @@ -11,7 +11,7 @@ Peptides A short chain of amino acids. Octadecyl(C18) - An alkyl radical C~18~H~37~ derived from an octadecane by removal of one hydrogen atom. + An alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom. Mass Mass is a measure of the amount of matter that an object contains. In comparison to often used term weight, which is @@ -59,4 +59,33 @@ Collision-induced dissociation (CID) A mass spectrometry technique to induce fragmentation of selected ions in the gas phase. Also known as Collision induced dissociation. +TOPP + The OpenMS Proteomics Pipeline. + +TOPPAS.app + TOPPAS allows to create, edit, open, save, and run TOPP workflows. + +MSGFPlusAdapter + Adapter for the MS-GF+ protein identification (database search) engine. More information is available [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html). + +LuciphorAdapter + Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass + spectrometry data. More information is available [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_LuciphorAdapter.html). + +pyOpenMS + pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and + metabolomics data in Python. For pyOpenMS documentaion visit [this](https://pyopenms.readthedocs.io/en/latest/) link. + +TOPP Tools + All {term}`TOPP` tools can be found [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html). + +UTILS + Besides TOPP, OpenMS offers a range of other tools. They are not included in TOPP as they are not part of typical + analysis pipelines. More information is present in [OpenMS UTILS Documentation)(https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html). + +TOPPView + TOPPView is a viewer for MS and HPLC-MS data. More information is available in [TOPPView documentation](topp/toppview.md). + +[Nightly Snapshot](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html) + Untested installers and containers are known as the nightly snapshot. ``` diff --git a/docs/guides/contributors-quickstart-guide.md b/docs/guides/contributors-quickstart-guide.md index a6bb3ccc..81dd3732 100644 --- a/docs/guides/contributors-quickstart-guide.md +++ b/docs/guides/contributors-quickstart-guide.md @@ -7,12 +7,12 @@ To contribute to OpenMS: - Learn how to [build OpenMS](../installations/build-openms-from-source.md). - Check out the [OpenMS tutorial for developers](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/OpenMS_tutorial.html). -For any questions, please [contact us](../contact-us.md) at [open-ms-general]((https://sourceforge.net/projects/open-ms/lists/open-ms-general) mailing list. +For any questions, please [contact us](../contact-us.md) at [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) mailing list. ## Technical documentation ```{note} -Untested installers and containers are known as the nightly snapshot, are released every night. They generally pass +Untested installers and containers are known as the {term}`nightly snapshot`, are released every night. They generally pass automated continuous integration tests but no manual tests. ``` diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 6e7fadf6..b611400a 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -7,7 +7,7 @@ information, consult [OpenMS API Reference](https://abibuilder.informatik.uni-tu ## What is OpenMS [OpenMS](https://www.openms.de/) is a free, open-source C++ library with Python bindings. It is commonly used for liquid -chromatography-mass spectrometry (LC-MS) data management and analyses. OpenMS provides an infrastructure for the rapid +chromatography-mass spectrometry ({term}`LC-MS`) data management and analyses. OpenMS provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is available under the [three clause BSD licence](https://github.com/OpenMS/OpenMS/blob/develop/LICENSE) and runs under Windows, macOS, and Linux operating systems. @@ -17,16 +17,16 @@ Before using OpenMS, become familiar with the following terms: | Tool and Utilities | Description | |--------------------|-------------| -|**TOPPView** |A design tool that is used to view and explore LC-MS data, alignments, groups, peptide identifications, and more.| -|**TOPPAS** |A graphical workflow design tool that is used to create pipelines from all TOPP tools (and UTILS).| -|**TOPP tools** |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)| -|**UTILS** |Similar to TOPP tools, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)| +|**TOPPView** |A design tool that is used to view and explore {term}`LC-MS` data, alignments, groups, peptide identifications, and more.| +|**TOPPAS** |A graphical workflow design tool that is used to create pipelines from all {term}`TOPP tools` (and {term}`UTILS`).| +|**TOPP tools** |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)| +|**UTILS** |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)| ## How to run a Tool -A good start are the example pipelines (select **File** > **Open example file** within TOPPAS). +A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`). -Read the documentation of the tools (see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of TOPPAS ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)). +Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)). Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell script for automation. @@ -42,19 +42,19 @@ The default parameters of each tool can usually be tweaked to fit the data and i file are shown here as well. 2. **Command line**: Very basic parameters can be set on the command line, e.g. `FileFilter -rt 1000:2000 .....` 3. Doing 2 for all parameters would create a very long list, thus, use so-called `.ini` files to provide full parameter - sets to TOPP tools. If no INI file is given, default parameters are used. To get a default `.ini` use + sets to {term}`TOPP tools`. If no INI file is given, default parameters are used. To get a default `.ini` use ` -write_ini ` e.g. `FileFilter -write_ini filefilter.ini` Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp/ini-file-editor.md), which is another GUI tool shipped with - OpenMS and similar to the one build into TOPPAS. + OpenMS and similar to the one build into {term}`TOPPAS`. ### How do I feed the INI file to a Tool? 1. **TOPPAS**: Once you changed the parameters of a node and clicked **Ok**, the parameters are in effect. Because - they are part of the TOPPAS workflow, they are saved together with the workflow. + they are part of the {term}`TOPPAS` workflow, they are saved together with the workflow. 2. **Command line** : Supply the INI file via the `-ini` flag, ` -ini ` @@ -63,4 +63,5 @@ The default parameters of each tool can usually be tweaked to fit the data and i ### What parameters to set and to what value? The answer is complex, in general, read the tool description, change the parameters and compare the results using -TOPPView if possible. If that does not help, [contact us](../../contact-us.md). Please include all the necessary details we need in order to help you. +{term}`TOPPView` if possible. If that does not help, [contact us](../../contact-us.md). Please include all the necessary +details we need in order to help you. diff --git a/docs/installations/build-openms-from-source.md b/docs/installations/build-openms-from-source.md index 6dc18d47..52298e1c 100644 --- a/docs/installations/build-openms-from-source.md +++ b/docs/installations/build-openms-from-source.md @@ -7,4 +7,4 @@ To build OpenMS, please follow the build instructions for: * [macOS](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/install_mac.html) * [Windows](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/install_win.html) -Instructions to build pyOpenMS can be found in the [pyOpenMS documentation](https://pyopenms.readthedocs.io/en/latest/build_from_source.html). +Instructions to build {term}`pyOpenMS` can be found in the [pyOpenMS documentation](https://pyopenms.readthedocs.io/en/latest/build_from_source.html). diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md index a40ec8df..61f99282 100644 --- a/docs/installations/installation-on-macos.md +++ b/docs/installations/installation-on-macos.md @@ -28,7 +28,7 @@ To install OpenMS on macOS, run the following steps: Copying to Applications -To use TOPP as regular app in the shell, add the following lines to the `~/.profile` file. +To use {term}`TOPP` as regular app in the shell, add the following lines to the `~/.profile` file. ```bash export OPENMS_TOPP_PATH= @@ -61,9 +61,9 @@ Follow [these](installation-on-gnu-linux.md#install-via-conda) instructions. cd /Applications/OpenMS- sudo xattr -r -d com.apple.quarantine * ``` -2. Bug with running Java based thirdparty tools like MSGFPlusAdapter and LuciphorAdapter from within **TOPPAS.app** +2. Bug with running Java based thirdparty tools like {term}`MSGFPlusAdapter` and {term}`LuciphorAdapter` from within **TOPPAS.app** - If you face issues while running Java based thirdparty tools from within TOPPAS.app, run the TOPPAS.app from within - the Terminal.app (e.g. with the `open` command) to get access to the path where Java is located. + If you face issues while running Java based thirdparty tools from within {term}`TOPPAS.app`, run the {term}`TOPPAS.app` + from within the Terminal.app (e.g. with the `open` command) to get access to the path where Java is located. Java is usually present in the `PATH` of the terminal. Advanced users can set this path in the `Info.plist` of/inside the TOPPAS.app. diff --git a/docs/installations/installation-on-windows.md b/docs/installations/installation-on-windows.md index 2e3fdcb2..c9848c77 100644 --- a/docs/installations/installation-on-windows.md +++ b/docs/installations/installation-on-windows.md @@ -3,7 +3,7 @@ Installation on Windows ## Install via Windows installer -To Install the binary package of OpenMS & TOPP: +To Install the binary package of OpenMS & {term}`TOPP`: 1. Download and execute the installer `OpenMS--Win64.exe` from the [archive](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) and follow its instructions. 2. Run the installer under the user account that later runs OpenMS. It is not advised to use admin account for From 7b735116d04ce161c467f0f6053063154e5017dc Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 22:53:20 +0530 Subject: [PATCH 09/10] fix: include faq --- docs/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 915ca0a2..c8f5be64 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -69,8 +69,8 @@ Contents :maxdepth: 2 :caption: Frequently Asked Questions - developer-faq.md - contributor-faq.md + faqs/developer-faq.md + faqs/contributor-faq.md .. toctree:: :maxdepth: 2 From 4d0f840530b7e72492b2940ab736d43dd1208bf9 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Sun, 29 May 2022 23:25:47 +0530 Subject: [PATCH 10/10] add: glossary more --- docs/glossary.md | 56 +++++++++++++++++++ docs/tutorials/TOPP/TOPP-tutorial.md | 16 +++--- .../TOPP/data-analysis-in-toppview.md | 10 ++-- .../TOPP/data-editing-in-toppview.md | 4 +- .../TOPP/topp-and-openms-introduction.md | 20 +++---- .../tutorials/TOPP/topp-for-advanced-users.md | 2 +- docs/tutorials/TOPP/toppview-introduction.md | 6 +- docs/tutorials/TOPP/views-in-toppview.md | 4 +- 8 files changed, 88 insertions(+), 30 deletions(-) diff --git a/docs/glossary.md b/docs/glossary.md index 2bf63216..6a94a2bb 100644 --- a/docs/glossary.md +++ b/docs/glossary.md @@ -88,4 +88,60 @@ TOPPView [Nightly Snapshot](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html) Untested installers and containers are known as the nightly snapshot. + +Proteomics + Proteomics is the large-scale study of proteins. + +Proteins + Proteins are vital parts of living organisms, with many functions, for example composing the structural fibers of + muscle to the enzymes that catalyze the digestion of food to synthesizing and replicating DNA. + +Mascot + Identifies peptides in MS/MS spectra via Mascot. Please find more information in the {term}`TOPP` [Documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MascotAdapter.html). + +HPLC-MS + Data produced by High performance liquid chromatography (HPLC) separates components of a mixture, whereas mass + spectrometry (MS) offers the detection tools to identify them. + +mzML + The mzML format is an open, XML-based format for mass spectrometer output files, developed with the full participation + of vendors and researchers in order to create a single open format that would be supported by all software. + +mzData + mzData was the first attempt by the Proteomics Standards Initiative (PSI) from the Human Proteome Organization (HUPO) + to create a standardized format for Mass Spectrometry data.[7] This format is now deprecated, and replaced by mzML. + +mzXML + mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for + Systems Biology. + +Spectra + Singluar of spectrum. + +Spectrum + A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used + to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to + elucidate the chemical identity or structure of molecules and other chemical compounds. + +m/z + mass to charge ratio. + +RT + Retention time (RT). + +ProteoWizard + ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. It provides a + framework for unified mass spectrometry data file access and performs standard chemistry and LCMS dataset computations. + +OMSSA + The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying {term}`MS/MS` + {term}`peptide` {term}`spectra` by searching libraries of known protein sequences. + +PepNovo + PepNovo is a de novo sequencing algorithm for {term}`MS/MS` {term}`spectra`. + +De novo peptide sequencing + A peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum + ({term}`MS/MS` or {term}`MS^3`) fragment ions, without comparison to a reference proteome. ``` + diff --git a/docs/tutorials/TOPP/TOPP-tutorial.md b/docs/tutorials/TOPP/TOPP-tutorial.md index 76e29b3f..90aea6f2 100644 --- a/docs/tutorials/TOPP/TOPP-tutorial.md +++ b/docs/tutorials/TOPP/TOPP-tutorial.md @@ -1,9 +1,10 @@ TOPP Tutorial ============ -This tutorial is an introduction to TOPP and TOPPView. Let's start with understanding the intent and concept of TOPP -compared to OpenMS. Later, we will move to the handling of TOPPView which is our central GUI. Apart from viewing data, -TOPPView can also be used to analyze it using selected TOPP tools; how-to is explained in the third part of the tutorial. +This tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and +concept of {term}`TOPP` compared to OpenMS. Later, we will move to the handling of {term}`TOPPView` which is our central +GUI. Apart from viewing data, {term}`TOPPView` can also be used to analyze it using selected {term}`TOPP tools`; how-to +is explained in the third part of the tutorial. Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release. # Concepts @@ -18,7 +19,7 @@ topp-and-openms-introduction # TOPPView Main Interface -In this part of the tutorial, we will learn about the main features of TOPPView and its basic uses. +In this part of the tutorial, we will learn about the main features of {term}`TOPPView` and its basic uses. ```{toctree} :maxdepth: 1 @@ -33,7 +34,8 @@ hotkeys-table # Calling TOPP tools from TOPPView -This part of the tutorial illustrates how to interactively analyse proteomics data using TOPP tools from within TOPPView. +This part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from +within {term}`TOPPView`. ```{toctree} :maxdepth: 1 @@ -57,8 +59,8 @@ topp-for-advanced-users # Scripting with TOPP -This part of the tutorial gives a detailed overview of the most important TOPP tools. First, some basics needed for -every TOPP tool are explained, then several example pipelines are shown. +This part of the tutorial gives a detailed overview of the most important {term}`TOPP tools`. First, some basics needed +for every {term}`TOPP tool` are explained, then several example pipelines are shown. ```{toctree} :maxdepth: 1 diff --git a/docs/tutorials/TOPP/data-analysis-in-toppview.md b/docs/tutorials/TOPP/data-analysis-in-toppview.md index 56ed18d4..f7732c08 100644 --- a/docs/tutorials/TOPP/data-analysis-in-toppview.md +++ b/docs/tutorials/TOPP/data-analysis-in-toppview.md @@ -1,21 +1,21 @@ Data Analysis in TOPPView ========================= -TOPPView also offers limited data analysis capabilities for single layers, which will be illustrated in the following +{term}`TOPPView` also offers limited data analysis capabilities for single layers, which will be illustrated in the following sections. The functionality presented here can be found in the **Tools** menu: ![TOPPView Tools Menu](../../images/tutorials/topp/TOPPView_tools_menu.png) ## TOPP Tools -Single TOPP tools can be applied to the data of the currently selected layer or to the visible data of the current layer. +Single {term}`TOPP tools` can be applied to the data of the currently selected layer or to the visible data of the current layer. The following example image shows the TOPP tools dialog: ![TOPPView Tools](../../images/tutorials/topp/TOPPView_tools.png) -To apply a TOPP tool, follow the instructions below: +To apply a {term}`TOPP tool`, follow the instructions below: -1. Select a TOPP tool and if necessary a type. +1. Select a {term}`TOPP tool` and if necessary a type. 2. Specify the command line option of the tool, that takes the input file name. 3. Specify the command line option of the tool, that takes the output file name. 4. Set the algorithm parameters manually or load them from an INI file. @@ -28,7 +28,7 @@ and sample description. ![Meta Data Browser](../../images/tutorials/topp/MetaDataBrowser.png) ```{tip} -Identification data, e.g. from a Mascot run, can be annotated to the spectra or features, too. After +Identification data, e.g. from a {term}`Mascot` run, can be annotated to the spectra or features, too. After annotation, this data is listed in the metadata. ``` diff --git a/docs/tutorials/TOPP/data-editing-in-toppview.md b/docs/tutorials/TOPP/data-editing-in-toppview.md index ac1925c1..85666f5e 100644 --- a/docs/tutorials/TOPP/data-editing-in-toppview.md +++ b/docs/tutorials/TOPP/data-editing-in-toppview.md @@ -1,11 +1,11 @@ Data Editing in TOPPView ======================== -TOPPView offers editing functionality for feature layers. +{term}`TOPPView` offers editing functionality for feature layers. After enabling the feature editing mode in the context menu of the feature layer, the following actions can be performed: -- Features can be dragged with the mouse in order to change the m/z and RT position. +- Features can be dragged with the mouse in order to change the {term}`m/z` and {term}`RT` position. - The position, intensity and charge of a feature can be edited by double-clicking a feature. - Features can be created by double-clicking the layer background. - Features can be removed by selecting them and pressing the DEL key. diff --git a/docs/tutorials/TOPP/topp-and-openms-introduction.md b/docs/tutorials/TOPP/topp-and-openms-introduction.md index 504d2bf7..bbd018e2 100644 --- a/docs/tutorials/TOPP/topp-and-openms-introduction.md +++ b/docs/tutorials/TOPP/topp-and-openms-introduction.md @@ -1,16 +1,16 @@ TOPP and OpenMS ============== -TOPP, the OpenMS Proteomics Pipeline provides a set of computational tools that can be easily combined into analysis +{term}`TOPP`, the OpenMS Proteomics Pipeline provides a set of computational tools that can be easily combined into analysis pipelines even by non-experts and then be used in proteomics workflows. These applications range from useful utilities -file format conversion, peak picking over wrapper applications for known applications (e.g. Mascot) to completely new -algorithmic techniques for data reduction and data analysis. TOPP is based on the OpenMS library and as more -functionality is added to new OpenMS releases, TOPP will naturally contain new or updated tools. +file format conversion, peak picking over wrapper applications for known applications (e.g.{term}`Mascot`) to completely new +algorithmic techniques for data reduction and data analysis. {term}`TOPP` is based on the OpenMS library and as more +functionality is added to new OpenMS releases, {term}`TOPP` will naturally contain new or updated tools. -In addition to offering a toolbox, TOPP contains TOPPView - the central graphical user interface - which allows the user -to view, inspect and manipulate proteomics data. TOPPView reads standard formats and allows the user not only to view -the data, but also to interactively call TOPP tools and display the results. As such it is a powerful tool for -interactive data manipulation. +In addition to offering a toolbox, {term}`TOPP` contains {term}`TOPPView` - the central graphical user interface - which +allows the user to view, inspect and manipulate {term}`proteomics` data. {term}`TOPPView` reads standard formats and +allows the user not only to view the data, but also to interactively call {term}`TOPP tools` and display the results. +As such it is a powerful tool for interactive data manipulation. -In this tutorial, let's understand in detail the capabilities of TOPPView and the TOPP tools using real data sets and -standard analysis tasks. +In this tutorial, let's understand in detail the capabilities of {term}`TOPPView` and the {term}`TOPP tools` using real +data sets and standard analysis tasks. diff --git a/docs/tutorials/TOPP/topp-for-advanced-users.md b/docs/tutorials/TOPP/topp-for-advanced-users.md index 306df58c..770ec5f6 100644 --- a/docs/tutorials/TOPP/topp-for-advanced-users.md +++ b/docs/tutorials/TOPP/topp-for-advanced-users.md @@ -27,7 +27,7 @@ INI settings portable. ## Using external tools in workflows -OpenMS supports the wrapping of external tools (like msconvert from ProteoWizard), thus allowing to build scripts and/or +OpenMS supports the wrapping of external tools (like msconvert from {term}`ProteoWizard`), thus allowing to build scripts and/or TOPPAS pipelines containing external tools. ```{seealso} diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md index 961f2132..7ac5e984 100644 --- a/docs/tutorials/TOPP/toppview-introduction.md +++ b/docs/tutorials/TOPP/toppview-introduction.md @@ -1,13 +1,13 @@ TOPPView Introduction ===================== -TOPPView is a viewer for MS and HPLC-MS data. It can be used to inspect files in mzML, mzData, mzXML and several other -text-based file formats. +{term}`TOPPView` is a viewer for {term}`MS` and {term}`HPLC-MS` data. It can be used to inspect files in {term}`mzML`, +{term}`mzData`, {term}`mzXML` and several other text-based file formats. In each view, several datasets can be displayed using the layer concept. This allows visual comparison of several datasets as well as displaying input data and output data of an algorithm together. -TOPPView is intended for visual inspection of the data by experimentalists as well as for analysis software by +{term}`TOPPView` is intended for visual inspection of the data by experimentalists as well as for analysis software by developers. ![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png) diff --git a/docs/tutorials/TOPP/views-in-toppview.md b/docs/tutorials/TOPP/views-in-toppview.md index c1db0b64..4153b0c4 100644 --- a/docs/tutorials/TOPP/views-in-toppview.md +++ b/docs/tutorials/TOPP/views-in-toppview.md @@ -1,8 +1,8 @@ Views in TOPPView ================= -TOPPView offers three types of views – a 1D view for spectra, a 2D view for peak maps and feature maps, and a 3D view -for peak maps. All three views can be freely configured to suit the individual needs of the user. +{term}`TOPPView` offers three types of views – a 1D view for {term}`spectra`, a 2D view for peak maps and feature maps, +and a 3D view for peak maps. All three views can be freely configured to suit the individual needs of the user. ## Action Modes and Their Uses