created 5 clinical metaproteomics tutorials

CONTRIBUTORS.yaml

@@ -476,6 +476,10 @@ dbrites:
     name: Daniela Brites
     joined: 2022-03
 
+dechendb:
+    name: Dechen Bhuming
+    joined: 2023-06
+
 delphine-l:
     name: Delphine Lariviere
     email: [email protected]
@@ -968,6 +972,10 @@ jxtx:
 katherinecox:
     name: Katherine Cox
     joined: 2023-06
+
+katherine-d21:
+    name: Katherine Do
+    joined: 2023-08
 
 katrinleinweber:
     name: Katrin Leinweber

topics/proteomics/README.md

@@ -1,5 +1,9 @@
 GalaxyP Training material
 =================
+<details>
+<summary>
+
+# List of proteomics tutorials
 
 topic | features
 :-- | :--:
@@ -12,9 +16,18 @@ topic | features
 [RNA-seq Database creation](tutorials/proteogenomics-dbcreation/tutorial.md)| [:book:](tutorials/proteogenomics-dbcreation/tutorial.md)
 [Proteogenomics Database searching](tutorials/proteogenomics-dbsearch/tutorial.md)| [:book:](tutorials/proteogenomics-dbsearch/tutorial.md)
 [Proteogenomics Novel Peptide Analysis](tutorials/proteogenomics-novel-peptide-analysis/tutorial.md)| [:book:](tutorials/proteogenomics-novel-peptide-analysis/tutorial.md)
-[metaQuantome-Taxonomy](tutorials/metaquantome-taxonomy/tutorial.md)| [:book:](tutorials/metaquantome-taxonomy/tutorial.md)
-[metaQuantome-Function](tutorials/metaquantome-function/tutorial.md)| [:book:](tutorials/metaquantome-function/tutorial.md)
-[EncyclopeDIA](tutorials/encyclopedia/tutorial.md)| [:book:](tutorials/encyclopedia/tutorial.md)
+[metaQuantome-Taxonomy](tutorials/metaquantome-taxonomy/tutorial.md) | [:book:](tutorials/metaquantome-taxonomy/tutorial.md)
+[metaQuantome-Function](tutorials/metaquantome-function/tutorial.md) | [:book:](tutorials/metaquantome-function/tutorial.md)
+[EncyclopeDIA](tutorials/encyclopedia/tutorial.md) | [:book:](tutorials/encyclopedia/tutorial.md)
+[Clinical-Metaproteomics-Database-generation](tutorials/clinical-mp-database-generation/tutorial.md) | [:book:](tutorials/clinical-mp-database-generation/tutorial.md)
+[Clinical-Metaproteomics-Discovery](tutorials/clinical-mp-discovery/tutorial.md) | [:book:](tutorials/clinical-mp-discovery/tutorial.md)
+[Clinical-Metaproteomics-Data-Verification](tutorials/clinical-mp-data-verification/tutorial.md) | [:book:](tutorials/clinical-mp-data-verification/tutorial.md)
+[Clinical-Metaproteomics-Quantitation](tutorials/clinical-mp-quantitation/tutorial.md) | [:book:](tutorials/clinical-mp-quantitation/tutorial.md)
+[Clinical-Metaproteomics-Data-Interpretation](tutorials/clinical-mp-data-interpretation/tutorial.md) | [:book:](tutorials/clinical-mp-data-interpretation/tutorial.md)
+[N-Tails](./tutorials/ntails/workflows/) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows)
+[Secretome Prediction](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows)
+
+</summary> 
 
 The Galaxy community offers many different ways of training. The table above lists all available training features of a specific topic to give you a fast and comprehensive overview.
 
@@ -23,19 +36,22 @@ The Galaxy community offers many different ways of training. The table above lis
  - :eyes: The training course is available as [Galaxy tour](https://github.com/galaxyproject/galaxy-tours)
  - :page_facing_up: The training course and material is available as Galaxy page (:thumbsup: hands-on training).
  - :book: The training course and material is available as annotated text (:thumbsup: hands-on training).
- - :mortar_board: Slides as Introduction
+ - :mortar_board: Slides as Introduction (:thumbsup: Slides)
 
-### Workflows
 
-The GalaxyP GTN project also offers a selection of published GalaxyP workflows. The presented workflows are adapted to specific questions in proteomics, which are not answered in the more basic tutorials.
+## Workflows
+
+The GalaxyP GTN project also offers a selection of published GalaxyP workflows. The presented workflows are adapted to specific
+questions in proteomics,which are not answered in the more basic tutorials.
 You are free to use and modify all workflows for your scientific question.
 
-topic | features
-:-- | :--:
-[N-Tails](./tutorials/ntails/workflows/) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows)
-[Secretome Prediction](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows)
+## Disclaimer
+Thanks for your interest in the GTN GalaxyP training material project. We only recently started working on this
+repository.We try to integrate more and more topics over time. Keep an eye out for new material from time to time.
+
+
+
+</details>
 
-### Disclaimer
-Thanks for your interest in the GTN GalaxyP training material project. We only recently started working on this repository. We try to integrate more and more topics over time. Keep an eye out for new material from time to time.
+If you want to join the discussion about new material to integrate, please post your thoughts on this [issue page](https://github.com/galaxyproject/training-material/issues/237). We are most thankful for any feedback!
 
-If you want to join the discussion about new material to integrate, please post your thoughts [here](https://github.com/galaxyproject/training-material/issues/237). We are most thankful for any feedback!

topics/proteomics/metadata.yaml

@@ -36,7 +36,9 @@ subtopics:
   - id: property-prediction
     title: "Prediction of peptide properties"
     description: "These tutorials explain in-silico analyses of different peptide properties."
-
+  - id: clinical-metaproteomics
+    title: "Metaproteomics analysis of clinical data"
+    description: "These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results."
 references:
   -
     authors: "Kumar D, Yadav AK and Dash D"

topics/proteomics/tutorials/clinical-mp-data-interpretation/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/proteomics/tutorials/clinical-mp-data-interpretation/tutorial.bib

@@ -0,0 +1,42 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}