diff --git a/topics/proteomics/tutorials/encyclopedia/tutorial.bib b/topics/proteomics/tutorials/encyclopedia/tutorial.bib new file mode 100644 index 00000000000000..754c04639efb8e --- /dev/null +++ b/topics/proteomics/tutorials/encyclopedia/tutorial.bib @@ -0,0 +1,30 @@ + +# 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 {% Batut2018 %} + +@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} +} \ No newline at end of file diff --git a/topics/proteomics/tutorials/encyclopedia/tutorial.md b/topics/proteomics/tutorials/encyclopedia/tutorial.md new file mode 100644 index 00000000000000..8ca9ccbdbd678b --- /dev/null +++ b/topics/proteomics/tutorials/encyclopedia/tutorial.md @@ -0,0 +1,332 @@ +--- +layout: tutorial_hands_on + +title: Title of the tutorial +zenodo_link: '' +questions: +- Which biological questions are addressed by the tutorial? +- Which bioinformatics techniques are important to know for this type of data? +objectives: +- The learning objectives are the goals of the tutorial +- They will be informed by your audience and will communicate to them and to yourself + what you should focus on during the course +- They are single sentences describing what a learner should be able to do once they + have completed the tutorial +- You can use Bloom's Taxonomy to write effective learning objectives +time_estimation: 3H +key_points: +- The take-home messages +- They will appear at the end of the tutorial +contributors: +- contributor1 +- contributor2 + +--- + + +# Introduction +{:.no_toc} + + + +General introduction about the topic and then an introduction of the +tutorial (the questions and the objectives). It is nice also to have a +scheme to sum up the pipeline used during the tutorial. The idea is to +give to trainees insight into the content of the tutorial and the (theoretical +and technical) key concepts they will learn. + +You may want to cite some publications; this can be done by adding citations to the +bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations +must be in bibtex format. If you have the DOI for the paper you wish to cite, you can +get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org). + +With the example you will find in the `tutorial.bib` file, you can add a citation to +this article here in your tutorial like this: +{% raw %} `{% cite Batut2018 %}`{% endraw %}. +This will be rendered like this: {% cite Batut2018 %}, and links to a +[bibliography section](#bibliography) which will automatically be created at the end of the +tutorial. + + +**Please follow our +[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)** + +> ### Agenda +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Title for your first section + +Give some background about what the trainees will be doing in the section. +Remember that many people reading your materials will likely be novices, +so make sure to explain all the relevant concepts. + +## Title for a subsection +Section and subsection titles will be displayed in the tutorial index on the left side of +the page, so try to make them informative and concise! + +# Hands-on Sections +Below are a series of hand-on boxes, one for each tool in your workflow file. +Often you may wish to combine several boxes into one or make other adjustments such +as breaking the tutorial into sections, we encourage you to make such changes as you +see fit, this is just a starting point :) + +Anywhere you find the word "***TODO***", there is something that needs to be changed +depending on the specifics of your tutorial. + +have fun! + +## Get data + +> ### {% icon hands_on %} Hands-on: Data upload +> +> 1. Create a new history for this tutorial +> 2. Import the files from [Zenodo]({{ page.zenodo_link }}) or from +> the shared data library (`GTN - Material` -> `{{ page.topic_name }}` +> -> `{{ page.title }}`): +> +> ``` +> +> ``` +> ***TODO***: *Add the files by the ones on Zenodo here (if not added)* +> +> ***TODO***: *Remove the useless files (if added)* +> +> {% include snippets/import_via_link.md %} +> {% include snippets/import_from_data_library.md %} +> +> 3. Rename the datasets +> 4. Check that the datatype +> +> {% include snippets/change_datatype.md datatype="datatypes" %} +> +> 5. Add to each database a tag corresponding to ... +> +> {% include snippets/add_tag.md %} +> +{: .hands_on} + +# Title of the section usually corresponding to a big step in the analysis + +It comes first a description of the step: some background and some theory. +Some image can be added there to support the theory explanation: + +![Alternative text](../../images/image_name "Legend of the image") + +The idea is to keep the theory description before quite simple to focus more on the practical part. + +***TODO***: *Consider adding a detail box to expand the theory* + +> ### {% icon details %} More details about the theory +> +> But to describe more details, it is possible to use the detail boxes which are expandable +> +{: .details} + +A big step can have several subsections or sub steps: + + +## Sub-step with **msconvert** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. {% tool [msconvert](toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1) %} with the following parameters: +> - {% icon param-collection %} *"Input unrefined MS data"*: `output` (Input dataset collection) +> - *"Do you agree to the vendor licenses?"*: `Yes` +> - *"Output Type"*: `mzML` +> - In *"Data Processing Filters"*: +> - *"Apply peak picking?"*: `Yes` +> - *"Apply m/z refinement with identification data?"*: `Yes` +> - *"(Re-)calculate charge states?"*: `no` +> - *"Filter m/z Window"*: `Yes` +> - *"Filter out ETD precursor peaks?"*: `Yes` +> - *"De-noise MS2 with moving window filter"*: `Yes` +> - *"Demultiplex overlapping or MSX spectra"*: `Yes` +> - In *"Scan Inclusion/Exclusion Filters"*: +> - *"Filter MS Levels"*: `Yes` +> - In *"General Options"*: +> - *"Sum adjacent scans"*: `Yes` +> - *"Output multiple runs per file"*: `Yes` +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **msconvert** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. {% tool [msconvert](toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1) %} with the following parameters: +> - {% icon param-collection %} *"Input unrefined MS data"*: `output` (Input dataset collection) +> - *"Do you agree to the vendor licenses?"*: `Yes` +> - *"Output Type"*: `mzML` +> - In *"Data Processing Filters"*: +> - *"Apply peak picking?"*: `Yes` +> - *"Apply m/z refinement with identification data?"*: `Yes` +> - *"(Re-)calculate charge states?"*: `no` +> - *"Filter m/z Window"*: `Yes` +> - *"Filter out ETD precursor peaks?"*: `Yes` +> - *"De-noise MS2 with moving window filter"*: `Yes` +> - *"Demultiplex overlapping or MSX spectra"*: `Yes` +> - In *"Scan Inclusion/Exclusion Filters"*: +> - *"Filter MS Levels"*: `Yes` +> - In *"General Options"*: +> - *"Sum adjacent scans"*: `Yes` +> - *"Output multiple runs per file"*: `Yes` +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **SearchToLib** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. {% tool [SearchToLib](toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/0.9.5.0) %} with the following parameters: +> - {% icon param-file %} *"Spectrum files in mzML format"*: `output` (output of **msconvert** {% icon tool %}) +> - {% icon param-file %} *"Library: Chromatagram .ELIB or Spectrum .DLIB"*: `output` (Input dataset) +> - {% icon param-file %} *"Background proteome protein fasta database"*: `output` (Input dataset) +> - In *"Parameter Settings"*: +> - *"Set Acquisition Options"*: `No - use default options` +> - *"Set Tolerance Options"*: `No - use default options` +> - *"Set Percolator Options"*: `No - use default options` +> - *"Set Peak Options"*: `No - use default options` +> - *"Set Window Options"*: `No - use default options` +> - *"Set Modifications Options"*: `No - use default options` +> - *"Set Search Options"*: `No - use default options` +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **EncyclopeDIA Quantify** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. {% tool [EncyclopeDIA Quantify](toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/0.9.5.0) %} with the following parameters: +> - {% icon param-file %} *"Spectrum files in mzML format"*: `output` (output of **msconvert** {% icon tool %}) +> - {% icon param-file %} *"Library: Chromatagram .ELIB or Spectrum .DLIB"*: `elib` (output of **SearchToLib** {% icon tool %}) +> - {% icon param-file %} *"Background proteome protein fasta database"*: `output` (Input dataset) +> - In *"Parameter Settings"*: +> - *"Set Acquisition Options"*: `No - use default options` +> - *"Set Tolerance Options"*: `No - use default options` +> - *"Set Percolator Options"*: `No - use default options` +> - *"Set Peak Options"*: `No - use default options` +> - *"Set Window Options"*: `No - use default options` +> - *"Set Modifications Options"*: `No - use default options` +> - *"Set Search Options"*: `No - use default options` +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + + +## Re-arrange + +To create the template, each step of the workflow had its own subsection. + +***TODO***: *Re-arrange the generated subsections into sections or other subsections. +Consider merging some hands-on boxes to have a meaningful flow of the analyses* + +# Conclusion +{:.no_toc} + +Sum up the tutorial and the key takeaways here. 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