-
Notifications
You must be signed in to change notification settings - Fork 872
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
c0fb78a
commit 34e20ae
Showing
4 changed files
with
832 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} | ||
|
|
||
| <!-- This is a comment. --> | ||
|
|
||
| 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: | ||
|
|
||
|  | ||
|
|
||
| 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. We encourage adding an overview image of the | ||
| pipeline used. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| --- | ||
| layout: workflow-list | ||
| --- |
Oops, something went wrong.