cheatsheet

[bgruening]

During our last course we got this feedback give table with file formats and tools (what for, what in, what out). I guess this is a general good idea which we can extend to a cheatsheet.

[millen2223]

@bgruening @bebatut @hexylena Is this one project available to work on it, or have somebody been working on? Can I be assigned it? I thought about creating kind of cheatsheets similar to what I have seen before for R, python and SQL since I saw Galaxy for the first time.

[bebatut]

nobody is actually working on that project. so @millen2223 feel free to take it :smile:

[millen2223]

@bebatut thank you!

[millen2223]

Short plan for a cheatsheet

1. Create tool list based on known tools https://github.com/galaxyproject/tools-iuc/tree/master/tools
   2. Think of short descriptions and visualizations
   3. Organize the tools into self-explanatory groups. Each group should address a common problem or task. Ideas to create groups: make a poll among gitter Galaxy community consider "Tool recommendations" based on machine learning
   4. Sketch a possible layout and upload pptx. draft for a discussion and correction based on issue #718

[bebatut]

Sounds like good idea @millen2223. Maybe you could start from the tools used in the tutorials. It would help reducing the number of tools. Otherwise the source for tools in Galaxy is mostly there: https://toolshed.g2.bx.psu.edu/

[millen2223]

@bebatut This is just the way I thought when looked for best ways to group tools. I still have doubts, but somewhere I wanted to begin with, so I decided to place tools from "Send data" the smallest group with their descriptions in a table. Yes, this is a really good idea to look at tools used in tutorials, for example "tools for Galaxy newcomers" based on introduction tutorials. I also think there will be multiple cheatsheets later. Another important thing is that some tools maybe are not often used ones. Tool "cURL send cURL POST requests" have git repo but it is perhaps hidden and I cannot make look at them, only at short description made on Galaxy.

[millen2223]

@bebatut Could you please, look at my draft for the first table? This is only a start table for tools from the "Peaks and Genes tutorial". I also made second page to list formats and their descriptions there. If it at least first sight looks OK, I will continue working on it. And if not, I will try to edit it as needed.

[millen2223]

Hi @bgruening, @hexylena, @bebatut, I finished the first one cheatsheet based "Peaks and Genes tutorial" to imagine an example of how one might look like. Also, I added in the table link to every tool because of older versions I saw in the tools list In the end layout might be different. What do you think of it? https://github.com/millen2223/Galaxy-cheatsheets/blob/main/Peaks_and_Genes_cheatsheet/CheatSheet%20based%20on%20Peaks%20and%20Genes_last.pdf

[hexylena]

Very cool @millen2223! We'll have to think how and where to integrate this into the GTN.

[millen2223]

@hexylena Thank you a lot for your feedback!!

[millen2223]

I added as I promised pptx and pdf versions :)

• https://github.com/millen2223/Galaxy-cheatsheets/blob/main/Peaks_and_Genes_cheatsheet/Peaks_and_Genes_cheatsheet_last.pptx

• https://github.com/millen2223/Galaxy-cheatsheets/blob/main/Peaks_and_Genes_cheatsheet/Peaks_and_Genes_cheatsheet_last.pdf

[hexylena]

I was thinking about this again today because of a Teacher Training course I'm currently taking for my work. We have a lot of these "important things to remember" and I have the feeling a lot of them are essentially "definitions", we're defining a term (maybe a file format, maybe a process like 'assembly') and they feel a lot like flashcards somehow. It came up in the course to use flashcards to help students remember topics, so, maybe we should combine this somehow. We annotate tutorials (optionally!!) with Important Terms they should know, and from that at the end of the tutorial have some flash cards and a cheatsheet table.

Hey @millen2223 it seems the links are broken, is that expected? I wanted to compare what I was thinking to your implementation but it might be gone?

[millen2223]

@hexylena I just changed visibility, please check it again

[millen2223]

It is interesting what you wrote about, and I haven't seen flashcards for software or an environment though I used them multiple times to learn words or while preparing for an exam. I find them so good for conciseness and speed when revising a topic as a game. As for me, remembering flashcards on the computer or phone will be easier for a student than a cheat sheet. On the other hand, a cheat sheet, is more visible because then you can access all definitions when searching for a term that you have forgotten. By the way, I often made a quiz, closing one side of the list and writing term definitions on the other, and then checking definitions I got incorrectly. This type helps to run through the paper fast and improve weak points... Maybe a checklist with flashcards of terms would be good? I will be glad to support any ideas @hexylena please say if something else comes to mind.

[hexylena]

Both is an option! It's great to hear that you used something like that when you were learning, so if we can offer this data in a structured way maybe we can have all of the above automatically generated/updated. I wonder what's the easiest way to annotate this data in tutorials, maybe just tutorial metadata like we do with the abbreviations. There we could define something like

key_tools:
  - title: UCSC Main
    description: retrieve and export data from the Genome Browser annotation track database 
    input: |
      In a table browser select dataset, define region
      of interest (genome | position + identifiers) then
      retrieve or display the data
    output: |
      File type as a plain textplain text - data is in ASCII
      format, or as *.*.gzip gzip compressed archive
      format for Linux/Unix ![](../images...)
    example: | 
      Retrieve list of genes of an
      animals, viruses, insects for i.e.
      mice etc.

and then from that generate the flashcards (there's several open standards we can use), cheatsheet, etc? What do you think @bebatut? Or this could be a global file in the GTN with quick descriptions of the tools, and then the header metadata could be

key_tools: [ucsc_main, grep1, cut]

and we do the same.

[hexylena]

I think we have a couple categories of this type of information that students might want to study, key_tools, key_terms (what is 'mapping'? general, unstructured definitions), and maybe also the abbreviations we have defined. For key tools the data is very general, I could definitely see keeping a single source of that for all of the GTN.

For the key terms it might make sense to annotate on the tutorial the term/definition in a special box or so? That way we keep the definition close to its use and we can show a nice box directly where the term is used defining that term? (And of course it's all opt-in but it can provide a better learning experience when available?)