Ideas for more sandbox.bio tutorials for statistical genetics and python

[mragsac]

Hello there! I've been following sandbox.bio for a while and wanted to contribute some tutorials. I wanted to port over some of the materials from a class I helped teach at the University of California, San Diego. The class was CMM262: Quantitative Methods in Genetics taught in Winter 2020 and Winter 2021.

Here are some of the ideas that I had as potential things to implement with a pull request:

• Learning about plink for statistical genetics applications and running basic quality control steps (e.g., evaluating missingness in SNPs and samples, evaluating minor allele frequency (MAF), Hardy-Weinberg Equilibrium (HWE))
• Setting up an environment with conda on the command line with the miniconda install and installing a bioinformatics CLI tool with bioconda in a newly-created environment for a project
• Basic plotting in python with pandas and matplotlib for common bioinformatics figures (e.g., scatter plots, violin plots, bar plots)

I was wondering if tutorials for these things would be helpful or if others are already working on them. Thanks for reading this issue!

[robertaboukhalil]

Thanks @mragsac, a plink tutorial would be fantastic!

Let me first make sure I can get Plink running inside the browser environment and I'll get back to you.

For the others, conda is quite tricky to get working in the environment. Plotting tutorials is definitely something we want to add, but first we want to support Python tutorials with a better environment, e.g. an IDE instead of typing one command at a time

[robertaboukhalil]

@mragsac I can confirm Plink v1.9 runs just fine on sandbox.bio, feel free to start writing your tutorial!

Here are useful pointers on the format: https://github.com/sandbox-bio/sandbox.bio/blob/main/CONTRIBUTING.md#tutorial-structure

Feel free to send over drafts and I can publish them as unlisted for you to preview (I'm working on making this more automated for the future 😅).

[mragsac]

@robertaboukhalil Hooray! Sounds good! I'll get started on porting the plink things over!

As for having an IDE-like environment for people to learn in, what about using VS Code in the browser or Jupyter Lab with some sort of bindr instance connected to the sandbox.bio repo? 😅

[robertaboukhalil]

Great, looking forward to it!

Yes, I am thinking of VS Code for the in browser IDE, but for Python I'm planning to use Pyodide or JupyterLite as it lets you run Python directly in the browser!

[robertaboukhalil]

@mragsac I just made some updates to make it easier to write tutorials: https://github.com/sandbox-bio/sandbox.bio?tab=readme-ov-file#local-development-setup

Basically, instead of writing markdown files without seeing the results, you can now preview the tutorial while writing it! Please give that a try and let me know how it goes.

[robertaboukhalil]

Update: as of yesterday evening, Plink is now available on sandbox.bio

[mragsac]

Awesome! I'm slowly working on the tutorial and have found your updated documentation to be super helpful!

[robertaboukhalil]

Great to hear that, thanks!