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The Xarray landing page
https://xarray.dev
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[User story proposal] Xarray for Genomics #346

Open jhamman opened 1 year ago

jhamman commented 1 year ago

This is a proposal for a genomics use case story for Xarray. The story will be published on Xarray's blog (https://xarray.dev/blog).

Why?

We've seen Xarray is used in a number of genomics applications (e.g. @alimanfoo's blog post) and we've seen some discussion about more in-depth applications. A user story blog post showing how Xarray can be used to represent and analyze genomics data would help socialize the concept across the Xarray developer and genomics communities.

What?

We are targeting a short and non-technical post that illustrates how Xarray is (or could be) used in your genomics context. Below is a template outline that you should feel free to modify:

  1. Who am I?
  2. What problem am I trying to solve?
  3. How does Xarray help?
  4. Why did I choose Xarray?
  5. Current pain points (or ways that Xarray could better serve your use case)
  6. Technology I use around Xarray
  7. Anything else to know?
  8. Links and references

Feel free to insert images or short code blocks if they help you tell your story.

How?

Xarray's blog using Markdown with some front-matter. You can copy one of the existing posts to get started or you can write in a google-doc-like-thing and ask us to do the markdown formatting. If you copy a previous post, use a name like user-story-genomics or whatever makes sense for your application.

xref: https://github.com/xarray-contrib/xarray.dev/issues/272

jhamman commented 1 year ago

@alimanfoo, @ryan-williams - are either of you interested in writing a post here? If not, can you suggest someone who may be a good candidate?

jhamman commented 1 year ago

@jpivarski cc'ing you here since you seem to be engaged in both Anndata and Xarray discussions recently.

jpivarski commented 1 year ago

Thanks! I'll keep an eye on this and comment if it helps the discussion.

jhamman commented 1 year ago

@tomwhite - I'm curious if you would be interested in writing up a short post on Sgkit's use of Xarray?

tomwhite commented 1 year ago

@jhamman Yes, I can write something for this.

jhamman commented 1 year ago

@tomwhite - fantastic! We're ready to move the user stories along so whenever you have a draft, we're happy to help get it on the site.

jhamman commented 1 year ago

@tomwhite - circling back here. Are you still interested in writing something up here?

tomwhite commented 1 year ago

Hi @jhamman - realistically, I don't think I'm going to be able to write something for this in the near future I'm afraid.

alimanfoo commented 1 year ago

Hi @jhamman, sorry I missed this initially. FWIW we spent the last year building out a new API for accessing and analysing malaria genomic data in the cloud, and have used xarray extensively. We're also nearly finished a training course which walks through how to use the data and API for a range of analytical tasks common to genomic surveillance of mosquitoes. The training course website is a jupyter book and has lots of examples where xarray is used. We included a training module on xarray specifically because we used xarray so much. If it's still useful I'd be happy work work up a user story around this for you.

jhamman commented 1 year ago

@alimanfoo - that would be amazing! Let me know if I can help in any way. No specific time crunch on our end but we're ready to publish your user story as soon as you are.