Base branch for new kinase talkorials

[dominiquesydow]

Description

Add a new batch of 7 6 kinase-focused talktorials (emphasizing on kinase similarity).

Per notebook, create new branch (tk-t024-kinsim-seq) and set up PR (T024 - Title).

Todos

• [TK/DS] Add kinase-focused template Add kinase-focused talktorial template #116
• [DS] T023 - What is a kinase? T023 What is a kinase? #120
• [TK] T024 - Kinase similarity: Sequence T024 Kinase similarity: sequence #117
• [DS] T025 - Kinase similarity: Structure (kinome-specific) T025 Kinase similarity: KiSSim fingerprint #121
• [DS] T026 - Kinase similarity: Interactions T026 Kinase similarity: IFP #122
• [TK] T027 - Kinase similarity: Ligand profiles T027 Kinase similarity: ligand-profile #118
• [TK/DS] T028 - Kinase similarity: Compare perspectives T028 Kinase similarity: compare perspectives #123
  • Try to formulate discussion more generalized so that notebook fits also for other kinase sets
• [TK] T029 - Predicting affinity using kissim (ML) T029 Predicting affinity using kissim #119
• Formatting looks correctly on the Sphinx render (bold, italics, figure placing)
• Regenerate READMEs
• Check which input each notebook gets (UniProt, kinase name) - can we streamline with?
• [DS] After merging this PR, open small new PR where we update all relative image paths to URLs (otherwise problem with website I think); concerns T023 and T026

https://app.reviewnb.com/volkamerlab/teachopencadd/pull/115/

Questions

• ???

Status

• Ready to go

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[t-kimber]

Dear @dominiquesydow and @AndreaVolkamer ,
I finished checking the HTML rending for this set of notebooks. Going through them a month later made me love them even more <3
The CI seems to be failing, but besides this small (wink wink) issue, this PR is ready to be merged IMO!
What a nice project it has been :)

[dominiquesydow]

Dear @dominiquesydow and @AndreaVolkamer , I finished checking the HTML rending for this set of notebooks. Going through them a month later made me love them even more <3

Thank you, @t-kimber, for making them HTML-ready ❤️ I share your sentiment towards our kinase talktorials :)

The CI seems to be failing, but besides this small (wink wink) issue, this PR is ready to be merged IMO!

That made me laugh a lot, given that I am trying to fix the CI fails for T018 just now :D

What a nice project it has been :)

Absolutely agreed! :)

[t-kimber]

Just mentioning here that the CI is now passing (even though it doesn't look like it ;) ) and that this PR is officially ready for the world. Hallelujah!

[t-kimber]

Added library: dataframe_image, see https://github.com/dexplo/dataframe_image
Why? Convert pandas styler dataframe to png.
Conda installation:
conda install -c conda-forge dataframe_image

We will drop this option and load images instead.
If one needs an external package, look at this discussion #184

Libraries for loading images, see https://towardsdatascience.com/what-library-can-load-image-in-python-and-what-are-their-difference-d1628c6623ad

[t-kimber]

Approve? Ohh yes, 100% !! ❤️ 💟 😍

[t-kimber]

The kinase similarity collection is ready, with thumbnails and everything 🎉

[dominiquesydow]

@t-kimber just triggering the CI again, so that we know our notebooks have not picked up any dependency conflicts in the meantime (because external packages were updated or something like this).