T023 What is a kinase?

[dominiquesydow]

Description

• Talktorial ID: T023
• Title: What is a kinase?
• Original authors: @dominiquesydow
• Reviewer(s): @t-kimber, @AndreaVolkamer
• Date of review:

https://app.reviewnb.com/volkamerlab/teachopencadd/pull/120

Todos

Content

• Theory
  • Kinase dataset
  • Kinase similarity descriptor: XXX
• Practical
  • Retrieve and preprocess data
  • Show kinase coverage
  • Compare kinases
  • Visualize similarity as kinase matrix
  • Visualize similarity as phylogenetic tree

Content review

• Potential labels or categories (e.g. machine learning, small molecules, online APIs): XXXXXXXX
• One line summary: XXXXXXXXXX
• The table of contents reflects the talktorial story-line; order of #, ##, ### headers is correct
• URLs are linked with meaningful words, instead of pasting the URL directly or linking words like here.
• I have spell-checked the notebook
• Images have enough resolution to be rendered with quality, without being too heavy.
• All figures have a description
• Markdown cell content is still in-line with code cell output (whenever results are discussed)
• I have checked that cell outputs are not incredibly long (this applies also to DataFrames)
• Formatting looks correctly on the Sphinx render (bold, italics, figure placing)

Code review

• Time it took to execute (approx.):
• Variable and function names follow snake case rules (e.g. a_variable_name vs aVariableName)
• Spacing follows PEP8 (run Black on the code cells if needed)
• Code line are under 99 characters each (run black -l 99)
• Comments are useful and well placed
• There are no unpythonic idioms like for i in range(len(list)) (see slides)
• All 3rd party dependencies are listed at the top of the notebook
• I have marked all code cell with output referenced in markdown cells with the label # TODO: CI
• I have identified potential candidates for a code refactor / useful functions
• All import ... lines are at the top (practice part) cell, ordered by standard library / 3rd party packages / our own (teachopencadd.*)
• I have update the relative paths to absolute paths.
• List here unfamiliar libraries you find in the imports and their intended use:

Questions

• TBA

Status

• Ready to go

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[AndreaVolkamer]

@dominiquesydow and @t-kimber

I added an outline for how we could structure the short intro to kinases in general, then we could use the practical part to compile the input data for the remaining notebooks.
Potentially the practical part could also include some automated queries to create some of the mentioned figures, but this is optional.

[t-kimber]

We will address this PR in the kinase-talkorials branch to avoid too many conflicts (see PR #115).