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T027 Kinase similarity: ligand-profile #118

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merged 7 commits into from
Aug 24, 2021

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@t-kimber t-kimber commented Aug 10, 2021

Description

https://app.reviewnb.com/volkamerlab/teachopencadd/pull/118

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

@t-kimber t-kimber mentioned this pull request Aug 10, 2021
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@t-kimber t-kimber self-assigned this Aug 10, 2021
@t-kimber t-kimber changed the title T027 Kinase similarity ligand-profile T027 Kinase similarity: ligand-profile Aug 10, 2021
@t-kimber t-kimber added the enhancement New feature or request label Aug 10, 2021
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@t-kimber t-kimber merged commit 57ce05f into kinase-talkorials Aug 24, 2021
@t-kimber t-kimber deleted the tk-t027-kinsim-lig branch August 27, 2021 09:32
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