Faith Okamoto

👋🏽 My CV is available. 👋🏽

• Knowing what to leave out

  this is one of my positive ones

  By Faith Okamoto

  Posted on September 26, 2026

  I spend a while complaining about what people should add to their code. (Comments. You should add comments. Also a README. Also documentation. Also… but I repeat myself.) I thought it might be interesting to look at what people should leave out. And since this is a topic that benefits... [Read More]

  Tags:

  • published-code-critique
  • gitignore

• Keeping track of results by commit

  easy and useful

  By Faith Okamoto

  Posted on September 12, 2026

  I develop, implement, and test algorithms as part of my research.1 On a day-to-day basis, that looks like a lot of fiddling. Fiddle, test, fiddle, test. How do I keep track of what’s what in my notebook? Mostly, I notate results alongside their commit hash. [Read More]

  Tags:

  • process
  • notebook

• The work is not in vain

  things I need to hear

  By Faith Okamoto

  Posted on September 7, 2026

  If you read this blog, then you know that I evangelize proper documentation with zeal more commonly associated with religious crusades1. I’m here to tell you today that I have received a sign. [Read More]

  Tags:

  • meta
  • documentation

• Sharing accessible code

  for the greater good

  By Faith Okamoto

  Posted on August 29, 2026

  I’m on a paper that should be submitted Tuesday.1 This meant I spent a good portion of Thursday reading through the nearly finalized text. I’ll discuss one of my comments here. [Read More]

  Tags:

  • publications
  • code-availability

• Thanks for telling me how to contribute

  (that's not sarcastic I mean it)

  By Faith Okamoto

  Posted on August 15, 2026

  I recently added a CONTRIBUTING.md file to the tool I work on. Thought I’d check out what other tools have. After about thirty seconds of trying to think of a well-used bioinformatics tool which isn’t Minimap2 (I’ve done that before) I came up with BioPython. [Read More]

  Tags:

  • published-code-critique
  • documentation
  • guidelines

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