Faith Okamoto

👋🏽 My CV is available. 👋🏽

• Not every speedup is snazzy

  An optimization is an optimization

  By Faith Okamoto

  Posted on May 16, 2026

  I’ve been doing optimizations because my code that used to be winning on speed is now losing on speed. Or, actually, it was half-winning last I checked, but that was after several rounds of optimizations. Thought I’d write on it. [Read More]

  Tags:

  • optimization
  • algorithms

• Maybe it should do less

  an ode to simplicity

  By Faith Okamoto

  Posted on May 2, 2026

  Yeah, I work on the behemoth that is vg, but this post is about the benefits of task-specific tools. Instead of a be-all end-all multi-functional soup. [Read More]

  Tags:

  • pipeline
  • usability

• Code is for running, not just reading

  (though reading is important)

  By Faith Okamoto

  Posted on April 25, 2026

  I usually start my published code critiques by copying the previous post, just to get the formatting, which means I’m now noticing that last month’s critique was after the first time I watched Project Hail Mary. I’ve now watched it thrice. You may not have guessed that this bioinformatics PhD... [Read More]

  Tags:

  • published-code-critique
  • runnable

• Self-documenting data files

  Not just code should be usable

  By Faith Okamoto

  Posted on April 11, 2026

  I recently achieved that unicorn of collaborative science code: I passed off a section of my work to someone who’d never touched it before, and she figured it out without more than me just pointing her at my files. Thus, I thought I should write about a key component of... [Read More]

  Tags:

  • data
  • self-documenting

• Commit your clunkers

  Yes, even those ones

  By Faith Okamoto

  Posted on March 29, 2026

  I just got back from a conference talk which reminded me that I had a screed. So, a screed1. I want you to commit your clunkers2. [Read More]

  Tags:

  • version-control
  • screed

• Older Posts