The Curious Engineer

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Living in an Ivory Basement

ivory.idyll.org/blog

Stochastic thoughts on science, testing, and programming.

SciencePythonTesting / QA

’10’15’20’25
Posts
51 from 18 Sep 2006 to 7 Aug 2025
Posting
now and then
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personal blog
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2025 1

  1. Announcing taxburst, an update of the Krona software for taxonomy exploration

2024 6

  1. Announcing: the chill-filter Web site - DNA sample composition at a glance!
  2. Why Rust is an increasingly beloved part of my programming toolbox
  3. Recent advances in the sourmash ecosystem (August 2024)
  4. Speeding sourmash the heck up
  5. The history of the "Tragedy of the Commons"
  6. Sourmash and branchwater licensing: thoughts on extractive engagement with projects

2023 7

  1. snakemake for doing bioinformatics - inputs and outputs and more!
  2. snakemake for doing bioinformatics - using wildcards to generalize your rules
  3. conda & mamba on shared clusters works better now!
  4. A brief overview of automation and parallelization options in UNIX/on an HPC
  5. snakemake for doing bioinformatics - a beginner's guide (part 2)
  6. snakemake for doing bioinformatics - a beginner's guide (part 1)
  7. sourmash has a plugin interface!

2022 7

  1. Reading "Orwell's Roses" by Rebecca Solnit
  2. So! You want to search all the public metagenomes with a genome sequence!
  3. Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers
  4. The second Common Fund Data Ecosystem hackathon - May 9-13, 2022!
  5. Storing 64-bit unsigned integers in SQLite databases, for fun and profit
  6. The First Common Fund Data Ecosystem Hackathon
  7. On minimum metagenome covers, and calculating them for your own data.

2021 12

  1. A bioinformatics training career panel in the DIB Lab
  2. Using snakemake to do simple wildcard operations on many, many, many files
  3. A biotech career panel in the DIB Lab
  4. Scaling sourmash to millions of samples
  5. New sourmash databases are available!
  6. Moving sourmash towards more community engagement - a funding application
  7. Searching all public metagenomes with sourmash
  8. sourmash 4.1.0 released!!
  9. sourmash 4.0 is now available! Low low cost if you buy now!
  10. sourmash v4.0.0 release candidate 1 is now available for comment!
  11. Transition your Python project to use pyproject.toml and setup.cfg! (An example.)
  12. A snakemake hack for checkpoints

2020 7

  1. Improved workflows-as-applications: tips and tricks for building applications on top of snakemake
  2. sourmash databases as zip files, in sourmash v3.3.0
  3. Software and workflow development practices (April 2020 update)
  4. How to give a bad online talk
  5. Some snakemake hacks for dealing with large collections of files
  6. Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.
  7. sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes

2019 10

  1. Finding problematic bacterial/archaeal genomes using k-mers and taxonomy
  2. How does sourmash's lca classification routine compare with GTDB classifications?
  3. Sourmash LCA databases now available for the GTDB taxonomy
  4. An initial report on the Common Fund Data Ecosystem
  5. Comparing two genome binnings quickly with sourmash
  6. How to encourage participation in teleconferences
  7. Using GitHub for janky project reporting - some code
  8. Some questions and thoughts on journal peer review.
  9. Things to think about when developing shotgun metagenome classifiers
  10. Our submission for the NHGRI Human Genome Reference Center call

2006 1

  1. Index105