Announcing taxburst, an update of the Krona software for taxonomy exploration
Announcing taxburst for metagenome taxonomy!
Living in an Ivory Basement
Stochastic thoughts on science, testing, and programming.
Latest posts
Announcing: the chill-filter Web site - DNA sample composition at a glance!
what's in my sample, dude?
Why Rust is an increasingly beloved part of my programming toolbox
Rust is nice!
Recent advances in the sourmash ecosystem (August 2024)
sourmash is faster and better than before!
Speeding sourmash the heck up
Faster things are always nice, right?
The history of the "Tragedy of the Commons"
No, just no.
Sourmash and branchwater licensing: thoughts on extractive engagement with projects
What licenses should be used, for what purpose?
snakemake for doing bioinformatics - inputs and outputs and more!
Slithering your way into bioinformatics with snakemake - inputs and outputs and more!
snakemake for doing bioinformatics - using wildcards to generalize your rules
Slithering your way into bioinformatics with snakemake, wildcard version
conda & mamba on shared clusters works better now!
conda is great!
A brief overview of automation and parallelization options in UNIX/on an HPC
Automating things! Parallelizing them!
snakemake for doing bioinformatics - a beginner's guide (part 2)
Slithering your way into bioinformatics with snakemake, round 2.
snakemake for doing bioinformatics - a beginner's guide (part 1)
Slithering your way into bioinformatics with snakemake
sourmash has a plugin interface!
Enabling plugins in sourmash, for less directed & more incoherent progress!
Reading "Orwell's Roses" by Rebecca Solnit
This is a good book!
So! You want to search all the public metagenomes with a genome sequence!
Searching all the things - faster!
Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers
Munging GitHub issue trackers for fun!
The second Common Fund Data Ecosystem hackathon - May 9-13, 2022!
We're running another hackathon!
Storing 64-bit unsigned integers in SQLite databases, for fun and profit
Storing unsigned longs in SQLite is possible, and can be fast.
The First Common Fund Data Ecosystem Hackathon
We ran a successful pilot hackathon, and we will run a second one soon!
On minimum metagenome covers, and calculating them for your own data.
You, too, can run our software!
A bioinformatics training career panel in the DIB Lab
Careers in training!
Using snakemake to do simple wildcard operations on many, many, many files
snakemake is awesome
A biotech career panel in the DIB Lab
Careers outside of universities!
Scaling sourmash to millions of samples
Bigger and better!
New sourmash databases are available!
Databases are now available for GTDB!
Moving sourmash towards more community engagement - a funding application
CZI EOSS4 application for sourmash support
Searching all public metagenomes with sourmash
Searching all the things!
sourmash 4.1.0 released!!
sourmash v4.1.0 is here!
sourmash 4.0 is now available! Low low cost if you buy now!
sourmash v4.0.0 is here!
sourmash v4.0.0 release candidate 1 is now available for comment!
sourmash v4.0.0 is coming!
Transition your Python project to use pyproject.toml and setup.cfg! (An example.)
Updating old Python packages, in this year of the PSF 2021!
A snakemake hack for checkpoints
snakemake checkpoints r awesome
Improved workflows-as-applications: tips and tricks for building applications on top of snakemake
Writing applications around workflow systems, take 2.
sourmash databases as zip files, in sourmash v3.3.0
Use compressed databases directly!
Software and workflow development practices (April 2020 update)
How we develop software and workflows in the DIB Lab, in 2020.
How to give a bad online talk
A bad example...
Some snakemake hacks for dealing with large collections of files
snakemake4life
Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.
Using k-mers and taxonomy to find contamination in metagenomes
sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes
Using k-mers and taxonomy to find contamination in metagenomes
Finding problematic bacterial/archaeal genomes using k-mers and taxonomy
Some things in Genbank look ...odd.
How does sourmash's lca classification routine compare with GTDB classifications?
GTDB databases again!
Sourmash LCA databases now available for the GTDB taxonomy
GTDB databases!
An initial report on the Common Fund Data Ecosystem
Helping DCCs get FAIRer
Comparing two genome binnings quickly with sourmash
Comparing two sets of MAGs, for fun and profit!
How to encourage participation in teleconferences
Participation is good!
Using GitHub for janky project reporting - some code
We scripted GitHub for lightweight project reporting
Some questions and thoughts on journal peer review.
What's up with current peer review practice?
Things to think about when developing shotgun metagenome classifiers
Thoughts on goals and tradeoffs in classifying shotgun metagenome data.
Our submission for the NHGRI Human Genome Reference Center call
We wrote a big grant proposal!