Speeding sourmash the heck up

The history of the Tragedy of the Commons

Sourmash and branchwater licensing: thoughts on extractive engagement with projects

snakemake for doing bioinformatics - inputs and outputs and more

snakemake for doing bioinformatics - using wildcards to generalize your rules

conda & mamba on shared clusters works better now

A brief overview of automation and parallelization options in UNIX on an HPC

snakemake for doing bioinformatics - a beginner’s guide (part 2)

snakemake for doing bioinformatics - a beginner’s guide (part 1)

sourmash has a plugin interface

Reading Orwell’s Roses by Rebecca Solnit

So You want to search all the public metagenomes with a genome sequence

Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers

The second Common Fund Data Ecosystem hackathon - May 9-13, 2022

Storing 64-bit unsigned integers in SQLite databases, for fun and profit

The First Common Fund Data Ecosystem Hackathon

On minimum metagenome covers, and calculating them for your own data.

A bioinformatics training career panel in the DIB Lab

Using snakemake to do simple wildcard operations on many, many, many files

A biotech career panel in the DIB Lab

Scaling sourmash to millions of samples

New sourmash databases are available

Moving sourmash towards more community engagement - a funding application

Searching all public metagenomes with sourmash

sourmash 4.1.0 released

sourmash 4.0 is now available Low low cost if you buy now

sourmash v4.0.0 release candidate 1 is now available for comment

Transition your Python project to use pyproject.toml and setup.cfg (An example.)

A snakemake hack for checkpoints

Improved workflows-as-applications: tips and tricks for building applications on top of snakemake

sourmash databases as zip files, in sourmash v3.3.0

Software and workflow development practices (April 2020 update)

How to give a bad online talk

Some snakemake hacks for dealing with large collections of files

Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.

sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes

Finding problematic bacterial archaeal genomes using k-mers and taxonomy

How does sourmash’s lca classification routine compare with GTDB classifications?

Sourmash LCA databases now available for the GTDB taxonomy

An initial report on the Common Fund Data Ecosystem

Comparing two genome binnings quickly with sourmash

How to encourage participation in teleconferences

Using GitHub for janky project reporting - some code

Some questions and thoughts on journal peer review.

Things to think about when developing shotgun metagenome classifiers

Our submission for the NHGRI Human Genome Reference Center call

News from the NIH Data Commons Pilot Phase Consortium

Critically assessing open science - the CAOS meeting.

Sustaining open source: thinking about communities of effort

My recent reading re sustaining open communities