Hello!
I'm Edmund Miller, a PhD candidate with a broad range of interests, primarily in Functional Genomics. I got into bioinformatics after realizing I didn't have golden hands at the bench during undergrad.
That taste of programming got me dabbling in writing smart contracts and web apps. Through my research experience I acquired a taste for processing data with reproducible, high-throughput workflows.
I saw the light in March 2020 when I found nf-core and tossed aside the reptilian workflow manager for Nextflow. I love a good crossover episode of technologies and I'm always trying to push the envelope.
Start here
If you're here for bioinformatics tooling, reproducible workflows, or Emacs-shaped developer ergonomics, these are the best next steps.
Posts
How I turned a Jupyter notebook into a full-fledged Python package for UpSet plots
nf-core containers automation: how it'll all work behind the curtain
What Seqera Containers is and why we want to move to it.
Set up Pixi with conda-forge and Bioconda on an HPC cluster or laptop, install Nextflow, define tasks, and import an existing environment.yml.
Configure Apheleia in Doom Emacs to format Snakemake files with snakefmt, including a Nix package and the exact set-formatter! setup.
How I hack on Nextflow scripts using Emacs
I compared GoatCounter, Umami, Plausible, and Fathom to find personal-site analytics without creepy tracking or another yak-shaving project.
Set up Astro in Doom Emacs with astro-ts-mode, Tree-sitter, lsp-mode, Apheleia and Prettier, plus Tailwind CSS IntelliSense.
Set up age.el and rage in Doom Emacs, configure SSH key paths, and save org-journal entries as encrypted .org.age files when EasyPG hangs.
Or is it like v5 at this point?