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
What's the move for something that gives you feedback and isn't creepy
The beauty of Astro is it's like the Nextflow of web frameworks
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?