Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!

I've added an AI policy to ripgrep that was shamelessly copied from uv's policy. I plan to add this to the rest of my projects, but if anyone wants to offer feedback on wording, now would be a good time! github.com/BurntSushi/r...

lucumr.pocoo.org/2026/4/11/th... from Armin seems pretty related.

The Center Has a Bias

Why a measured position on AI tends to lean towards actually trying it.

lucumr.pocoo.org

Deeply worried about deskilling in bioinformatics and software development. In parallel, also worried about low quality code being churned out rapidly by folks using these tools without doing proper quality control on the outputs 😬

Jordan Nafa@ajordannafa.com · 3mo ago

The more I use AI for development, the more concerned I am about the fact that knowing what makes an effective prompt and the appropriate, opiniated, guardrails necessary to consistently get high quality output is much harder if you don't have quite a bit of experience doing things by hand first.

We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 3mo ago

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan https://www.biorxiv.org/content/10.64898/2026.05.14.725045v1

still WIP but: better design-book examples incoming: meodai.github.io/design-book/

I've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

youtu.be

coming soon in a github.com/bearcove/figue near you

me: maybe i will finally write some of that code <gets immediately tarpitted for six hours trying to fix something in dev setup, is now 11:30>

I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html

This semester I developed and taught a course on applied population genomics. Lab activities proceed from the basics of the command line and Git to variant calling with workflow managers and a suite of downstream analyses (e.g., ADMIXTURE). All materials can be found here: elinck.org/genomics_eco...

From @davidmoreau.bsky.social & Kristina Wiebels in @plos.org #Computational #Biology | Nine quick tips for #software #containerization | I like all Tips, but particularly Tip 9: Plan for sharing & longevity | #Bioinformatics #Education #PLOSCBQT | 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

Nine quick tips for software containerization

Software containerization has become a cornerstone of modern computational biology, enabling researchers to package code, dependencies, and execution environments in portable and reusable units. Conta...

journals.plos.org

From @robert.bio @helenechiapello.bsky.social @mthomaschollier.bsky.social & col. in @plos.org #Computational #Biology | Training biologists in #Unix command-line skills: From curriculum to interactive online tutorials|#Education #OpenEducationalResources | 🖥️ 🧪 ⬇️ journals.plos.org/ploscompbiol...

Training biologists in Unix command-line skills: From curriculum to interactive online tutorials

As the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly tho...

journals.plos.org

In about an hour using Claude Code (see disclaimer in repo) I put together code to do something that is a pain in the ass to do manually - find a good genome in NCBI then see what decent population level WGS data exist for that genome assembly in NCBI SRA: github.com/brantfairclo.... I'm impressed.

[blog] A Better R Programming Experience Thanks to Tree-sitter Did you know how Tree-sitter's support for R help you get ✨ reformatting through Air and linting through Jarl; ✨ auto-completion or help on hover in the Positron IDE; ✨ better search for R on GitHub; ✨ and more! By @maelle […]

Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes https://www.biorxiv.org/content/10.64898/2026.03.29.711974v1

The #SnakemakeHackathon2026 has ended, we are still preparing our preprint release. But, our host has prepared a note on their homepage: https://go.tum.de/946236 🥳 #Snakemake #ReproducibleComputing

Snakemake Hackathon 2026 – faster and further improved reproducible data analysis

Snakemake Hackathon 2026 delivers even faster and further improved support for reproducible data analysis. The 2026 Snakemake Hackathon brought together about 40 experts in Munich to deliver major improvements, new features, and performance enhancements for reproducible data analysis. Their community driven work strengthens Snakemake’s scalability, usability, and support for modern scientific workflows.

mdsi.tum.de

We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Click to learn more about our goal with this fund and to donate! www.givecampus.com/schools/Univ...

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter

The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.

github.com

Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....

GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.

A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt

github.com

At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa.... It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍

Johannes Köster@johanneskoester.bsky.social · 5mo ago

Today, the #SnakemakeHackathon2026 at the TU Munich ended with the release of Snakemake 9.17! I want to thank all participants and my co-organizers! You have been incredibly dedicated and we improved a ton of things throughout the ecosystem.

I'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! Computational lab. Message me if interested, and can apply here: indiana.peopleadmin.com/postings/32547

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

Came across the phrase "cognitive DDOS" to describe our present culture. Understood instantly what it meant.

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

COMBINE-lab - The skeptic’s guide to generative AI assisted coding

An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

combine-lab.github.io

Excited for this. Teaching popgen is one of my favourite parts of my job and I've wondered about doing an online version of the class for sometime. Teaming up with @jrossibarra.bsky.social to do this is wonderful.

Jeffrey Ross-Ibarra@jrossibarra.bsky.social · 6mo ago

Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!

Playing with sandbox.bio. This was remarkably cathartic.

A succinct and useful list of rules for teaching data science, including some of my favourites: "teach with real data" and "have students do projects". #databs #datasky

Tiffany Timbers@tiffanytimbers.bsky.social · 6mo ago

"Ten simple rules for teaching data science": arxiv.org/abs/2602.02874 A new preprint by @minecr.bsky.social and myself. We'd love any feedback!

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework? Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.

Richard Lenski@relenski.bsky.social · 12mo ago

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime. telliamedrevisited.wordpress.com/2025/08/12/s... STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.