Something a little different for this week’s recap. I’ve been thinking a lot lately about the practice of data science education in this era of widely available (and really good!) LLMs for code. Commentary at the top based on my own data science teaching experience, with a deep dive into a few recent papers below.

The majority of developers use LLMs to help write code, present company included. When I’m working in languages I know well, they're fantastic at handling the grunt work: generating boilerplate, suggesting completions, and writing tedious tests and documentation.

I'm still catching up on papers from my late 2024 backlog. This week’s recap highlights autonomous microbial sensors for detecting TNT in soil, genome size estimation from long reads, STABIX for indexing and compressing GWAS summary statistics, and Clair3-RNA for deep learning-based small variant calling on long-read RNA-seq data.

OpenAI introduced the ability to create custom GPTs back in November 2023. I wanted to try to create one of these, and in the spirit of learning in public this post describes how I made it. But first, what does it do?Gene Info Custom GPT Gene Info custom GPT The Gene Info custom GPT takes a list of human gene symbols as input.

Happy New Year! I’m still catching up on papers from my late 2024 backlog.

Background Bluesky, atrrr, local LLMs I’ve written a few posts lately about Bluesky — first, Bluesky for Science, about Bluesky as a home for Science Twitter expats after the mass eXodus, another on using the atrrr package to expand your Bluesky network. I’ve also spent some time looking at R packages to provide an interface to Ollama.

I had good intentions to give NaNoWriMo a try this year but didn’t get very far. Instead I gave OpenAI’s Creative Writing Coach GPT a try for a (very) short story I had in mind, inspired by my frustration trying to access closed-access research articles for a review article I’m preparing.

The Baader–Meinhof phenomenon (aka the frequency illusion) is the name for that thing that happens when you buy a new car, and suddenly you notice that same model car everywhere you drive.

This week’s recap highlights the Evo model for sequence modeling and design, biomedical discovery with AI agents, improving bioinformatics software quality through teamwork, a new tool from Brent Pedersen and Aaron Quinlan (vcfexpress) for filtering and formatting VCFs with Lua expressions, a new paper about the NHGRI-EBI GWAS Catalog, and a review paper on designing and engineering synthetic genomes.

A few days ago I wrote about translating R package help documentation using a local LLM (e.g. llama3.x)… …when Mick Watson commented: I was already thinking of wiring up something like this using local AI models — something to summarize podcasts, conference recordings, etc. The relatively new (as of this writing) Gemini 2.0 Flash model will do this for you for YouTube videos. But what if you wanted to do this offline using a local LLM?

Last week I posted about a web app that turns a GitHub repo into a single text file for LLM-friendly input. This is great for capturing LLM-friendly text from a GitHub repo, but what about any other arbitrary website or PDF? I was catching up on Simon Willison’s newsletter reading about an app he made with Claude artifacts that uses the Jina Reader API to generate Markdown from a website. You don’t need to use the API to do this.