Lab notebook, 11 entries, newest first
To follow up on a previous post and answer a question I get surprisingly often - how I manage to get so much done - I want to share a loose collection of ideas that I've found particularly helpful. Software engineering in 2026 comes with a uniquely demanding…
Software is principally concerned with abstractions. Instead of writing binary, we have programming languages that abstract away the machine-readable details. Instead of repeating thousands of lines of code to perform some action, we abstract the action as a…
When I was growing up, many of my friends' parents worked in aerospace and defense. Later, when I entered the software industry, many of my peers followed the same path. Their salaries were almost always higher than mine. I had, and still have, many friends w…
Modern omics workflows require pulling thousands of files from dozens of vendors, each with their own identifiers and formats. We solve this by treating every external resource as a vendor artifact, unified by a consistent OCI-like interface. Here we define a…
Circa 2018 I was working on R&D for my employer's medical device product. AI was integral to the platform, and that project fell in my lap. Back then, nothing in the ML stack worked unless you were willing to get your hands dirty. If you were serious about ML…
Lately I've been thinking about why machine learning with biological data feels harder than it should. The research moves slowly not because scientists lack ideas, but because the infrastructure around data is fractured. Every archive, every consortium, every…
I've ended up writing a fair amount of code to poke at different public bioinformatics APIs: GDC, GTEx, UCSC, ENA, PDB, gnomAD, and a few others. I needed to answer questions like: What do these endpoints actually return? Are their IDs stable? What does the e…
For more than a decade, digital pathology has suffered from a strange paradox: a landscape full of powerful individual tools, but almost no cohesive ecosystem. Each project solves one slice of the computational-pathology workflow, but none of them span the co…
Digital pathology has quietly fallen decades behind every other data-intensive field. Despite the enormous clinical and research value locked inside whole slide imaging, the surrounding software ecosystem looks more like a collection of isolated experiments t…
In the summer of 2025, I had the privilege of working in my school's research lab as a fellow. One of the professors there was leading a project that relied heavily on microscopy, and her research fellows produced textbook-beautiful tissue slides. I'd often p…
A few times a week I receive an email from an approximately 20-year-old developer currently enrolled in college or planning to be shortly. Sometimes they are interested in biomedical, but most express a desire to enter a cross-domain STEM field with software…