Job search 2025 post-mortem and advice
The comp bio job market is scarier than usual: 2023 was a biotech bankruptcy bloodbath, 2024 was a little better, and as far as layoffs, 2025 has been worse. Academic and government sectors are also r...
How long does it take to run gpt-oss:20b?
<p>gpt-oss is OpenAI's open-weight models designed for powerful reasoning, agentic tasks, and versatile developer use cases. You can easily use it via Ollama and read more about it in their blog post....
Announcing taxburst, an update of the Krona software for taxonomy exploration
<p>Announcing taxburst for metagenome taxonomy!</p>...
Announcing taxburst, an update of the Krona software for taxonomy exploration
<p>Announcing taxburst for metagenome taxonomy!</p>...
Hunting collisions with ntHash
<div> <nav id="TableOfContents"> <ul> <li><a href="https://bacpop.org/blog/index.xml#a-quick-introduction">A quick introduction</a></li> <li><a href="https://bacpop.org/blog/index.xml#the-ultravio...
Analyzing ICE Detention Data from 2021 to 2025
The ability to code and explore big datasets are generally useful skills that transfer well beyond our work of biomedical spatial omics analysis. In this blog post, I analyze publicly available datase...
A recap of virtual cell releases circa June 2025
In October 2024, I twote that “something is deeply wrong” with what we now call virtual cell models. A lot has happened since then: modelers are advancing new architectures and mining new sources of i...
DEE2 database gets HDF5
<p>Here I’ll show you how to download and work with the new HDF5 datasets from DEE2 (dee2.io).</p><div class="section level2" id="introduction"><p style="margin: 0px 0px 10px;">HDF5 files are provide ...
Five flavors of stratified LD score regression (Part 1, Vanilla)
Linkage disequilibrium score regression (LDSC) is a workhorse technique at the intersection of quantitative genetics and functional genomics. The core use of S-LDSC is to detect and quantify functiona...
The Future of At-Home Oncology Testing: Tiny Drops, Big Insights?
<p>The journey for an oncology patient often involves a relentless cycle of clinic visits, treatments, and crucially to the work I am involved with, blood draws for diagnosis, monitoring and MRD. This...