What Uncle Bob's "I Don't Read Code Anymore" Taught Me About Testing
I've come across a post by Uncle Bob on X ( link ) (the author of Clean Code ) that has a couple thousand reposts. It states that he does not read cod…
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Spatial Transcriptomics Plus Topological Data Analysis: A Complete End-to-End Tutorial with squidpy and GUDHI
Build a real spatial transcriptomics pipeline on Visium mouse brain, then go one step past every tutorial: use persistent homology to find spatial str…
A UMAP With Arrows Is Not a Benchmark. This Is
How I built a three-task evaluation framework for RNA velocity trajectory inference -- measuring global ordering, pairwise rank preservation, and robu…
Engineering CellFateBench: A Reproducible Python Benchmark for Single-Cell Genomics Reasoning
CellFateBench is a scientific software and benchmark-engineering project for evaluating reasoning over single-cell genomics workflows. The project was…
A MOGONET-Style Multi-Omics Biomarker Pipeline: Why a Near-Random Graph Net Still Earns Its Place
TL;DR (Quick Answer) This is an honest engineering write-up of a MOGONET-style multi-omics consensus biomarker pipeline built as an internal R&D p…
From Repo Scanner to Audit Architecture: What Changed in STEM BIO-AI Through v1.7.8
Three technical changes that made the scanner less Python-shaped, the warning model more stable, and the reports more inspectable. The last time I wro…
When Control Becomes Authority: Calibration Governance in STEM BIO-AI 1.7.x
Control slowly becomes authority when nobody marks the boundary. That is the calibration problem I kept running into while building STEM BIO-AI. At fi…
From Score to Workflow: Turning STEM BIO-AI Into a Local Audit System
Earlier in this series, I wrote about why bio/medical AI repositories need more than benchmarks, what I learned after auditing 10 public repositories,…