We often buy developer kits with grandiose industrial ambitions, only to leave half the shields sitting in parts drawers gathering dust. Recently, while clearing off my workbench, I grabbed an Elegoo Uno R3 clone paired with a ubiquitous 16×2 LCD keypad shield. The original plan was a quick telemetry display, but old gaming instincts took… Read More: The Project: Dino Runner on 16×2 Character LCD »
Part 5 of 5. Four posts of reasons are enough. This one is about what it looks like when you actually use the thing, and about the name, which people ask about more often than they ask about normalization. Fair enough. One small note first. The command examples below use the usual command line options,… Read More: Using SimurgArray, and the bird behind the name »
Part 4 of 5. Right now SimurgArray lives in a private repository on my own Git server. It has a license, a changelog, a user guide, wheels, a Docker image and a version number that just became 2.0.0. In other words, it looks public. It is not, yet. Publishing code is easy. Publishing it responsibly… Read More: SimurgArray going public: what it takes, and a calendar »
Part 3 of 5. “Benefit to humanity” is a big phrase for a tool that mostly reads binary files. I will try to keep this post the right size. SimurgArray will not cure anything. What it can do is lower a few barriers that currently decide who gets to do genetics research and how much… Read More: SimurgArray: What good could it do? »
Part 2 of 5. Whenever someone tells me they are writing their own genotype caller, my first instinct is to ask whether they have looked around. So it is only fair that I answer the same question about myself. I did look around. There is a lot of good work out there. Some of it… Read More: Are there SimurgArray alternatives? Yes. Why build it anyway? »
Part 1 of 5. Every genotyping array tells a small story before it tells you anything about DNA. A glass slide goes into a scanner, the scanner writes two IDAT files per sample (one red, one green), and a few hundred thousand bead intensities wait for someone to turn them into genotypes. That someone is… Read More: Why SimurgArray should exist? »
An end-to-end rare-disease variant triage platform: a Nextflow pipeline, three execution backends behind one API call, Terraform for two cloud tracks, and a phenotype-driven ranking measured against 10,178 published cases. Including the model metric that collapsed to exactly random once I removed the feature doing all the work.
https://github.com/lynchaos/biapy-hub https://lynchaos-biapy-hub-app-hlcmfj.streamlit.app/ If you have spent your machine learning career optimizing ResNets or YOLO on ImageNet and COCO, here is an inconvenient truth: standard computer vision has spoiled you. In standard computer vision, a batch is usually an RGB triplet where . The pixels are isotropic, the spatial coordinates are Euclidean, the lighting is roughly… Read More: Beyond the 2D Bounding Box: Why Bioimage Deep Learning Is… »
A Raspberry Pi Zero 2 W paired with a Sense HAT V2 runs a fully self-contained, edge-native machine learning weather station with no cloud, GPU, or heavy ML frameworks. The system uses pure NumPy implementations of Recursive Least Squares, Kalman filtering, conformal prediction, and drift detection, staying under 150 MB RAM. The station continuously updates… Read More: I turned a Raspberry Pi into a tiny weather intelligence… »
Repository: github.com/lynchaos/generative-microscopy Why this sketch I wanted to find out whether I could make something that genuinely looked like microscopy footage. Not cells bouncing around a canvas, but Saccharomyces cerevisiae behaving the way it actually behaves under a coverslip, seen through real glass and real light. The sketch began life as a generic n-body attraction… Read More: Building a fake microscope: simulating a yeast wet mount »