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Computational Biology

Articles and publications tagged Computational Biology across the Atmosphere.

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Kemal YaylaliSep 30, 2026

SimurgArray going public: what it takes, and a calendar

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...

Bioinformaticsbuild-in-public

Kemal YaylaliSep 30, 2026

SimurgArray: What good could it do?

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...

BioinformaticsComputational Biology

Kemal YaylaliSep 30, 2026

Are there SimurgArray alternatives? Yes. Why build it anyway?

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...

BioinformaticsComputational Biology

Kemal YaylaliSep 30, 2026

Why SimurgArray should exist?

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...

BioinformaticsComputational Biology

Kemal YaylaliSep 12, 2026

rarelens: building a rare-disease variant triage platform, and the four things I got wrong

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.

AIBioinformatics

Kemal'sAug 24, 2026

Beyond the 2D Bounding Box: Why Bioimage Deep Learning Is a Completely Different Beast and How BiaPy Tames It

[latexpage]https://github.com/lynchaos/biapy-hubhttps://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 $(B, 3, H, W)$ where $H, W \le 1024$. The pixels are isotropic, the spatial coordinates...

AIComputational Biology

Kemal'sAug 1, 2026

Building a fake microscope: simulating a yeast wet mount

[latexpage] 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...

2Computational Biology

Kemal'sJul 20, 2026

What rebuilding five aging papers from scratch actually proves

A reproducible, cloud-scale reanalysis of five peer-reviewed studies on cellular aging, reprogramming, and rejuvenation, and an honest account of what survived contact with a shared pipeline.

Data ScienceMachine Learning

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