tag: bioinformatics

Release note for QuEStVar v0.1.0. Python package for paired equivalence and difference testing, now stable on PyPI.

Zero-dependency FASTA indexing that matches samtools byte-for-byte while running up to 17x faster. Built in Zig with SIMD and mmap. Also: a proof of concept that needs Zig 0.14, has no gzip support, and cannot extract sequences yet.

The search engine space is crowded, fast-moving, and genuinely competitive. DIA-NN, Spectronaut, FragPipe, MaxQuant, and Sage each carved a niche. A Zig-based search engine is not the right next step. The gap between engines might be.

The story behind ProteoForge, a framework for finding differential proteoforms in bottom-up proteomics data. Why protein-level averages hide biology, how missing data broke every tool we tried, and what we found when we applied it to a hypoxia dataset.

Nextflow and Snakemake both get the big things right and the small things wrong. A bioinformatics-specific engine with no runtime and a single static binary might fix the part that actually costs time.

I already knew Rust. I'm learning Zig anyway. Not because it's better, but because it fits a specific kind of work: small, fast tools that live forever in pipelines. An early take, not a manifesto.

Probabilistic dropout analysis for label-free proteomics. Handles missing values by modeling dropout curves instead of imputing.

Deep learning for MS2 spectrum and retention time prediction. Accurate enough for rescoring and library generation.