Bioinformatician. At work I write the software behind genomic surveillance of foodborne and zoonotic bacteria — Salmonella, Listeria, Klebsiella — for One Health outbreak investigation: typing, distances, trees, and the pipelines that run them. In my spare time I build self-hosted tools for working with AI coding agents.

Mostly Rust, where a cgMLST matrix of tens of thousands of genomes has to fit in a coffee break. Published under genpat-it.

• cgDist — distances between cgMLST/wgMLST profiles counted in SNPs and indels, not just differing alleles, by aligning the alleles that differ. Finer resolution where outbreak clusters are decided. de Ruvo et al. (2025), bioRxiv, 10.1101/2025.10.16.682749.
• chewcall — a cgMLST/wgMLST allele caller with SIMD Smith-Waterman scoring: 10.7–22.3× faster than chewBBACA, with the same DNA sequences called.
• mm2-geo — geometry-guided band doubling for minimap2's gap-filling DP: faster, with identical variant-calling F1.
• cgmlst-dists-rs · cgmlst-dists-py — pairwise Hamming matrices for cgMLST: AVX-512 in Rust (~6× the C cgmlst-dists, byte-identical), GPU in Python.
• dist2mst-rs · grapetree-rs · ohe-rs — minimum spanning trees, GrapeTree's engine and one-hot encoding of allele profiles, rewritten for speed.
• CoreGuard — compares SNP calls from several variant-calling pipelines against a ground truth and shows where they disagree.
• cohesive-llm — a self-hostable platform that writes Nextflow DSL2 pipelines from a description, with its benchmark.
• Platform comparison — bacterial and viral genomic-surveillance platforms compared, every value backed by a cited source.

Several of these are on Bioconda (cgmlst-dists-py, dist2mst, dist2mst-rs, ohe-rs).

Argus is a self-hosted workspace around the AI coding agents and other processes already running in tmux: terminal sessions, files, reports, alerts and hand-offs together, on desktop or phone, with no hosted control plane. It came out of long genomics jobs and agents running on a lab server that I wanted to follow from anywhere.

• Argus Fleet, powered by Panoptes — one board for several Argus machines, ordered by which one needs you.
• argus-sync — a folder of an Argus server kept in sync with your computer, both ways, on macOS, Windows and Linux.

• Assembly Studio — browser-based 3D CAD assembly with optional FreeCAD verification.
• FreeCAD Timing Belt Generator — parametric timing belts for the common tooth profiles.
• AgID LLM UI — an experimental machine-readable design system for Italian public-administration interfaces.

I care about tools that are inspectable, durable and useful beyond the machine on which they were created.