Chorus article — "Chatting with genomic oracles" + reproduction harness

This repository holds the Genomics×AI blog post 2026-006, "Chorus: chatting with genomic oracles" and everything an independent agent (or person) needs to reproduce every quantitative claim in it from scratch.

The goal: a fresh agent reads the article, installs Chorus, runs the prompts/recipes, and checks each claim against an expected value + tolerance — then reports PASS / FAIL / COULD-NOT-TEST. If it all passes, the article is reproducible end-to-end.

📖 Read the article (figures render inline on GitHub): article/2026-006_chorus.md

Layout

Path	What
article/2026-006_chorus.md	The article, in blog-publishable format (Hugo frontmatter + shortcodes). Source of truth for the prose and the prompts.
reproduce/PROMPT.md	The one-shot reproduction prompt — copy it to a fresh agent (or follow it yourself) to reproduce the whole package: install, run the article's prompts, verify each claim, regenerate the figures, report a verdict. Start here.
reproduce/claims.yaml	Machine-actionable manifest — one entry per claim: the conversational prompt, a deterministic Python recipe, the expected value, the tolerance, and the PASS criterion.
reproduce/REPRODUCE.md	Long-form version of the prompt: install, tokens, MCP, then run each claim and compare.
reproduce/CLAUDE.md	Drop-in guidance so an agent run in this repo knows its job.
figures/	The three article figures + their sources. Fig 2/Fig 3 are regenerated from Chorus (numbers match claims.yaml); Fig 1 ships as a design brief. See figures/README.md.

Reproducibility status (2026-06-17)

Every claim in the article reproduces against Chorus main at/after commit 9f21266 (PRs #91 install fixes, #92 fine-mapping/LD fixes, #93 variant-scoring window fix — all merged 2026-06-17). Earlier commits will not reproduce the fixed-input-oracle magnitudes (ChromBPNet, Borzoi) via the conversational path — install main (or pin ≥ 9f21266). Regenerating the multi-oracle figure (Fig 3) additionally needs the per-oracle native-window fixes (PRs #94/#95), which are on main — so the simplest guidance is just install main.

Provenance of the expected values: an independent reproduction review (see chorus/audits/2026-06-16_blogpost_reproduction_report.md).

Quick start (verifying agent)

Hand reproduce/PROMPT.md to a fresh agent — it is self-contained. Or do it by hand:

# 1. Install chorus (main has all reproducibility fixes)
git clone https://github.com/pinellolab/chorus.git && cd chorus
mamba env create -f environment.yml && mamba activate chorus && pip install -e .
chorus setup --oracle alphagenome && chorus setup --oracle chrombpnet && chorus setup --oracle legnet   # one --oracle per call; + tokens (see PROMPT.md)
# 2. Reproduce
#    Follow reproduce/PROMPT.md (or REPRODUCE.md); for each entry in reproduce/claims.yaml,
#    run the prompt (or python_recipe) and compare to expected ± tolerance.

Tokens

• HF_TOKEN — required (AlphaGenome is gated). Accept the licence at google/alphagenome-all-folds.
• LDLINK_TOKEN — required for Analysis B (fine_map_causal_variant LD fetch). Free at ldlink.nih.gov.

License

Article text: CC-BY (matching the blog). Code references: Chorus is MIT.