fgx — FinnGen eXplore

Note

Part of the jx experiment - not an official FinnGen or GeneGenie project.

An experiment in agent-driven scientific data exploration, built around FinnGen and partner human-genetics datasets exposed through the GeneGenie results API — FinnGen R14 + UK Biobank + MVP meta-analyses, eQTL Catalogue R8, Open Targets 25.12, GTEx, Genebass, GenCC, Monarch (29 datasets at last count).

fgx is a curated catalog of marimo notebooks for human-genetics analysis, plus a thin skill that lets an agent compose new analyses from them. Each notebook is both a runnable demonstration and a source of pure functions other notebooks can import and reuse directly. Given a new human-genetics question, the agent picks relevant notebooks, composes their functions into a new notebook, executes it in a live kernel, and hands back a self-contained, re-runnable result.

GeneGenie ships https://genegenie.broadinstitute.org/api/v1/* with bearer auth, predictable paths, and TSV by default — that collapses the data-access layer to httpx.get, so there is no Python SDK, no MCP server, no schema cache.

The catalog

Each notebook ships with a committed session snapshot under notebooks/__marimo__/session/ so the molab preview renders cell outputs without re-executing.

Notebook	Role	Preview
nb01_pcsk9_walkthrough.py	Gene -> credible sets -> lead variant -> colocalization
nb02_variant_phewas.py	Variant PheWAS across endpoints
nb03_phenotype_locus_zoom.py	Phenotype-driven locus zoom
nb04_gene_exome_burden.py	Gene-based exome burden results
nb05_pign_cdg.py	Gene -> exome + curated gene_disease -> recessive-Mendelian companion to nb04 (PIGN-CDG / MCAHS1); imports prepare_deleterious from nb04
nb06_variant_pqtl_function.py	Variant -> pQTL credible sets -> direction-of-effect across proteins (ADAM17 / IBD demo replay)
nb07_data_catalog.py	Catalog introspection (/datasets, /resources, /resource_metadata) for "what's available?"
nb08_genetics_primer.py	Educational walkthrough from GWAS and fine-mapping through colocalization, exome results, molecular QTLs, and gene-disease curation
nb09_polygenic_heart_disease.py	Polygenic coronary heart disease: locus landscape, effect sizes, colocalization, pathways, and exome evidence
nb10_diabetes_susceptibility.py	Type 2 diabetes susceptibility: locus landscape, effect sizes, TCF7L2 colocalization, and MODY gene curation
nb11_protective_cancer_variants.py	Protective cancer variants across resources, with locus clustering and PheWAS classification of clean protection versus disease trade-offs

The machine-readable catalog table is catalog.toml's [[vignette]] blocks - each notebook, its reusable helpers, and what it does - which the vignette-catalog-compose-notebook skill reads.

Related public catalogs of the same pattern: jx for JUMP Cell Painting, prx for PROSPECT chemical genetics, and dmx for DepMap Breadbox.

Getting started

Create an API key at genegenie.broadinstitute.org (MCP/API KEYS -> Create key), then cp .env.example .env and paste your key in.

This catalog follows the vignette-catalog-skills pattern. The skill stores are gitignored, so a fresh clone has only skills-lock.json; restore the on-disk skill content first:

uv --version  # or: curl -LsSf https://astral.sh/uv/install.sh | sh
npx skills@1.5.20 add carpenter-singh-lab/vignette-catalog-skills -s vignette-catalog-compose-notebook -s vignette-catalog-scaffold -a claude-code -a codex -y
npx skills@1.5.20 add marimo-team/skills -s marimo-notebook -a claude-code -a codex -y
npx skills@1.5.20 add marimo-team/marimo-pair -s marimo-pair -a claude-code -a codex -y

Then open Claude Code or Codex in this repo and ask to get started. The vignette-catalog-compose-notebook skill launches nb01_pcsk9_walkthrough in a live marimo kernel and handles later analysis in the same workflow.

License

BSD 3-Clause — see LICENSE.