Basecase
I built Basecase, an AI-assisted genomic research workspace that connects natural-language questions directly to an interactive genome browser.
Core trick
Model-generated annotations are written as genome-browser tracks anchored to exact coordinates and variant positions, each linked to its evidence source.
Description
I built Basecase, an AI-assisted genomic research workspace that connects natural-language questions directly to an interactive genome browser. The system handles disease, gene, variant, regulatory, conservation, transcript, genomic-range, and VCF-based queries using grounded biological evidence. Researchers need more than prose: answers become useful when genes, variants, ranges, and annotations remain inspectable and actionable in the browser. Basecase therefore supports linked loci, multiple selected regions, live reasoning summaries, evidence sources, precise variant anchors, and agent-generated annotation tracks. This matters because it creates a faster, more transparent workflow for moving from a biological question to evidence that can be independently examined.
README excerpt
# Basecase An evidence-centered genome browser with an agentic research workspace. ## Development Requirements: [Bun](https://bun.sh/), [uv](https://docs.astral.sh/uv/), and an Anthropic API key in `.env`. Install dependencies: ```sh bun install uv sync --directory backend ``` Start the frontend and API together: ```sh bun run dev ``` The evidence agent uses Claude Sonnet 5 at medium effort through Anthropic's Messages API. Grounded Open Targets and UCSC results are provided to Claude as application context. Set `ANTHROPIC_API_KEY` in the repository `.env` file. - Frontend: http://localhost:5173 - API: http://localhost:8000 - API docs: http://localhost:8000/docs The initial browser opens the hg38 BRCA1 locus with live MANE, GENCODE, ClinVar, ENCODE cCRE, and phyloP data from UCSC. Use **Add track** to search other supported UCSC tracks. Useful checks: ```sh bun run build bun run lint bun run test ``` ## Structure - `frontend/` — Vite, React, TypeScript, TanStack Router, and shadcn/ui - `backend/` — FastAPI, Pydantic, Ruff, ty, and Python 3.12 managed by uv