Drosophila Stocks

BioContextAI - Registry

An MCP server that lets AI assistants query Drosophila melanogaster stock centers — Bloomington (BDSC), Kyoto/DGRC, Vienna (VDRC), Korea (KDRC), NIG-FLY, FlyORF, and the National Drosophila Species Stock Center (NDSSC) — by genotype or by gene, using FlyBase's freely redistributable data.

FlyBase already integrates the stock records (genotype, stock number, holding center) for all of these collections. This server indexes that bulk data locally for fast search and generates deep links into each center's own ordering system for the parts FlyBase does not track (live availability, price, shipping).

Tools

Tool	What it does
search_stocks_by_genotype	Substring/token search over genotype strings, optional center filter
search_stocks_by_gene	Resolve a gene (symbol/synonym/FBgn) via FlyBase, then find stocks mentioning it
get_stock	Look up one stock by FBst ID or CENTER:NUMBER (e.g. BDSC:1234)
list_stock_centers	List supported centers with codes and homepages
resolve_gene	Resolve a gene symbol to a FlyBase gene record
get_dataset_info	Report the loaded FlyBase release, record count, and cache age

Every stock result includes center_code, stock_number, genotype, flybase_url, and a best-effort order_url.

Install & run

Requires Python ≥ 3.10.

uvx drosophila-stocks-mcp          # stdio transport (Claude Desktop, Cursor, VS Code)

Claude Desktop

Settings → Developer → Edit Config, then add:

{
  "mcpServers": {
    "drosophila-stocks": {
      "command": "uvx",
      "args": ["drosophila-stocks-mcp@latest"],
      "env": { "UV_PYTHON": "3.12" }
    }
  }
}

Remote / HTTP hosting (for claude.ai custom connectors)

claude.ai's web app only accepts remote MCP servers over HTTPS — it can't launch a local stdio process the way Claude Desktop/Code can. To use this server there, run it with the streamable-http transport somewhere publicly reachable:

MCP_HOST=0.0.0.0 MCP_TRANSPORT=streamable-http uvx drosophila-stocks-mcp

A Dockerfile is included for deploying to any container platform (Google Cloud Run, Koyeb, Render, a VPS, ...). It listens on $PORT if set (the convention most of those platforms use), or $MCP_PORT/8000 otherwise:

docker build -t drosophila-stocks-mcp .
docker run -p 8000:8000 -e PORT=8000 drosophila-stocks-mcp

Once it's live at a public HTTPS URL (e.g. https://your-host/mcp), add it in claude.ai as a custom connector: Settings → Connectors → Add custom connector.

Configuration

Env var	Purpose	Default
FLYBASE_STOCKS_URL	Override the bulk stock file URL (e.g. pin a release)	discovered from FlyBase's current release directory
FLYBASE_STOCKS_FILE	Use a local .tsv/.tsv.gz instead of downloading	—
FLYBASE_SYNONYM_URL	Override the bulk gene-synonym file URL	discovered from FlyBase's current release directory
FLYBASE_SYNONYM_FILE	Use a local synonym .tsv/.tsv.gz instead of downloading	—
DROSOPHILA_STOCKS_CACHE	Cache directory	~/.cache/drosophila-stocks-mcp
DROSOPHILA_STOCKS_MAX_AGE_DAYS	Re-download after this many days	30
MCP_TRANSPORT	stdio, streamable-http, or sse	stdio

On first use the server downloads the FlyBase precomputed stock file, caches it, and indexes it in memory. Subsequent runs use the cache until it ages out. If a refresh download fails, a stale cache is used rather than erroring. FlyBase's bulk files are release-stamped (e.g. stocks_FB2026_02.tsv.gz, no stable _current filename), so the exact filename is discovered from the current release's directory listing rather than guessed.

Data sources & limitations

• Stock records come from FlyBase's bulk stocks_FB<release>.tsv.gz file (free for academic use; cite FlyBase).
• Gene resolution (symbol/synonym → FBgn) uses FlyBase's bulk fb_synonym_fb_<release>.tsv.gz file, restricted to D. melanogaster genes — FlyBase's REST API has no symbol-lookup endpoint. A gene summary is then fetched opportunistically from the REST API (/gene/summaries/auto/{fbgn}); id/symbol/name/synonyms always come from the bulk file regardless. As of this writing, that REST endpoint sits behind an AWS WAF bot challenge that returns an empty 202 to any non-browser client, so summary is currently always None in practice — this is handled gracefully (no error), not a bug in this server, and may resolve itself if FlyBase changes their WAF rules.
• s3ftp.flybase.org (the bulk-file host) reliably returns an empty 202 to plain HTTP/1.1 requests but a real 200 over HTTP/2, so this server requires httpx[http2] and always connects over HTTP/2.
• search_stocks_by_gene matches the gene's symbol/synonyms as whole tokens in the genotype string. This is precise for most alleles but can miss lines that carry a gene only inside an un-symboled construct; use search_stocks_by_genotype for exhaustive curation. Precise allele→gene→stock linkage via the Chado schema is a planned enhancement.
• Availability/price/shipping are not in FlyBase. The order_url deep-links you to the center's own system to check and order. Every deep-link template was verified against the live site's actual rendered content (not just a non-404 status — see tests/test_live.py): BDSC, KYOTO, VDRC, and FLYORF all resolve to a real, correctly-parameterized search for the specific stock. VDRC's link is a storefront search (not a direct product page, since its stock numbers aren't catalog product IDs) that requires stripping the "v" prefix FlyBase stores; FlyORF's link goes through its separate KonaKart webshop (not flyorf.ch itself, which has no search), and only finds stocks that webshop's own catalog has indexed — some FlyBase-listed FlyORF stocks aren't in it, through no fault of the query. KDRC, NIG-FLY, and NDSSC have no direct-stock deep link and fall back to the center homepage (KDRC's is http://, not https:// — its HTTPS vhost is misconfigured and serves a server error).

Development

uv venv && source .venv/bin/activate
uv sync
pre-commit install
pytest          # runs fully offline against tests/fixtures/

Citation

If you use this in research, please cite FlyBase and the specific stock center(s) you order from, in addition to this tool.

License

MIT. Stock data © FlyBase and the respective stock centers, used under their academic-use terms.