bioscope — AI cell-biology research assistant on Claude Code
bioscope is a TypeScript CLI that turns a gene symbol, UniProt accession, or PubMed ID into a structured cell-biology research brief. It is built end-to-end on Claude Code and exercises every extension surface the platform exposes.
- Custom MCP server exposing 7 tools across 4 public bioinformatics APIs (UniProt, NCBI E-utilities, Ensembl REST, Reactome) with a 24-hour on-disk cache and per-host rate limiting.
- 4 custom slash commands:
/explain-gene,/pathways-for,/lit-review,/summarize-pmid. - 2 scoped sub-agents:
literature-reviewer,pathway-analyst. - Pre / post tool-use hooks for autoformatting and protected-path enforcement.
- Headless Claude Agent SDK app — same pipeline outside the TUI:
bioscope analyze genes.txt. - GitHub Actions workflow running
claude -pnon-interactively to auto-comment on PRs.
Tech. TypeScript · Node · MCP · Claude Code · Claude Agent SDK · Vitest · GitHub Actions.
// bioscope MCP server — tool registration (excerpt)
import { Server } from "@modelcontextprotocol/sdk/server/index.js";
import { lookupUniprot, searchPubmed, findPathways } from "./tools";
const server = new Server({ name: "bioscope", version: "0.3.0" });
server.setRequestHandler(ListToolsRequestSchema, async () => ({
tools: [
{ name: "lookup_uniprot", description: "Fetch protein record by accession." },
{ name: "search_pubmed", description: "PubMed search; returns PMIDs + abstracts." },
{ name: "find_pathways", description: "Reactome pathways for a gene symbol." },
{ name: "get_ensembl_gene", description: "Ensembl REST gene/transcript metadata." }
]
}));