bioresearcher-deep-researchlisted

# Bioresearcher Deep Research Reference-based biomedical research: interview the user to clarify scope and align the research plan, split the topic into research aspects, investigate each aspect with biomcp tools, then synthesize a succinct, accurately cited report. Harness-agnostic: works with or without a subagent/Task tool. ## What it does - Clarifies the research question and proposes a structured research plan with 2-5 independent aspects for user feedback before execution. - Runs one focused worker per aspect - in parallel via the harness's subagent/Task tool when available, sequentially otherwise. - Workers query the biomcp MCP server (articles/PubMed, ClinicalTrials.gov, genes, variants, drugs, diseases, patents, GEO/SRA/GenBank, Ensembl/PDB) per `references/tool-selection.md`, collecting PMIDs, DOIs, NCT IDs, and patent IDs as they go into a per-aspect evidence ledger. - The orchestrator synthesizes a draft using semantic cite-key markers (`[@pmid:21639808]`), then the `render` script numbers every citation and generates the bibliography from the merged ledger, and `vet-references.py` audits the result (structural + NCBI) - producing `final_report.md` and, by default, `final_report.html` (the `no-html` prefix skips rendering). ## When to use (triggers) - "Deep research" / "research report" on any biomedical topic. - Literature review, PubMed search, "find papers on ...". - Clinical trial landscape ("trials for X", "phase 3 melanoma"). - Drug qu