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yeyuan98

@yeyuan98 source repo

5 published skills

  1. ▌
    Bioresearcher Onboard · yeyuan98 bundle
    Bootstraps a project-local biomcp MCP server runtime in .bioresearcher-runtime/: downloads portable Node.js 22 (if missing), vendors biomcp with fast mirror support (official or npmmirror), configures optional features (R, Biowasm, SQLite), and registers the server in OpenCode, Claude Code, Cursor, ZCode, Pi, CodeBuddy, or WorkBuddy. Use when biomcp is not installed, when biomedical tools are missing, or on requests like setup bioresearcher, install biomcp, or onboard.
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    Bioresearcher Plot Making · yeyuan98 bundle
    Biomedical visualization router and plotting engine: classifies research data and produces publication-ready scientific figures (structural protein-binder complexes, conformational dynamics, literature method summaries, developmental case registers, and evidence tables). Use when asked to plot, visualize, graph, or chart biomedical data, PDB complexes, binding modes, literature searches, or translational safety cases.
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    Bioresearcher Deep Research · yeyuan98 bundle
    Deep biomedical research orchestrator powered by the biomcp MCP server: clarifies the question, aligns research area plan with user, decomposes into 2-5 aspects, researches each aspect via subagents (sequential fallback), and synthesizes a fully cited report. Use for deep research, literature review, clinical trials, drugs, genes, variants, diseases, patents, PubMed, functional genomics, biomcp.
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    Bioresearcher Pubmed Weekly · yeyuan98 bundle
    Downloads the past week's PubMed daily update XML.gz files from ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/, streams-parses interleaved PubmedArticle and DeleteCitation records, and produces one combined Excel workbook plus a summary JSON. Use for weekly PubMed/NLM literature tracking, NCBI updatefiles retrieval, pubmedNNnNNNN.xml.gz parsing, PMID/DOI/journal/author extraction, deleted-PMID lists, or building a weekly biomedical literature table.
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    Bioresearcher Python Setup Uv · yeyuan98
    Sets up a project-local Python environment with the uv package manager: downloads uv binary from astral.sh, creates .venv, configures dependencies (pandas or scientific plotting: pymol-open-source, matplotlib, pymupdf, biopython), verifies install, and appends usage rules to AGENTS.md. Auto-races PyPI and CN mirrors. Use when uv/Python is missing, for plotting/analysis, or on requests like install uv, set up Python, prepare plotting packages, use a China mirror, or prepare .scripts/py/.
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