bio-research-forge

Evidence-first life-science workbench for MiniMax Code. The Plugin ships twelve Agent Skills plus three local stdio MCP servers: public biological APIs (with provenance), RNA result figures (PNG/PDF + plotted data), and bounded local molecular tools (PyMOL render / SnapGene / Cytoscape / Fiji).

It does not bundle genomes, expression matrices, credentials, or species-specific private portals. Private tables stay on the user's machine. Public queries are allowlisted and read-only. This package is the portable Agent Plugins 1.0 subset; it does not include Codex marketplace adapters, hooks, custom agents, LSP, Apps, OAuth, or TUI extensions.

Standalone source: https://github.com/Presisitence/bio-research-forge

Companion figure library (optional)

For a local scientific figure gallery beyond this plugin's RNA volcano / PCA / heatmap tools, see the optional companion Scientific Figure Library. It is not bundled here—install it separately (Node.js 22+; see that repo's QUICKSTART). Bio Research Forge keeps its own RNA figure pipeline; SFL is a separate local gallery. See ATTRIBUTION.md.

Try it

Look up Arabidopsis FLC in UniProt and NCBI. Then, using my local DEG table deg.csv
(columns gene, log2FoldChange, padj), draw a volcano plot (padj < 0.05, |log2FC| > 1)
and show the PNG in the conversation.

用公共 API 查拟南芥 FLC 的 UniProt / NCBI 记录，再用我本地的 deg.csv
（列 gene, log2FoldChange, padj）画火山图，padj < 0.05 且 |log2FC| > 1，并在对话里预览 PNG。

Expected result: the agent calls bio_api_query (UniProt / NCBI) then rna_figure_create (plot_type="volcano"). API replies include the source URL and retrieval time. The local table is not uploaded. Success writes <name>.png, <name>.pdf, and <name>.plot-data.csv; the PNG path is meant for inline preview. Missing R packages return a status error rather than a crash.

For a design or manuscript request, bio-research-orchestrator routes to specialist Skills (experimental-design-gate, manuscript-argument, evidence-review, …) and labels evidence as direct data / external / candidate / hypothesis.

Requirements

• Node.js 18+ on PATH (mcp.json starts each server with node and cwd: ${PLUGIN_ROOT}).
• Optional NCBI_API_KEY in the environment to raise NCBI rate limits. No key is shipped.
• Optional R with Rscript on PATH, or RSCRIPT_EXE, plus jsonlite, ggplot2, pheatmap (and ggrepel for volcano labels). Needed only for rna_figure_create.
• Optional local installs of PyMOL, SnapGene, Cytoscape, or Fiji (or PYMOL_EXE / SNAPGENE_EXE / CYTOSCAPE_EXE / FIJI_EXE). The bridge never installs software.
• Windows, macOS, and Linux.

Data and network

public-bio-api contacts named public scholarly APIs only. Arbitrary URLs, local files, credentials, and pepper-specific queries are rejected:

• eutils.ncbi.nlm.nih.gov
• rest.uniprot.org
• www.ebi.ac.uk (InterPro, Europe PMC)
• rest.ensembl.org
• alphafold.ebi.ac.uk
• data.rcsb.org
• string-db.org
• jaspar.elixir.no
• solgenomics.net (generic BrAPI crop-name metadata only)

rna-figure and local-bio-tools are local-only. User CSVs and structure files are not transmitted. No telemetry. No credentials in the package.

Skills and MCP

Skills (frontmatter name matches each directory): bio-research-orchestrator, public-bio-databases, experimental-design-gate, omics-workflow, rna-figure-workflow, quantitative-research, local-bio-toolkit, secure-compute-routing, manuscript-argument, scientific-figure-delivery, reproducible-analysis, evidence-review.

MCP tools: bio_api_catalog / bio_api_query / bio_api_health; rna_figure_status / rna_figure_create; local_bio_tool_status / pymol_render / local_bio_open.

License

AGPL-3.0-or-later. See LICENSE and ATTRIBUTION.md. This Plugin keeps the upstream source license; it is not relicensed to MIT. Public databases and optional desktop tools have their own terms.