Bio Research Forge

中文详细说明 | English

Bio Research Forge is a vendor-neutral life-science agent package. Its portable core follows Agent Plugins 1.0 and the Model Context Protocol (MCP), so it is not tied to Codex or to one model vendor.

It can be used in three ways:

1. Agent Plugins 1.0 clients discover the root plugin.json, skills/, and mcp.json;
2. any MCP client that supports local stdio servers can launch the three bundled MCP servers;
3. an agent with shell access but no MCP client can call the same tools through scripts/call-tool.mjs.

The optional .agents/ marketplace file and the nested plugins/bio-research-forge/.codex-plugin/ manifest are a Codex adapter. They do not define or own the portable core.

Portable package

Path	Purpose
plugin.json	Vendor-neutral Agent Plugins 1.0 manifest
skills/	Twelve portable Agent Skills
mcp.json	Portable definitions for three stdio MCP servers
scripts/print-mcp-config.mjs	Generates configuration for generic MCP, Claude, Cursor, or VS Code
scripts/call-tool.mjs	Lets any shell-capable agent list or call tools without a native MCP client
plugins/bio-research-forge/	Self-contained implementation and optional Codex package
.agents/plugins/marketplace.json	Optional Codex Marketplace adapter only

Quick start for any agent

Clone the repository, then generate the configuration format required by your client:

node scripts/print-mcp-config.mjs --client generic
node scripts/print-mcp-config.mjs --client claude
node scripts/print-mcp-config.mjs --client cursor
node scripts/print-mcp-config.mjs --client vscode

Copy the generated JSON into the client's MCP configuration. The generator resolves the repository's absolute path at runtime, including paths containing spaces.

For an agent without MCP support but with shell access:

node scripts/call-tool.mjs list-servers
node scripts/call-tool.mjs list-tools public-bio-api
node scripts/call-tool.mjs call public-bio-api bio_api_catalog "{}"

See the detailed cross-agent integration guide.

Included capabilities

• public biological APIs with provenance and evidence limits;
• local RNA volcano, PCA, heatmap, expression-boxplot, and enrichment-dotplot generation;
• safe PyMOL rendering and explicit opening of compatible files in SnapGene, Cytoscape, or Fiji;
• research design, omics, statistics, secure compute routing, manuscript argument, figure delivery, reproducibility, and independent review.

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.

Optional Codex adapter

Codex users can additionally install the repository marketplace:

codex plugin marketplace add "<repository-root>"
codex plugin add bio-research-forge@bio-research-forge

This adapter is optional. Removing it would not change the MCP wire protocol or the portable Agent Skills.

Verify

npm test
npm run test:render
npm run test:live

The repository excludes private datasets, private genome/transcriptome databases, dedicated pepper resources, credentials, and local reference documents. See privacy, attribution, and the verification report.