BioMCP

The open MCP platform for biology, bioinformatics, bioimaging, and scientific AI.

BioMCP follows a PowerMCP-style architecture: one installable distribution, one machine-readable registry, independent MCP servers, client configuration, diagnostics, tests, and a documentation site. The registry states what is installable, experimental, planned, or externally provided.

Server families

BioImage — local image inspection, intensity summaries, and thresholding primitives.

ImageJ / Fiji — bridge to an explicitly configured local ImageJ/Fiji installation.

LLM — OpenAI-compatible model access for agent workflows using environment-provided credentials.

BioNuclei — validated external scientific MCP adapter; BioMCP does not duplicate its scientific engine.

CellProfiler — planned adapter; not advertised as installable until an executable, tested integration exists.

Quick start

pip install biomcp
biomcp list
biomcp install --servers bioimage --clients generic
biomcp doctor

Image-analysis dependencies:

pip install 'biomcp[bioimage]'

Launch servers

biomcp run bioimage
biomcp run imagej
biomcp run llm

Each server is independently launchable over stdio, following the modular server-factory pattern used by PowerMCP.

Configure AI hosts

biomcp install --servers bioimage,imagej,llm --clients claude-desktop
biomcp install --servers bioimage,llm --clients codex

Use --dry-run to inspect changes before writing client configuration.

Local configuration

BIOMCP_IMAGEJ_EXECUTABLE points to ImageJ/Fiji.

BIOMCP_LLM_BASE_URL, BIOMCP_LLM_API_KEY, and BIOMCP_LLM_MODEL configure the LLM bridge. OPENAI_API_KEY is accepted as an API-key fallback.

Scientific boundary

BioMCP transports typed tool calls. It does not invent scientific measurements, benchmarks, or validation claims. Scientific computation remains under the authority of the underlying server.

Website

The product site lives in docs/ and is published by GitHub Pages.

Contributing

A new integration needs an executable server, registry metadata, tests, documentation, client configuration, and an explicit validation state before being promoted to installable or validated.

License

MIT.