Isabl MCP Server

MCP server providing AI agents access to the Isabl genomics platform.

11 tools for querying data, searching applications, aggregating results, and searching the built-in knowledge base (347 documents from Isabl's source code, documentation, and API specs).

Quick Start

# Run directly with uvx (no install needed)
uvx isabl-mcp

# Or install with pip
pip install isabl-mcp
isabl-mcp

Set your credentials:

export ISABL_API_URL="https://your-isabl-instance.com/api/v1/"
export ISABL_API_TOKEN="your-token-here"

Tools (11)

Data Access

Query output convention

For experiment/sample/individual queries, use a human-readable identifier by default:

• Prefer ["system_id"] for experiments
• Use ["identifier"] when system_id is not available
• Include pk only when explicitly requested

Example:

isabl_query(
    endpoint="experiments",
    filters={"projects": 102},
    output_fields=["system_id"]
)

For analysis summaries:

• If analysis is individual_level_analysis, show individual system_id (for example IID_H210514) instead of long targets/references experiment lists.
• If analysis is project_level_analysis, show project pk instead of long targets/references experiment lists.
• Build frontend links from ISABL_API_URL by removing /api/v1/ and adding query params (for example ?analysis=<pk>).
• Before displaying a table, include a one-line summary of what the table shows (scope, filters, and count when available).

Applications

Aggregation

Knowledge Base

Configuration

Development

uv sync --dev
uv run pytest
uv run isabl-mcp     # start server

License

MIT