MCP servers

smarts.bio speaks the Model Context Protocol (MCP), the open standard for connecting AI assistants to external tools. That means your favorite assistant can run smarts.bio queries, tools, pipelines, and file operations natively.

Two ways to connect

Hosted MCP (remote)

A managed server at mcp.smarts.bio that URL-based clients connect to directly with one-click OAuth. This is how you reach assistants that can't run a local process — ChatGPT, Claude on the web, and Gemini. Add this URL as a remote/custom connector:

Hosted MCP guide →

Local MCP (stdio)

The smarts CLI ships a local MCP server that runs on your machine, spawned by clients that can launch a process — Claude Desktop, Claude Code, Cursor, Windsurf, and the Gemini CLI. It reuses your CLI login, so there's no separate auth step.

Local MCP guide →

Available tools

Both servers expose the same focused tool set:

• smarts_query — ask the bioinformatics agent anything
• smarts_list_tools / smarts_run_tool — discover and run tools
• smarts_list_pipelines / smarts_run_pipeline / smarts_run_status — run and track pipelines
• smarts_list_files / smarts_read_file / smarts_open_file — browse, read, and view workspace files
• smarts_list_workspaces — list accessible workspaces