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proto-tools ships an MCP server, so an MCP-compatible agent such as Claude
Code or Cursor can discover the tool catalog, read a tool’s schemas, and run it, all through
natural language.
Currently our MCP server only runs locally over stdio. Agents such as Claude Code and Cursor
are supported. A hosted version reachable over HTTPS is in active development.
What the agent can do
An agent connected to the server works through the same contract the Python interface uses: discover a tool, inspect its typed schemas, then call it.Workspace
workspace_info reports which backend calls go to, how it is configured, and whether its
credentials are present.Discover
list_tools returns the catalog; search_tools matches a keyword against tool keys and
descriptions.Inspect
get_tool_schema and get_tool_example return a tool’s input, config, and output models.
get_tool_citation returns the BibTeX for the method it implements.Run
run_tool executes a tool and blocks until it finishes. Large outputs are written to disk and
returned as file paths.Deploy
On Modal,
deploy_tool provisions a tool that is not deployed yet, after asking you to
confirm the cost.Choosing a backend
The server runs against one backend, chosen when it starts, so listing and running agree about what is available. The default ismodal, and an agent can send a single call elsewhere with
run_on.
modal keeps model weights warm in your own workspace between calls, so repeat calls are
fast. Deploying and running bill your own Modal account, and deploy_tool asks you to approve
before anything is built.
local executes tools in the server’s own process, so there is nothing to deploy and every
registered tool is available. Each tool builds its isolated environment and downloads its weights
on first use, so a first call can take several minutes; later calls reuse both.
Next Steps
Installation
Install the
mcp extra, register the server with your agent, and select a backend.Server Functions
Reference for each function the server exposes, with its parameters and behavior.
Tools
The catalog of bioinformatics models the server exposes.
Modal Integration
How the server uses Modal, and what an agent can deploy on your behalf.