nonmem-mcp-server

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summarize_run

Generate comprehensive NONMEM run summaries by combining control stream, .ext, and .lst results to analyze pharmacometric model outputs.

Instructions

Generate a comprehensive summary of a NONMEM run by combining control stream, .ext, and .lst results.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "run_dir": "<run_dir>"
    },
    "name": "summarize_run"
  }
}

Input Schema

Name	Required	Description	Default
`run_dir`	Yes	Path to the run directory
`run_name`	No	Base name of the run files (e.g., 'run001'). If omitted, auto-detected from directory.

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

B3.1/5.0

Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions 'combining' files but fails to state whether this is a read-only operation, whether it creates output files on disk, what the return format is, or if it requires specific permissions. This leaves significant behavioral gaps.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, efficient sentence that front-loads the action ('Generate') and immediately qualifies the scope ('comprehensive summary') and methodology ('by combining...'). Every word serves a purpose with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite complete parameter documentation in the schema, the description omits critical context given the lack of annotations and output schema. It does not describe the return value format, structure of the summary, or side effects, which are essential for a tool that aggregates multiple file types.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 100% schema coverage, the baseline is 3. The description adds valuable domain context by specifying the exact file extensions processed (.ext, .lst), which helps clarify how the 'run_name' parameter is used to locate specific NONMEM output files, exceeding the basic schema definitions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool generates a comprehensive summary and identifies the specific resource (NONMEM run) and constituent files processed (control stream, .ext, .lst). However, it does not explicitly differentiate from siblings like 'get_run_results' or clarify why one would choose this over individual file parsers.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no explicit guidance on when to use this tool versus alternatives such as 'read_ext_file', 'read_lst_file', or 'get_run_results'. While the mention of 'combining' files implies a comprehensive use case, there are no when/when-not statements or alternatives named.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.