nonmem-mcp-server

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read_nm_dataset

Read and summarize NONMEM datasets to extract subject counts, observation records, dose information, missing values, and column structure for pharmacometric analysis.

Instructions

Read and summarize a NONMEM dataset: subject count, observation count, dose records, missing values, and column overview.

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": {
      "file_path": "<file_path>"
    },
    "name": "read_nm_dataset"
  }
}

Input Schema

Name	Required	Description	Default
`file_path`	Yes	Path to the dataset file
`input_columns`	No	Column names from $INPUT (optional, auto-detected if file has header)

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

A3.8/5.0

Behavior3/5

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

With no annotations provided, the description carries the full burden. It successfully discloses what the tool produces (the five summary statistics listed), but fails to mention safety properties (read-only), performance characteristics on large datasets, or error handling behavior.

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?

Single sentence efficiently structured with action first ('Read and summarize'), followed by specific outputs after the colon. Zero redundancy; every element specifies either the operation or a specific summary component produced.

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

Completeness4/5

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

Given no output schema exists, the description compensates effectively by enumerating the five summary components returned (subject count through column overview). However, it lacks mention of error conditions or output format structure, and should ideally note the read-only nature given absent annotations.

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

Parameters3/5

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

Schema description coverage is 100%, so the baseline is 3. The description adds domain context by specifying 'NONMEM dataset' which clarifies the expected file format for file_path, but does not elaborate on parameter syntax or validation rules beyond what the schema provides.

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

Purpose5/5

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

Description provides specific verb ('Read and summarize') and resource ('NONMEM dataset'), clearly distinguishing it from siblings like read_ext_file, read_lst_file, and read_nm_tables which handle output files rather than input datasets. The scope is precisely defined.

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

Usage Guidelines3/5

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

While the description implies exploratory data analysis use through the listed summary statistics (subject count, dose records, etc.), it lacks explicit guidance on when to use this versus read_nm_tables or parse_control_stream. No prerequisites or exclusions are stated.

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