nonmem-mcp-server

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read_nm_tables

Parse NONMEM table output files to compute summary statistics for key pharmacometric parameters like CWRES, PRED, IPRED, and ETAs.

Instructions

Parse NONMEM table output files (SDTAB, PATAB, etc.) and compute summary statistics for key columns (CWRES, PRED, IPRED, ETAs).

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_tables"
  }
}

Input Schema

Name	Required	Description	Default
`file_path`	Yes	Path to the table output file

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

B3.4/5.0

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 of behavioral disclosure. It mentions computing summary statistics and identifies specific columns processed, but does not specify the output format, whether the operation is read-only, or error handling behavior since no output schema exists to document the return structure.

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, information-dense sentence with no filler. It front-loads the action ('Parse') and efficiently combines file type examples, operation details, and specific column targets without redundancy.

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

Completeness3/5

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

For a single-parameter tool, the description adequately covers the input domain but leaves a gap regarding the return value structure since no output schema is present. It mentions 'summary statistics' but does not describe their format, granularity, or what happens when key columns are missing.

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?

While the schema has 100% coverage for the single file_path parameter, the description adds valuable semantic context by listing example file types (SDTAB, PATAB) and column names (CWRES, PRED, etc.), helping the agent understand what constitutes a valid NONMEM table file beyond the generic schema description.

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 parses NONMEM table output files and computes summary statistics, using specific domain terminology (SDTAB, PATAB, CWRES, PRED, IPRED, ETAs) that identifies the exact resource type and distinguishes it from siblings like read_ext_file or read_nm_dataset which handle different file formats.

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?

There is no explicit guidance on when to use this tool versus alternatives like parse_psn_results or read_nm_dataset, nor are there any stated prerequisites or exclusions. The specific file type examples provide implicit context but no direct usage instructions.

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