nonmem-mcp-server

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run_diagnostics

Perform comprehensive post-run diagnostics including boundary checks, condition number analysis, shrinkage assessment, precision evaluation, and convergence warnings for pharmacometric models without requiring NONMEM installation.

Instructions

Run comprehensive post-run diagnostics: boundary checks, condition number, shrinkage, precision (RSE), convergence warnings. No NONMEM needed.

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": "run_diagnostics"
  }
}

Input Schema

Name	Required	Description	Default
`run_dir`	Yes	Path to the run directory
`run_name`	No	Run name (auto-detected if omitted)

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

A3.7/5.0

Behavior3/5

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

With no annotations provided, the description carries full burden and successfully discloses the diagnostic suite performed and NONMEM independence. However, it lacks critical safety disclosure (read-only vs. destructive) and omits output format details (returns data vs. writes report files).

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?

Two dense sentences with zero waste: the first front-loads the comprehensive diagnostic scope with specific metrics, the second delivers a critical prerequisite constraint. Every word earns its place.

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?

Adequate for basic invocation given the simple 2-parameter schema, but incomplete regarding execution outcomes. Without annotations or output schema, the description should disclose whether results are returned as structured data, written to disk, or displayed, and whether the tool modifies the run directory.

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 coverage is 100% with clear descriptions for both run_dir and run_name (including auto-detection behavior). The description adds no parameter-specific semantics beyond what the schema already provides, warranting the baseline score.

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?

The description uses a specific verb ('Run') and resource ('post-run diagnostics'), enumerates exact diagnostic checks performed (boundary checks, condition number, shrinkage, precision/RSE, convergence warnings), and distinguishes from NONMEM-dependent siblings via 'No NONMEM needed'—critical context in this pharmacometrics toolset.

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?

Provides timing context ('post-run') and environment constraint ('No NONMEM needed'), but fails to explicitly differentiate from sibling analysis tools like summarize_run, check_run_status, or get_run_results which also operate on completed runs.

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