nonmem-mcp-server

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execute_psn_vpc

Run visual predictive checks for pharmacometric models using PsN to assess model performance through simulation-based diagnostics.

Instructions

Run VPC using PsN (async). Returns job ID for polling. Requires PsN + NONMEM.

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": {
      "model_path": "<model_path>"
    },
    "name": "execute_psn_vpc"
  }
}

Input Schema

Name	Required	Description
`model_path`	Yes	Path to the model file
`samples`	No	Number of simulations (default: 200)
`options`	No	Additional PsN VPC options

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

A3.5/5.0

Behavior3/5

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

With no annotations provided, the description carries the burden of disclosure. It successfully communicates async execution, job ID return, and external dependencies, but omits side effects (file creation), error behavior, or reversibility considerations important for a simulation execution tool.

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?

Three efficient sentences front-loaded with purpose: method declaration, return value, and prerequisites. No redundant or filler text; every clause provides essential operational context.

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 a specialized tool with no output schema and no annotations, as it compensates by describing the return value (job ID). However, given the complexity of VPC analysis and nested parameters, it could benefit from mentioning typical use cases or linking to polling mechanisms.

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%, providing detailed documentation for all parameters including nested options (predcorr, stratify_on, etc.). The description adds no parameter-specific guidance beyond the schema, meeting the baseline expectation.

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?

Clearly states the tool runs VPC (Visual Predictive Check) using PsN, with the async nature specified. Distinguishes from siblings like execute_psn_bootstrap by specifying the VPC method, though it could explicitly differentiate from generate_vpc_data.

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?

Mentions prerequisites (PsN + NONMEM) and implies polling is needed via 'Returns job ID for polling', but lacks explicit guidance on when to use this versus generate_vpc_data or which tool to use for polling (check_run_status).

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