nonmem-mcp-server

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translate_to_mrgsolve

Convert NONMEM control streams to mrgsolve model code for pharmacokinetic simulations, handling ADVAN routines, parameters, and model blocks.

Instructions

Translate a NONMEM control stream (.ctl/.mod) to mrgsolve model code. Handles ADVAN1-13, THETAs, OMEGAs, $PK, $DES, $ERROR.

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": {
      "ctl_path": "<ctl_path>"
    },
    "name": "translate_to_mrgsolve"
  }
}

Input Schema

Name	Required	Description
`ctl_path`	Yes	Path to NONMEM control stream
`output_path`	No	Where to save the mrgsolve .mod file (optional)
`parameter_values`	No	Override parameter values (e.g., from .ext final estimates)

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 the full burden. It adds valuable scope limitations (supports ADVAN1-13 specifically, handles $PK/$DES/$ERROR sections) but omits critical behavioral details: whether output_path overwrites existing files, what is returned when output_path is omitted, or dependency requirements. The capability disclosure is helpful but incomplete for safe invocation.

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 efficient sentences with zero redundancy. The first sentence front-loads the core transformation purpose; the second immediately qualifies supported subsystems. Every word serves to define scope or capability.

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 file-conversion tool with complete parameter schema documentation, the description adequately covers the transformation logic. However, given the lack of output schema and annotations, it should clarify the return behavior (e.g., 'returns file path or model code') and file system side effects to be fully complete.

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?

Input schema has 100% description coverage, establishing a baseline of 3. The description adds domain context by mentioning THETAs and OMEGAs, which semantically links to the parameter_values parameter (used for overriding these specific estimates), but does not elaborate on syntax requirements or validation rules beyond the schema.

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 explicitly states the transformation ('Translate'), source format ('NONMEM control stream'), and target format ('mrgsolve model code'). The mention of specific pharmacometric components (ADVAN1-13, THETAs, OMEGAs) clearly distinguishes this from sibling parse_control_stream (which only parses) and simulate_mrgsolve (which executes simulations).

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 domain specificity (NONMEM-to-mrgsolve conversion) implies usage context, there is no explicit guidance on when to choose this over parse_control_stream for analysis, nor warnings about prerequisites (e.g., mrgsolve availability). The description relies on the tool name to convey intent without explicit when/when-not rules.

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