// MCP TOOL REFERENCE

NONMEM TOOLS

22 tools from the Nonmem MCP Server, categorised by risk level.

// ALL 22 NONMEM TOOLS

READ 15 tools

Read compare_models Compare multiple NONMEM runs by OFV, delta-OFV, parameter counts, and AIC. Accepts a list of run directorie... Read parse_control_stream Parse a NONMEM control stream (.ctl/.mod) into structured components: $THETA, $OMEGA, $SIGMA, $EST options,... Read parse_psn_results Parse results from an existing PsN output directory (VPC or bootstrap). No PsN/NONMEM installation needed. Read summarize_run Generate a comprehensive summary of a NONMEM run by combining control stream, .ext, and .lst results. Read check_nonmem_setup Check NONMEM, PsN, R, and mrgsolve installation status and paths. Read check_psn_status Check status and progress of a PsN VPC or bootstrap job. Read check_r_setup Check R installation and required packages (mrgsolve, vpc, dplyr, ggplot2). Read check_run_status Check the status and progress of a submitted NONMEM run by job ID. Read get_run_results Get full parsed results of a completed NONMEM run by job ID. Read list_runs Scan a project directory for NONMEM run files and list their status (completed/failed/running). Read read_ext_file Parse a NONMEM .ext file to extract parameter estimates, standard errors, OFV, eigenvalues, and condition n... Read read_lst_file Parse a NONMEM .lst file for termination status, minimization success, shrinkage, condition number, and war... Read read_nm_dataset Read and summarize a NONMEM dataset: subject count, observation count, dose records, missing values, and co... Read read_nm_tables Parse NONMEM table output files (SDTAB, PATAB, etc.) and compute summary statistics for key columns (CWRES,... Read translate_to_mrgsolve Translate a NONMEM control stream (.ctl/.mod) to mrgsolve model code. Handles ADVAN1-13, THETAs, OMEGAs, $P...

DESTRUCTIVE 1 tools

Destructive cancel_run Cancel a running NONMEM job.

EXECUTE 6 tools

Execute execute_psn_bootstrap Run bootstrap using PsN (async). Returns job ID for polling. Requires PsN + NONMEM. Execute execute_psn_vpc Run VPC using PsN (async). Returns job ID for polling. Requires PsN + NONMEM. Execute run_diagnostics Run comprehensive post-run diagnostics: boundary checks, condition number, shrinkage, precision (RSE), conv... Execute simulate_mrgsolve Run a simulation using mrgsolve (R). No NONMEM needed. Provide model code or model file path. Execute generate_vpc_data Generate VPC data using mrgsolve + vpc R package. No NONMEM needed. Requires observed data and model. Execute submit_run Submit a NONMEM run (async). Returns a job ID for polling. Requires NONMEM installation.

// FAQ

How many tools does the Nonmem MCP server have? +

The Nonmem MCP server exposes 22 tools across 3 categories: Read, Destructive, Execute.

How do I enforce policies on Nonmem tools? +

Route the Nonmem server through the PolicyLayer gateway. Define allow, deny, or approval rules per tool in the dashboard; they are enforced on every call before it reaches the server.

What risk categories do Nonmem tools fall into? +

Nonmem tools are categorised as Read (15), Destructive (1), Execute (6). Each category has a recommended default policy.

Enforce policy on every Nonmem tool call.

Start from Nonmem, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

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