nonmem-mcp-server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NONMEM_NMFE_PATH | No | Path to the NONMEM nmfe executable (e.g., /opt/NONMEM/nm75/run/nmfe75). Required for executing NONMEM runs via the submit_run tool. |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| read_ext_fileA | Parse a NONMEM .ext file to extract parameter estimates, standard errors, OFV, eigenvalues, and condition number. |
| read_lst_fileA | Parse a NONMEM .lst file for termination status, minimization success, shrinkage, condition number, and warnings. |
| parse_control_streamA | Parse a NONMEM control stream (.ctl/.mod) into structured components: $THETA, $OMEGA, $SIGMA, $EST options, input columns, data file, and ADVAN/TRANS. |
| read_nm_datasetA | Read and summarize a NONMEM dataset: subject count, observation count, dose records, missing values, and column overview. |
| read_nm_tablesB | Parse NONMEM table output files (SDTAB, PATAB, etc.) and compute summary statistics for key columns (CWRES, PRED, IPRED, ETAs). |
| compare_modelsA | Compare multiple NONMEM runs by OFV, delta-OFV, parameter counts, and AIC. Accepts a list of run directories or .ext file paths. |
| summarize_runB | Generate a comprehensive summary of a NONMEM run by combining control stream, .ext, and .lst results. |
| list_runsA | Scan a project directory for NONMEM run files and list their status (completed/failed/running). |
| submit_runA | Submit a NONMEM run (async). Returns a job ID for polling. Requires NONMEM installation. |
| check_run_statusB | Check the status and progress of a submitted NONMEM run by job ID. |
| get_run_resultsB | Get full parsed results of a completed NONMEM run by job ID. |
| cancel_runA | Cancel a running NONMEM job. |
| run_diagnosticsA | Run comprehensive post-run diagnostics: boundary checks, condition number, shrinkage, precision (RSE), convergence warnings. No NONMEM needed. |
| execute_psn_vpcA | Run VPC using PsN (async). Returns job ID for polling. Requires PsN + NONMEM. |
| execute_psn_bootstrapA | Run bootstrap using PsN (async). Returns job ID for polling. Requires PsN + NONMEM. |
| check_psn_statusC | Check status and progress of a PsN VPC or bootstrap job. |
| parse_psn_resultsA | Parse results from an existing PsN output directory (VPC or bootstrap). No PsN/NONMEM installation needed. |
| check_nonmem_setupA | Check NONMEM, PsN, R, and mrgsolve installation status and paths. |
| translate_to_mrgsolveA | Translate a NONMEM control stream (.ctl/.mod) to mrgsolve model code. Handles ADVAN1-13, THETAs, OMEGAs, $PK, $DES, $ERROR. |
| simulate_mrgsolveA | Run a simulation using mrgsolve (R). No NONMEM needed. Provide model code or model file path. |
| generate_vpc_dataA | Generate VPC data using mrgsolve + vpc R package. No NONMEM needed. Requires observed data and model. |
| check_r_setupA | Check R installation and required packages (mrgsolve, vpc, dplyr, ggplot2). |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
| review_model | Review a NONMEM model for errors, best practices, and improvement suggestions |
| interpret_results | Interpret NONMEM run results in pharmacological context |
| troubleshoot_run | Diagnose why a NONMEM run failed or produced warnings |
| suggest_next_model | Suggest what to try next in model development based on current results |
| write_methods_section | Draft a Methods section for a publication based on the final model |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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