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NMGUI2 v2.9 — User Guide

A complete feature reference for pharmacometricians. Each section states where the feature lives and how to use it. If you are coming from Pirana, see the quick-mapping table at the end.

Contents

  1. Required and optional software
  2. Orientation — window layout
  3. Models tab
  4. Files tab
  5. Model detail panel
  6. Tree tab
  7. Evaluation tab
  8. VPC tab
  9. Uncertainty tab
  10. Sim Plot tab
  11. History tab
  12. Settings tab
  13. Dialogs
  14. Global keyboard shortcuts
  15. Files written by NMGUI2
  16. Mapping: Pirana → NMGUI2

1. Required and optional software

NMGUI2 is a pure Python/PyQt6 desktop app. It never spawns a browser and never contacts a server (other than an optional GitHub update check). The app launches and can browse, compare and evaluate models even with nothing else installed.

Required for the core app

Tool Minimum Install
Python 3.10 python.org / brew / apt
PyQt6, pyqtgraph, numpy, matplotlib, scipy — pip install -r requirements.txt

Required to run NONMEM models from inside NMGUI2

Tool Minimum Notes
NONMEM 7.4 Licensed install from ICON
PsN 5.0 execute, vpc, bootstrap, scm, sir, cdd, npc, sse must be on PATH
Perl 5.16 macOS/Linux: system Perl. Windows: Strawberry Perl

Paths can be overridden in Settings if autodetection fails.

Required for VPC generation

Tool Install
R ≥ 4.0 (Rscript on PATH) brew install r / apt install r-base / cran.r-project.org
R package vpc install.packages("vpc")
R package xpose install.packages("xpose")
R package tidyverse required by xpose
R package ggplot2 required by vpc/xpose

One-liner:

Rscript -e 'install.packages(c("vpc","xpose","tidyverse","ggplot2"), repos="https://cran.r-project.org")'

The VPC tab shows a green ✓ / red ✗ per package at startup.

Required for Uncertainty tab

PsN bootstrap and sir commands. Loading existing results folders works without PsN.

2. Orientation — window layout

┌─────────────────────────────────────────────────────────────┐
│  NMGUI  v2.9.0           PROJECTDIR / run12   [?About] [RS] │
├─────┬───────────────────────────────────────────────────────┤
│  M  │                                                       │
│  F  │           tab content                                 │
│  T  │                                                       │
│  E  │                                                       │
│  V  │                                                       │
│  U  │                                                       │
│  ~  │                                                       │
│  H  │                                                       │
│  ⚙  │                                                       │
├─────┴───────────────────────────────────────────────────────┤
│  status bar                                                 │
└─────────────────────────────────────────────────────────────┘
  • Left sidebar — nine tabs: Models (M) / Files (F) / Tree (T) / Evaluation (E) / VPC (V) / Uncertainty (U) / Sim Plot (~) / History (H) / Settings (⚙).
    Keyboard: ⌘1–⌘9 (macOS) / Ctrl+1–Ctrl+9 (Win/Linux).
  • Top bar — app name, version, current directory / model breadcrumb, About button, Open RStudio button.
  • Status bar — model count, active directory, last scan time, transient action messages.
  • Theme — dark / light / follow system, toggled in Settings.

3. Models tab

Shortcut: ⌘1 / Ctrl+1. This is the home view.

Directory controls (top row)

Control Action
Browse… Pick a folder; scans for .mod / .ctl files
⭮ Rescan (⌘R / Ctrl+R) Re-scan after external changes
+ Bookmark / Bookmarks ▾ Save / recall directories
All / Completed / Failed Status filter buttons
Search box Free-text filter on stem, comment, notes, tag
New model… (⌘N / Ctrl+N) Create a new NONMEM control file from a template

New model

Click New model… or press ⌘N / Ctrl+N to open the New Model dialog:

  • Model name — stem (no extension). Must start with a letter; letters, digits, _ and - allowed. The destination path is shown live below the field.
  • Template — choose from 26 built-in NONMEM templates (see below).
  • $DATA path — type or Browse… to pick a dataset file. Stored as a relative path when inside the working directory.
  • Preview… — renders the full control file text before writing.
  • OK — writes <stem>.mod, rescans the directory, and auto-selects the new model with the Editor tab open.

Available templates

Category Template Notes
Analytical $PRED subroutine blank Minimal $PRED scaffold
Analytical 1-CMT oral (ADVAN2 TRANS2) KA, CL, V with IIV
Analytical 1-CMT IV bolus (ADVAN1 TRANS2) CL, V with IIV
Analytical 2-CMT oral (ADVAN4 TRANS4) KA, CL, Q, V2, V3
Analytical 2-CMT IV bolus (ADVAN3 TRANS4) CL, Q, V1, V2
Analytical 3-CMT IV bolus (ADVAN11 TRANS4) CL, Q2, Q3, V1, V2, V3
Analytical 3-CMT oral (ADVAN12 TRANS4) KA, CL, Q3, Q4, V2, V3, V4
ODE — Tier 1 1-CMT Michaelis-Menten IV (ADVAN6) Non-linear (Vmax/Km) elimination
ODE — Tier 1 1-CMT Michaelis-Menten oral (ADVAN6) MM elimination + oral absorption
ODE — Tier 1 2-CMT time-varying CL oral — sigmoid Imax (ADVAN6) Auto-induction / inhibition
ODE — Tier 1 QE-TMDD 1-CMT IV (ADVAN6) Quasi-equilibrium TMDD
ODE — Tier 1 Wagner 1-CMT IV — TMDD Rtot constant (ADVAN6) Simplified TMDD (fixed Rtot)
ODE — Tier 1 Dual first-order absorption 1-CMT (ADVAN6) Two parallel absorption depots
ODE — Tier 1 Parallel first-order absorption + lag 1-CMT (ADVAN6) Two depots, lag on one
ODE — Tier 1 Transit compartment absorption 1-CMT (ADVAN6) N=3 transit CMTs, Savic 2007
ODE — Tier 2 QE-TMDD 1-CMT oral (ADVAN6) SC/oral TMDD
ODE — Tier 2 QE-TMDD 2-CMT IV (ADVAN6) 2-CMT TMDD with peripheral
ODE — Tier 2 Zero-order absorption + MM elimination (ADVAN6) Extended-release + non-linear
ODE — Tier 2 Simultaneous first+zero order absorption 1-CMT (ADVAN6) Mixed-release
ODE — Tier 2 2-CMT IV + urine compartment (ADVAN6) Dual DVID: plasma + urine
PK/PD Direct Emax PK/PD (ADVAN1) E = E0 + EMAX·C/(EC50+C); dual DVID
PK/PD Sigmoid Emax PK/PD (ADVAN1) Hill equation; GAM estimated; dual DVID
PK/PD IDR Type I — inhibit Kin (ADVAN6) Drug inhibits response production
PK/PD IDR Type II — inhibit Kout (ADVAN6) Drug inhibits response elimination
PK/PD IDR Type III — stimulate Kin (ADVAN6) Drug stimulates response production
PK/PD IDR Type IV — stimulate Kout (ADVAN6) Drug stimulates response elimination

All ODE templates use ADVAN6 TOL=6, TV-parameterisation, combined proportional+additive residual error, and diagonal OMEGA. Dataset notes are embedded as comments where the template requires special columns (RATE, DVID).

PK/PD templates require a DVID column (1 = PK concentration, 2 = PD response). Two separate EPS terms with the same W-scaling trick are used, one per endpoint. The IDR templates initialise the response compartment at steady state (A_0(2) = KIN/KOUT) so that a pre-dose equilibration period is not needed.

Table columns

Column Source Notes
★ metadata Star / unstar with Space or right-click
Stem file e.g. run12
Status tag metadata Base / Candidate / Final / Reject (coloured)
OFV .lst / .ext Final objective function value
ΔOFV — Relative to reference model
Min. .lst ✓ converged, ✗ failed, — not run
Cov .lst Covariance step result
Cond# .lst Condition number
Method $EST FO / FOCE / FOCEI / IMP / SAEM / BAYES / SIM
#ID dataset Individuals
#obs dataset Observations
#par .lst Estimated parameters
AIC — OFV + 2 × #par
Runtime .lst Reported or measured
Comment metadata Editable in Info panel

Row colours: green = converged, red = failed / terminated, orange = stale (source newer than .lst) or boundary warning.

Reference model

Right-click → Set as reference model. All ΔOFV values recompute against it. Clear via right-click → Clear reference model.

Right-click context menu

Item Action
Run Run the model with current Run panel settings
Toggle star Also Space
Duplicate… Clone with incremented run number
Set / Clear reference model
Compare with… Two-model parameter comparison dialog
Copy .mod path Path to clipboard
Copy folder path Folder path to clipboard
Open folder Open in Finder / Explorer / xdg-open
View .lst Raw listing in search-enabled viewer
View .ext Parameter estimates by iteration (if run exists)
View run record… Immutable audit record
NMTRAN messages… NM-TRAN compilation warnings/errors
QC Report… PASS/WARN/FAIL HTML checklist (completed models only)
Run Report… HTML rendering of Output tab (completed models only)
Workbench… Multi-model comparison table
Delete… Remove .mod + all paired output files (confirms before deleting; excludes dataset)

Keyboard (model table)

Key Action
↑ / ↓ Move row
Enter Jump to Output sub-tab
Space Toggle star

4. Files tab

Shortcut: ⌘2 / Ctrl+2.

A built-in file browser for the current working directory, with a content viewer for all common NONMEM file types.

Navigation bar (top)

[←]  PROJECTDIR  /  run12        [All] [.mod] [.ctl] [.lst] [.tab] [.csv] [.ext] [.cov] [.cor] [.phi] [+]
Element Action
← back button Return to previous directory; disabled at root
Breadcrumb Shows current path relative to working directory root
All pill Show all files (default)
Extension pills Click to show only files with that extension; folders always remain visible regardless of filter
[+] pill Add a custom extension filter via a text prompt

Multiple extension pills can be active simultaneously. Clicking All clears all extension selections. Filter state persists across sessions.

File list

  • Folders appear first (bold, 📁 prefix), sorted A-Z.
  • Files appear below, sorted by name by default; click column headers (Name / Size / Modified) to resort.
  • Hidden folders (name starts with .) are not shown.
Interaction Result
Single-click file Load preview in right pane
Single-click folder Highlight only (no preview)
Double-click folder Navigate into it; breadcrumb and back button update
Double-click file Open with the OS default application (Finder / Explorer / xdg-open)

Content viewer (right pane)

Toolbar shows the current filename and context-sensitive controls:

File type View Controls
.mod, .ctl Syntax-highlighted text Find bar, Edit / Save / Discard
.lst, .phi, other text Monospace text Find bar, Edit / Save / Discard
.csv Spreadsheet (sortable, virtualised — no row cap) Table / Plot pills, Edit / Save / Discard
.tab (NONMEM TABLE) Spreadsheet (sortable, virtualised — no row cap) Table / Plot pills (read-only)

Plot view (.csv / .tab) — full Data Explorer:

  • Any column on X and Y.
  • Colour-by any column (categorical or continuous).
  • Multi-filter (AND) — add rows of column op value.
  • Paginated data table view.

Edit mode — toggle with the Edit button:

  • Text files become editable; Save writes back, Discard reloads.
  • .csv cells become editable; saves back with the original delimiter.
  • .tab files remain read-only (NONMEM output).

Find bar (text files only) — highlights all occurrences; jumps to first match.

5. Model detail panel (right-hand pane)

Visible when a model is selected in the Models tab. Five sub-tabs:

5.1 Parameters

Full THETA / OMEGA / SIGMA table. Parameter names parsed from comments in the control stream. Columns: estimate, SE, RSE%, 95% CI, SD (for variance parameters). Handles BLOCK(n) and BLOCK(n) SAME correctly.

  • THETA / OMEGA / SIGMA blocks are collapsible — click the section header.
  • Export CSV… — full table.
  • Export HTML… — self-contained report for sharing.

5.2 Editor

Syntax-highlighted .mod editor. Save writes the file and marks the model stale (orange row). Never overwrites .lst.

5.3 Run

Launch any PsN tool on the current model.

  • Tool dropdown — execute / vpc / bootstrap / scm / sir / cdd / npc / sse.
  • Extra args — free-form arguments appended verbatim.
  • Run detached (Linux/macOS) — launch under nohup in a new OS session. The job continues even if NMGUI2 closes or the SSH connection drops. Auto-checked when running over SSH. Output written to <run_id>.nmgui.log in the project folder.
  • Run — opens a floating popup window per model (unchecked), or adds a row to the Active & Recent Runs table (checked).

Run popup window

Each run gets its own independent floating window:

  • Status line — pulsing ● while running; shows live iteration / OFV for execute runs; shows N/M progress for multi-run tools. On completion shows ✓/✗ with termination reason.
  • Elapsed timer.
  • Live console — stdout/stderr stream.
  • Stop button — Gentle (SIGTERM) or Force kill (SIGKILL).
  • Open run dir — reveals the run subdirectory in the file manager.

Active & Recent Runs table

Shows all runs for the current project folder:

  • Live rows — click to raise the popup window.
  • Detached rows — click to open a Watch Log window (live tail with elapsed timer and Stop button).
  • Historical rows — loaded from nmgui_run_records.json; persist across restarts.
  • Interrupted — runs that were active when the app closed appear as "? Interrupted".

Detached run reconciliation

On the next NMGUI2 startup or directory rescan, finished detached runs are automatically reconciled — status, timestamps, and OFV are retrieved from the log file. A status bar message reports the outcome.

5.4 Info

  • Dataset card — path, row count, columns, integrity warnings (missing file, non-monotonic TIME, duplicate doses, extreme DV, high BLQ proportion).
  • Annotation card — status tag (Base / Candidate / Final / Reject) and comment, both visible in the table.
  • Notes card — free-form multiline notes; persisted in ~/.nmgui/model_meta.json.

5.5 Output

Structured HTML rendering of the .lst in-panel:

  1. Summary strip — stem, OFV, minimisation, covariance, method, runtime.
  2. Estimation steps (chained $EST) — one row per step: OFV, ΔOFV between steps, runtime, significant digits, termination reason.
  3. NM-TRAN warnings.
  4. Convergence — iteration history from .ext.
  5. Parameter estimates with SEs.
  6. ETABAR with p-values.
  7. Shrinkage (ETA and EPS).
  8. Correlation and covariance matrices.
  9. Eigenvalues and condition number.

Open in browser — exports full HTML to a temp file and opens it externally.

6. Tree tab — model lineage

Shortcut: ⌘3 / Ctrl+3.

Interactive force-directed node graph of model genealogy. Parent is taken from the PsN metadata line ;; 1. Based on: NNN or from the manually-set parent in Info → Annotation.

  • Scroll to zoom, drag to pan.
  • Double-click a node — selects that model in the Models tab.
  • Starred models: gold border. Final models: green border.

7. Evaluation tab — GOF and diagnostics

Shortcut: ⌘4 / Ctrl+4.

Select a model in the Models tab first. NMGUI2 auto-loads the first sdtab* table file found next to the .mod. Manual override via Browse…. Exclude MDV=1 is on by default.

Four pills across the top switch sections:

7.1 GOF

2×2 panel: DV vs PRED | DV vs IPRED | CWRES vs TIME | CWRES vs PRED — with unity / zero reference lines.

Inner pill strip also exposes:

  • CWRES histogram — with normal density overlay and Save PNG.
  • QQ plot — CWRES vs theoretical quantiles; Shapiro–Wilk statistic and 95% band; Save PNG.
  • NPDE distribution — histogram + normal overlay; shown only when the table contains an NPDE column; Save PNG.
  • ETA vs Covariate — scatter of each ETA against continuous covariates with LOESS overlay. Recognises ETA, ET and PHI column prefixes (including NONMEM-truncated ET12 etc.).

7.2 Individual Fits

Paginated DV / IPRED / PRED vs TIME per subject. Configurable columns per page. Space / arrow keys page through.

7.3 OFV Waterfall

Ranked ΔOFV bar chart across all completed models in the current directory. Useful at the end of a model-building sequence.

7.4 Convergence

Parameter trajectories from the .ext file for the selected model — one trace per estimated parameter.

8. VPC tab

Shortcut: ⌘5 / Ctrl+5.

8.1 Backends

Two R backends:

  • vpc — Ronny Keizer's package; binned PI / CI bands.
  • xpose — tidyverse-based rendering.

Availability shown as ✓ / ✗ per package at the top of the panel.

8.2 Inputs

Field Purpose
VPC folder PsN vpc output directory (contains m1/, vpc_results.csv)
Run directory For xpose backend; contains sdtab, .ext, .phi
Use PsN settings (default on) Inherits binning, stratification, pred-corr, LLOQ from PsN output; override individual fields by unchecking
Stratify Column name; validated against header before running; warns if > 20 levels
PI (low / high) Prediction interval percentiles
CI (low / high) Confidence interval percentiles
LLOQ Lower limit of quantification
Bins Bin count (when overriding PsN)
Log Y axis Toggle
Prediction-corrected (pcVPC) Toggle

8.3 Run flow

  1. Click Generate VPC. A script is generated and run via Rscript.
  2. Console streams stdout/stderr live.
  3. On success, the PNG is displayed inline.
  4. Save high-res PNG… — re-runs at 4× resolution.
  5. Save PDF… — re-runs with a pdf() device (vector output).
  6. Stop — terminates the R process.

8.4 R script

Toggle the R Script view to edit the generated script before running — add custom ggplot themes, colours, or annotations. Reset restores the template.

9. Uncertainty tab — Bootstrap & SIR

Shortcut: ⌘6 / Ctrl+6.

Two sub-sections: Bootstrap / SIR (switched by the top pill).

9.1 Bootstrap

  1. Select a model in the Models tab (carried over).
  2. Run bootstrap (spawns PsN bootstrap) or Load results folder… (existing raw_results_*.csv).
  3. Pre-run options: Samples, Threads, Stratify by.

Outputs:

  • Parameter table — original estimate, bootstrap median, bias%, 2.5–97.5 percentile CI.
  • Forest plot — normalised distributions.
  • Diagnostics: completion rate, bias, parameter correlations, CI validity, boundary proximity.
  • Overall assessment — PASSED / ACCEPTABLE / WARNING / FAILED.

9.2 SIR

Same layout. Uses PsN sir. Fields:

Field PsN option Default
Samples -samples 1000
Resamples -resamples 1000
Threads -threads 4
Output dir -directory sir_<stem> next to model

Outputs:

  • Effective sample size (ESS) and resampling efficiency.
  • Degeneracy detection.
  • Weighted percentile CIs.
  • Overall assessment with one-line interpretation.

9.3 Console

Live PsN output streamed to the console at the bottom. Reset clears.

10. Sim Plot tab

Shortcut: ⌘7 / Ctrl+7.

Plots prediction intervals from NONMEM Monte Carlo simulation output. Requires a NONMEM table file that contains a replicate column (REP, IREP, SIM, SIMNO, SIM_NUM, etc. — auto-detected).

10.1 Data card

  • Browse / Load — pick any NONMEM table file or CSV (no row-count cap).
  • X column and Y column selectors.
  • Replicate column — auto-detected or manually selected.
  • Observed data — optionally load a second file to overlay observed DV points.

10.2 Filters card (expanded by default)

Up to 6 independent column filters (==, !=, >, <, >=, <=), ANDed together. Use to subset by compartment, dose group, sex, or any other column. Exclude MDV=1 checkbox in this card.

10.3 PI Bands card

Up to 4 simultaneous prediction interval ribbons, each configured on a single-line card:

Control Purpose
Visibility checkbox Show / hide the band
Lo% / Hi% spinboxes Percentile pair (e.g. 5 / 95)
Colour swatch Click to open colour picker
Alpha spinbox Transparency (0–1)
Remove (×) button Delete this band

Add band — adds a new row. Preset dropdown restores a named set (4 presets cover common pharmacometric conventions).

10.4 Appearance card

  • Median line — colour and line width; computed as the 50th percentile across replicates.
  • Log Y axis — toggle for concentration-time plots.
  • LOESS smoothing — smooth all PI boundaries and the median line; Span spinbox controls bandwidth (0.05–1.0, default 0.30).

10.5 Generate / Save

  • Generate — runs quantile calculations in a background thread; UI stays responsive.
  • Save PNG — 300 DPI PNG via matplotlib.

11. History tab

Shortcut: ⌘8 / Ctrl+8.

Chronological log of every PsN run started from NMGUI2 (last 200 entries, global across all projects).

Column Meaning
Status Running / Completed / Failed
Stem Model
Tool execute / vpc / bootstrap / …
Command Full command line
Started / Duration Timestamps

Double-click any row to open the full Run Record dialog.

12. Settings tab

Shortcut: ⌘9 / Ctrl+9. All settings persist in ~/.nmgui/settings.json.

  • Theme — Dark / Light / Follow system.
  • Font size — base font point size.
  • Paths — manual overrides for PsN execute, NONMEM binary, R Rscript, RStudio.
  • Directory bookmarks — add / remove / reorder.
  • GitHub update check — optional; pings /releases/latest once per launch; compares versions numerically.
  • Debug logging — verbose output to ~/.nmgui/nmgui_debug.log.
  • Open .nmgui/ folder — reveals the config directory in the file manager.

13. Dialogs

13.1 New Model

Opens from New model… button or ⌘N / Ctrl+N in the Models tab. See §3 for full description.

13.2 Compare

Right-click → Compare with…, pick a second model. Side-by-side parameter table with ΔOFV, ΔAIC, ΔBIC, Δ#par, LRT p-value (sign-aware), and a verdict string. Export CSV / HTML.

13.3 Workbench

Right-click → Workbench… or toolbar button. Sortable table of all completed models: OFV, ΔOFV, AIC, BIC, #par, LRT p-value, minimisation, covariance. Choose the reference from a dropdown. Export CSV.

13.4 QC Report

Right-click → QC Report… (completed models only). Self-contained HTML with PASS / WARN / FAIL checklist: termination, covariance, condition number, max %RSE, parameter correlations (|r| ≥ 0.95), shrinkage, ETABAR, OMEGA near boundary.

13.5 Duplicate

Right-click → Duplicate…. Clones .mod with an incremented run number; optionally copies dataset reference.

13.6 LST viewer

Right-click → View .lst. Raw listing in a monospaced, search-enabled viewer window.

13.7 NM-TRAN messages

Right-click → NMTRAN messages…. Parsed compilation warnings and errors — useful for catching WARNING: DES COMPARTMENT NOT USED and similar.

13.8 Run record

Right-click → View run record…. Immutable audit record per run:

  • Run UUID.
  • SHA-256 hash of the control stream and dataset.
  • NONMEM / PsN / NMGUI versions.
  • Start/end timestamps and duration.
  • Final OFV, minimisation status, covariance status.
  • Full command line.
  • Export JSON for archival.

13.9 About

App version, Python / PyQt6 / numpy versions, environment summary, credits.

13.10 Keyboard shortcuts reference

A floating card of all shortcuts, accessible from the About dialog.

14. Global keyboard shortcuts

Action macOS Win / Linux
Models tab ⌘1 Ctrl+1
Files tab ⌘2 Ctrl+2
Tree tab ⌘3 Ctrl+3
Evaluation tab ⌘4 Ctrl+4
VPC tab ⌘5 Ctrl+5
Uncertainty tab ⌘6 Ctrl+6
Sim Plot tab ⌘7 Ctrl+7
History tab ⌘8 Ctrl+8
Settings tab ⌘9 Ctrl+9
Open directory ⌘O Ctrl+O
Rescan directory ⌘R Ctrl+R
New model ⌘N Ctrl+N
Navigate model table ↑ / ↓ ↑ / ↓
Jump to Output panel Enter Enter
Toggle star Space Space

15. Files written by NMGUI2

Global state — ~/.nmgui/ (created on first launch):

File Contents
settings.json Theme, paths, window geometry, splitter sizes
model_meta.json Stars, status tags, comments, notes, parent overrides
bookmarks.json Directory bookmarks
runs.json Global run history (last 200 entries across all projects)
nmgui_debug.log Debug log

Per-project files — written inside each project folder:

File Contents
nmgui_run_records.json Immutable run audit trail (last 500 entries); drives the Active & Recent Runs table
<run_id>.nmgui.log stdout/stderr of a detached run; tailed by the Watch Log window
<run_id>.nmgui.pid PID and metadata of a running detached job; removed on completion

Delete ~/.nmgui/ to reset global settings. Per-project run records are not affected.

16. Mapping: Pirana → NMGUI2

Pirana feature NMGUI2 equivalent
Run overview spreadsheet Models tab
Run comparison / ΔOFV Right-click → Compare with… or Workbench…
Model tree / ancestry Tree tab (⌘3)
Execute / bootstrap / VPC buttons Run sub-tab and VPC tab
Xpose diagnostic plots Evaluation tab — native, no R required for GOF / CWRES / QQ / ETA plots
.lst reader Output sub-tab, or right-click → View .lst for raw
NONMEM messages Right-click → NMTRAN messages…
Bootstrap results Uncertainty tab → Bootstrap
SIR results Uncertainty tab → SIR
Audit / archival Right-click → View run record… and QC Report…
Annotation, star, status tag Info sub-tab → Annotation, Space to star
File browser Files tab (⌘2) — with subfolder navigation and content preview
Simulation plot / PI ribbons Sim Plot tab (⌘7)
Create new model file New model… button / ⌘N — 26 built-in templates
SSH / nohup workflow Run detached checkbox in the Run sub-tab

NMGUI2 v2.9 · Developed with Anthropic Claude · GitHub