NMGUI2

A standalone desktop application for NONMEM pharmacometric modelling workflows

NMGUI2 is a PyQt6 desktop application that brings together everything a pharmacometrician needs in one window: browse and compare NONMEM models, evaluate goodness-of-fit, run PsN tools, analyse bootstrap and SIR results, visualise model lineage, and read .lst output — without switching between terminals, text editors and R.

It runs entirely offline on macOS, Windows and Linux. No browser. No server. No internet connection required during use.

Features
User guide — full reference for every tab, dialog, and required R/PsN package
Dependencies overview
Quick start
Installation — macOS
Installation — Windows
Installation — Linux
First use
Updating NMGUI2
Keyboard shortcuts
Configuration files
Troubleshooting
Contributing
Author
Acknowledgements
License
Changelog

Features

Models tab

Scans a directory for .mod / .ctl files and displays all models in a sortable, filterable table
Columns: OFV, ΔOFV (relative to best or user-selected reference), minimisation status, covariance step, condition number, estimation method, individuals, observations, parameters, AIC, runtime
Colour-coded rows: green = successful, red = failed/terminated, orange = boundary/stale
Filter buttons: All, Completed, Failed — plus free-text search
Right-click context menu on any model: run, toggle star, duplicate, set reference model, compare with another model, copy paths, open folder, view .lst, view .ext, open QC report, open run report, view run record, show NM-TRAN messages, workbench, delete (excludes dataset)
Keyboard navigation: ↑↓ move rows, Space toggles star, Enter jumps to Output

Model detail panel

Parameters — full THETA/OMEGA/SIGMA table with names (parsed from control stream comments), estimates, SE, RSE%, 95% CI, SD for variance parameters. Handles BLOCK(n) and BLOCK(n) SAME designs correctly. Export to CSV and HTML report.

Editor — syntax-highlighted .mod editor with save functionality.

Run — launch any PsN tool (execute, vpc, bootstrap, scm, sir, cdd, npc, sse) with custom arguments. Each run opens its own floating popup window with a live console, iteration/OFV progress indicator, elapsed timer, and Stop button (gentle SIGTERM or force SIGKILL). Multiple models run simultaneously. A "Run detached" checkbox (Linux/macOS) launches the job under nohup so it survives SSH disconnection or NMGUI2 closure — automatically pre-checked when running over SSH. The Active & Recent Runs table shows live, detached, and historical runs; history persists per project folder across restarts.

Info — comment, status tag (base/candidate/final/reject), notes — all persisted in project metadata.

Output — structured HTML rendering of the .lst file in-app:

Summary card with key results
Estimation steps table for chained $EST runs (e.g. FO → FOCE-I → IMP), showing per-step OFV, ΔOFV, runtime, significant digits and termination status
NM-TRAN warnings section
Convergence table (iteration history)
Parameter estimates with SEs and names
ETABAR statistics with p-values
Shrinkage (ETA and EPS)
Correlation and covariance matrices
Eigenvalues and condition number
"Open in browser" exports full HTML

Files tab

A three-pane file browser built into NMGUI, positioned directly below the Models tab (Ctrl+2).

Left panel — extension filter checkboxes pre-populated with .mod, .ctl, .lst, .tab, .csv, .ext, .cov, .cor, .phi. Custom extensions can be added and removed. Filter state persists across sessions.
Middle panel — sortable file list showing name, size and last-modified date for all files in the current project directory matching the active filters.
Right panel — content viewer:
- Text files: monospace editor with syntax highlighting for .mod / .ctl (reuses the NMHighlighter). Inline find bar (Ctrl+F equivalent).
- .csv and .tab files: spreadsheet table. NONMEM TABLE NO. header lines are automatically detected and skipped. Large files are capped at 5 000 rows.
- Edit / Save / Discard for text files and .csv files. .tab files remain read-only.

Ancestry tree (Tree tab)

Interactive node graph of model lineage based on ";; 1. Based on:" PsN metadata or manually set parent. Zoom, pan, double-click any node to select that model in the Models tab. Visual indicators for starred and final models.

Model Evaluation (Evaluation tab)

Comprehensive diagnostic plots and data exploration:

GOF 2×2 — DV vs PRED, DV vs IPRED, CWRES vs TIME, CWRES vs PRED with unity/zero reference lines
Individual fits — paginated DV/IPRED/PRED vs TIME per subject, customisable columns per page
CWRES histogram — with normal distribution overlay
QQ plot — CWRES vs theoretical quantiles with Shapiro-Wilk test and 95% confidence band
ETA vs covariate — scatter plots of ETAs against continuous covariates
OFV waterfall — ranked ΔOFV bar chart across all models
Convergence traces — parameter trajectories from .ext file
Data explorer — interactive scatter plot with multi-filter capability, grouping/colouring by any column, paginated data table view

Auto-loads sdtab files when a model is selected. Shows truncation warning if data exceeds 15,000 rows.

VPC tab

Generate Visual Predictive Checks via two R backends:

vpc (R package by Ronny Keizer)
xpose (tidyverse-based)

Features:

Prediction-corrected VPC (pcVPC) option
Stratification by any column with validation (checks column exists, warns if >20 levels)
Configurable prediction intervals, confidence intervals, LLOQ, number of bins
Log Y axis option
Editable R script with syntax highlighting — modify before running
Live console output during R execution
PNG output displayed in-app
R package availability detection on startup

Uncertainty tab

Analyse parameter uncertainty via Bootstrap or SIR:

Bootstrap analysis

Run new bootstrap via PsN or load existing results folder
Configurable samples, threads, stratification
Automated parsing of raw_results.csv
Diagnostic checks:
- Completion rate (% successful runs)
- Bias assessment (median vs original estimate)
- Parameter correlations
- CI validity (does CI include point estimate?)
- Boundary proximity warning (OMEGAs clustering near zero)
Parameter table with 95% CI from percentiles
Forest plot visualisation
Overall assessment: PASSED / ACCEPTABLE / WARNING / FAILED

SIR analysis

Run new SIR via PsN or load existing results folder
Configurable samples, resamples, auto-detected degrees of freedom
Parsing of raw_results.csv with resample weighting
Diagnostic checks:
- Effective sample size (ESS)
- Resampling efficiency
- Degeneracy detection
- Resample distribution analysis
Parameter table with weighted percentile CIs
Overall assessment with interpretation

Run History (History tab)

Full history of PsN runs with:

Status (running/completed/failed)
Duration
Command preview
Timestamp
Click to view full run record

Run Records (audit trail)

Every model run creates an immutable run record containing:

Unique run ID (UUID)
Model file SHA-256 hash (integrity verification)
Data file SHA-256 hash
NONMEM version, PsN version, NMGUI version
Start/end timestamps, duration
Final OFV, minimisation status, covariance status
Number of individuals, observations, parameters
Full command used

Access via right-click → "View run record" on any model. Records stored in ~/.nmgui/run_records.json.

Settings tab

Dark/light theme toggle (follows system or manual override)
Path configuration for NONMEM, PsN, RStudio
Directory bookmarks management
All settings persisted between sessions

Additional features

Bookmarks — save frequently-used directories for quick access
Model comparison — side-by-side parameter comparison dialog with aligned rows
Duplicate model — create copy with incremented run number
NM-TRAN messages — quick access to compilation warnings/errors
Stale detection — orange highlight when .mod or data file is newer than .lst
GitHub update check — optional notification when new version available
Debug logging — detailed logs written to ~/.nmgui/nmgui_debug.log for troubleshooting
Cross-platform — native look on macOS, Windows, Linux (including X11/MobaXterm)

Dependencies overview

Python packages

All Python dependencies are listed in requirements.txt and installed automatically:

Package	Purpose
PyQt6	GUI framework
pyqtgraph	Interactive plots
numpy	Numerical operations
matplotlib	CWRES histogram, QQ plot
scipy	Shapiro-Wilk test, confidence bands (optional but recommended)

External tools for running models

Dependency	Minimum version	Notes
NONMEM	7.4	Must be installed and licensed
PsN (Perl-speaks-NONMEM)	5.0	Must be on system PATH
Perl	5.16	Required by PsN

External tools for VPC generation

Dependency	Notes
R ≥ 4.0	Must be on system PATH (`Rscript` command must work)
RStudio	Optional but recommended
R package: vpc	`install.packages("vpc")`
R package: xpose	`install.packages("xpose")`
R package: tidyverse	`install.packages("tidyverse")` — required by xpose
R package: ggplot2	`install.packages("ggplot2")` — required by vpc/xpose

NMGUI2 (browsing, evaluating, comparing results) works without NONMEM, PsN, R or RStudio. These are only needed if you want to run models or generate VPCs from within the app.

Quick start

If you already have Python 3.10+, Git, and optionally R/PsN installed:

git clone https://github.com/robterheine/nmgui2.git
cd nmgui2
pip install -r requirements.txt
python3 nmgui2.py

For full installation instructions including NONMEM, PsN, and R, see the platform-specific sections below.

Installation — macOS

1. Install Xcode Command Line Tools

xcode-select --install

2. Install Homebrew (if not already installed)

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

3. Install Python 3

brew install python
python3 --version

4. Install R (required for VPC only)

brew install r

Or download from https://cran.r-project.org/bin/macosx/

Verify:

Rscript --version

5. Install RStudio (optional)

Download from https://posit.co/download/rstudio-desktop/ and add to /Applications.

6. Install required R packages

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

7. Install Perl (required by PsN — usually pre-installed on macOS)

perl --version

If missing:

brew install perl

8. Install PsN

Follow the official guide at https://uupharmacometrics.github.io/PsN/install.html

Verify:

execute --version

9. Clone and install NMGUI2

git clone https://github.com/robterheine/nmgui2.git
cd nmgui2
pip3 install -r requirements.txt

10. Run NMGUI2

python3 nmgui2.py

Optional: desktop launcher

Create ~/Desktop/NMGUI2.command:

#!/bin/bash
cd /path/to/nmgui2
python3 nmgui2.py

Make it executable:

chmod +x ~/Desktop/NMGUI2.command

Double-click in Finder to launch.

Installation — Windows

1. Install Python 3.10 or newer

Download from https://www.python.org/downloads/windows/

During installation, tick:

✅ Add Python to PATH
✅ Install pip

Verify in Command Prompt:

python --version
pip --version

2. Install R (required for VPC only)

Download from https://cran.r-project.org/bin/windows/base/

During installation, tick "Add R to system PATH" (or add manually: C:\Program Files\R\R-4.x.x\bin to PATH).

Verify:

Rscript --version

3. Install RStudio (optional)

Download from https://posit.co/download/rstudio-desktop/

4. Install required R packages

Open Command Prompt or RStudio and run:

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

5. Install Perl (required by PsN)

Download Strawberry Perl from https://strawberryperl.com/ — this includes all required modules.

Verify:

perl --version

6. Install PsN

Follow the official guide at https://uupharmacometrics.github.io/PsN/install.html

Verify:

execute --version

7. Install Git

Download from https://git-scm.com/download/win

8. Clone and install NMGUI2

Open Command Prompt:

git clone https://github.com/robterheine/nmgui2.git
cd nmgui2
pip install -r requirements.txt

9. Run NMGUI2

python nmgui2.py

Optional: desktop launcher

Create NMGUI2.bat in the nmgui2 folder:

@echo off
cd /d %~dp0
python nmgui2.py

Double-click to launch.

Installation — Linux

Shown for Ubuntu/Debian. For Fedora replace apt with dnf; for Arch replace with pacman.

1. Install system dependencies

sudo apt update
sudo apt install -y python3 python3-pip python3-venv git curl perl
python3 --version

2. Install Qt system libraries (required by PyQt6)

sudo apt install -y libxcb-xinerama0 libxcb-cursor0 libxkbcommon-x11-0 \
    libgl1-mesa-glx libegl1

3. Install R (required for VPC only)

sudo apt install -y r-base r-base-dev

For the latest R version, follow https://cran.r-project.org/bin/linux/ubuntu/

Verify:

Rscript --version

4. Install RStudio (optional)

Download the .deb installer from https://posit.co/download/rstudio-desktop/

sudo dpkg -i rstudio-*.deb
sudo apt --fix-broken install

5. Install required R packages

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

6. Install PsN

Follow the official guide at https://uupharmacometrics.github.io/PsN/install.html

Verify:

execute --version

7. Clone and install NMGUI2

git clone https://github.com/robterheine/nmgui2.git
cd nmgui2
pip3 install -r requirements.txt

Or with a virtual environment (recommended on systems with externally-managed Python):

git clone https://github.com/robterheine/nmgui2.git
cd nmgui2
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

8. Run NMGUI2

python3 nmgui2.py

Or if using a virtual environment:

source venv/bin/activate
python3 nmgui2.py

Optional: desktop launcher

Create ~/.local/share/applications/nmgui2.desktop:

[Desktop Entry]
Type=Application
Name=NMGUI2
Exec=/bin/bash -c "cd /path/to/nmgui2 && python3 nmgui2.py"
Terminal=false
Categories=Science;

Updating NMGUI2

On all platforms, from the nmgui2 directory:

git pull
pip install -r requirements.txt

The second command ensures any new dependencies are installed. If no new packages were added, it completes instantly.

If using a virtual environment on Linux:

source venv/bin/activate
git pull
pip install -r requirements.txt

Previous versions

Snapshot zips of older NMGUI releases are kept in the previous releases/ folder at the repository root — useful if you need to reproduce results generated with an earlier version. Each zip contains the full source tree at that tag; unzip into a separate directory and run as usual. Tagged releases from v2.5.0 onward are also available on the Releases page.

First use

Launch the app (python3 nmgui2.py)
Click Browse… or use ⌘O / Ctrl+O and navigate to a folder containing .mod files
Click + Bookmark to save the directory for quick access
Select a model row to view its parameters, output, and diagnostic plots
Go to Settings (⌘9 / Ctrl+9) to configure paths if PsN/NONMEM/RStudio are not auto-detected

Keyboard shortcuts

Action	macOS	Windows / 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
Navigate model table	↑ / ↓	↑ / ↓
Jump to Output panel	Enter	Enter
Toggle star	Space	Space

Configuration files

All settings are stored in ~/.nmgui/ (created automatically on first run):

File	Contents
`settings.json`	Theme, paths, window geometry, splitter sizes
`model_meta.json`	Stars, comments, status tags, notes, parent model
`bookmarks.json`	Directory bookmarks
`runs.json`	Run history (last 200 entries)
`nmgui_debug.log`	Debug log for troubleshooting

These files are written inside each project folder (not in ~/.nmgui/):

File	Contents
`nmgui_run_records.json`	Immutable audit trail of runs for that project (last 500 entries), used by 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 automatically on completion

To reset all settings: delete the ~/.nmgui/ folder. Run records in individual project folders are not affected.

Troubleshooting

App fails to launch — ModuleNotFoundError: No module named 'PyQt6' Dependencies did not install. Rerun pip install -r requirements.txt (or pip3 on macOS/Linux). If you see "externally-managed environment" on Linux/macOS, use a virtual environment (see the Linux section).

App launches but window is blank or scrollbars are native-grey Your Qt style is overriding the stylesheet. NMGUI2 forces Fusion at startup; if you see this, confirm you are on v2.5.0 (git pull && pip install -r requirements.txt).

"R: vpc ✗ xpose ✗" in the VPC tab Rscript is not on PATH or the R packages are not installed. Verify Rscript --version in a shell, then install packages with

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

execute --version not found PsN is not on PATH. On Linux/macOS, add the PsN bin directory to your shell profile (~/.zshrc, ~/.bashrc). On Windows, add it to the system PATH via Environment Variables.

NM-TRAN messages show "parser.py not available" Your nmgui2 repository is outdated. Run git pull.

Models tab shows models but OFV column is empty The .lst file is missing or incomplete — the run never finished or was deleted. Check the model's run directory.

Dark mode colours look wrong after toggling theme Fixed in v2.5.0. If you still see stale colours, restart the app.

Everything else — enable debug logging and share ~/.nmgui/nmgui_debug.log when filing an issue.

Contributing

Contributions are very welcome. See CONTRIBUTING.md for details.

Areas particularly in need of help:

Windows and Linux testing and bug reports
Additional NONMEM output parsing (BAYES, mixture models)
New diagnostic plot types
Documentation and tutorials
Translations

Author

Rob ter Heine Hospital pharmacist – clinical pharmacologist Radboud Applied Pharmacometrics · Radboudumc, Nijmegen, the Netherlands

Acknowledgements

Developed with Anthropic Claude.

License

MIT License — free to use, modify and distribute.

Changelog

v2.8.0

Files tab now supports plotting — selecting a .tab or .csv file shows a [ Table | Plot ] pill pair in the toolbar. Plot view is the full DataExplorer (scatter, LOESS, colour-by column, filters) that previously lived in the Evaluation tab. Column deduplication (from v2.7.9) now also applies in the Files tab viewer.
Evaluation tab simplified — "Data Explorer" pill removed; the tab is now a clean 4-pill diagnostics panel: GOF | Individual Fits | OFV Waterfall | Convergence.
Auto-select sdtab in Files tab — navigating to the Files tab with a model selected automatically highlights the model's sdtab in the file list.

v2.7.9

Sim Plot — fix crash on duplicate column names — NONMEM sdtab files that list the same column twice (e.g. IPRED appearing as both column 3 and 18) caused pd.to_numeric to raise arg must be a list, tuple, 1-d array, or Series because selecting a duplicate column returns a DataFrame instead of a Series. Duplicates are now renamed at load time (IPRED → IPRED, IPRED_2) and a warning is shown in the Data card label.

v2.7.8

Sim Plot — PI band row redesign — each band is now a single-line card (rounded, bordered) instead of a two-line layout; Alpha moved onto the same row as Lo/Hi; colour picker is now a circular 22×22 swatch; remove button is a round ghost pill that turns red on hover; "Add band" and "Add filter" buttons use a dashed-border style to communicate additive intent; band card spacing increased for breathing room; preset dropdown gains a tooltip warning it resets all bands. Changes are fully cross-platform (macOS/Windows/Linux).

v2.7.7

Eliminated -apple-system startup warning — Qt cannot resolve CSS-level font aliases like -apple-system; replaced with "Helvetica Neue", "Segoe UI", Arial, sans-serif which Qt can find on all platforms without the 71 ms alias-population penalty.

v2.7.6

SF Mono actually renders now — Qt registers SFNSMono.ttf under the internal family name .SF NS Mono (not SF Mono). The font priority list now uses the correct name, so macOS editors show SF Mono instead of Courier.
Removed system-ui from base stylesheet — Qt does not understand the CSS system-ui keyword and emitted a 74 ms warning on every startup. Replaced with -apple-system, "Segoe UI", "Helvetica Neue", Arial, sans-serif.

v2.7.5

SF Mono now loads on macOS — QFontDatabase.addApplicationFont() explicitly registers /System/Library/Fonts/SFNSMono.ttf (and the italic variant) at startup. Qt's normal font enumeration cannot see SF Mono; this one-time registration makes the SF Mono name resolvable so editors render in SF Mono instead of falling back to Menlo.

v2.7.4

Virtualised table viewer — CSV and NONMEM TABLE files in the Files tab are now backed by QAbstractTableModel + QTableView instead of QTableWidget. Qt only fetches data for visible rows, so files of any size (100k+ rows) open instantly and scroll smoothly. The 5 000-row cap and the "Showing first N rows" notice have been removed. Column sorting tries numeric comparison first, falling back to case-insensitive string sort.

v2.7.3

Font priority reordered — SF Mono is now first in the editor font chain: SF Mono → Consolas → DejaVu Sans Mono → JetBrains Mono → Cascadia Code → Liberation Mono → Menlo → Ubuntu Mono → Courier New. macOS users will see SF Mono by default.

v2.7.2

File list panel wider — Files tab middle pane default width increased from 240 → 320 px so filenames are no longer truncated on first open.
SF Mono added to the monospace font priority list (macOS 10.12+, the font used by Xcode and Terminal). On a standard Mac without JetBrains Mono installed the editors now use SF Mono instead of Menlo.

v2.7.1

Consistent monospace font — both the Models tab editor and the Files tab viewer now use a shared monospace_font() helper that calls QFont.setFamilies() with a priority list: JetBrains Mono → SF Mono → Cascadia Code → Cascadia Mono → Consolas → DejaVu Sans Mono → Liberation Mono → Menlo → Ubuntu Mono → Courier New. StyleHint.TypeWriter ensures a monospace fallback on minimal installs. Both editors render at 11 pt.

v2.7.0

New Files tab and Models tab right-click additions.

Files tab (Ctrl+2) — three-pane file browser: extension filter checkboxes (.mod, .ctl, .lst, .tab, .csv, .ext, .cov, .cor, .phi pre-populated; custom extensions addable), sortable file list (name / size / modified), and content viewer with syntax highlighting for .mod/.ctl, inline find, and spreadsheet view for .csv/.tab with NONMEM TABLE NO. header handling. Row cap of 5 000 with notice. Edit/Save/Discard for text and CSV files.
Run added to the top of the Models right-click menu — runs the selected model with current panel settings.
Open folder added to the right-click menu — opens the model's directory in Finder / Explorer / xdg-open.
View .ext added to the right-click menu (shown when a run exists) — opens the parameter-estimates-by-iteration file.
Delete… added to the bottom of the right-click menu — removes .mod and all paired output files; parses $DATA to identify and exclude the dataset. Confirmation dialog lists every file before deletion.
Navigation shortcuts shifted: Ctrl+2 = Files, Ctrl+3 = Tree, Ctrl+4 = Evaluation, Ctrl+5 = VPC, Ctrl+6 = Uncertainty, Ctrl+7 = Sim Plot, Ctrl+8 = History, Ctrl+9 = Settings.

v2.6.13

Run detached defaults to OFF — the "Run detached" checkbox now always starts unchecked, regardless of whether an SSH session is detected. Detached mode must be opted in to explicitly.

v2.6.12

Sim Plot default panel width increased to 600 px.

Splitter default — 380 → 600 px so the panel opens at the width where all spinbox values display fully without the user needing to drag the splitter
Panel max width — 500 → 700 px to allow further widening if desired

v2.6.11

Sim Plot spinboxes — adaptive width instead of fixed pixels.

Stop guessing font metrics — fixed-width spinboxes (64 px) still clipped values because macOS font size varies with display scaling; switched Lo%, Hi% and Alpha spinboxes to setMinimumWidth(62) + setMaximumWidth(110/90) with addWidget(stretch=1) so they expand to fill whatever space the panel provides
Result: spinboxes now use the full available panel width (typically 80–110 px each), guaranteeing values like "95.0" and "0.25" always display completely regardless of system font size or display scaling

v2.6.10

Sim Plot band row — fix checkbox expansion and spinbox clipping.

Checkbox fixed width — setFixedWidth(20) added to the visibility checkbox; without it, QCheckBox has Preferred size policy and silently absorbs all spare horizontal space, pushing the colour swatch and × button off-screen
row1.addStretch() — explicit stretch added at the end of the band row so any remaining panel width goes to blank space on the right, not to widgets
Spinboxes widened 58 → 64 px — on macOS the arrow buttons consume ~28 px, leaving 30 px text area at 58 px; "95.0" (4 chars) needs ~32 px and clipped to "9". At 64 px the text area is 36 px, enough for all expected values
Alpha row spacer uses literal 20 px — previously used sizeHint() which would not match the now-fixed checkbox width

v2.6.9

Sim Plot band row redesign — two-line layout with inline labels.

Root cause fixed — macOS QDoubleSpinBox has a minimum intrinsic rendering width (~58 px); forcing 46 px clipped the value to nothing. Pixel-squeezing six controls onto one line was the wrong architecture
Two-line band rows — each band now uses two compact lines: line 1 holds the visibility checkbox, Lo%, Hi%, colour swatch and remove button; line 2 holds Alpha. Inline labels ("Lo%", "Hi%", "Alpha") replace the old separate column-header row
Spinboxes now 58 px — wide enough for macOS to render "49.9" and "0.25" without clipping
Column-header row removed — no longer needed; inline labels provide the same context without alignment fragility
Colour swatch restored to 32 px — previous shrink to 26 px hit macOS button minimums

v2.6.8

Sim Plot band row layout overhaul — all controls now fully visible.

Removed % suffix from Lo/Hi spinboxes — the column header "Lo%" / "Hi%" already communicates the unit; dropping the suffix saves ~12 px per spinbox and lets the values render fully
Narrowed Lo/Hi spinboxes — 60 → 46 px (fits "49.9" at 1 decimal place)
Narrowed colour swatch — 32 → 26 px (still clearly a colour picker)
Narrowed alpha spinbox — 58 → 52 px
Narrowed remove button — 22 → 20 px
Tightened row spacing — 4 → 3 px between widgets
New band row total: 221 px (was 270 px) — fits comfortably in the available content width with ~40 px to spare, even accounting for the vertical scrollbar
Filter header fixed — Op and Value column labels now have explicit fixed widths (52 / 72 px) matching the data row, so "Op" is never clipped

v2.6.7

Sim Plot panel default width correction.

Wider default panel — splitter default increased from 300 → 380 px and max-width from 400 → 500 px; the vertical scrollbar was consuming ~15 px of horizontal space, causing the band row columns to clip even at 300 px; 380 px gives ~333 px usable content width, well clear of the 270 px band row

v2.6.6

Sim Plot left panel layout fixes.

Narrower band rows — Lo%/Hi% spinboxes reduced from 68 → 60 px, Alpha from 72 → 58 px so all columns (including the × button) fit without clipping
Narrower panel — default splitter position reduced from 360 → 300 px; max panel width reduced from 480 → 400 px
Span spinbox — widened from 62 → 70 px so "0.30" is never clipped

v2.6.5

Sim Plot LOESS smoothing option.

Smooth curves — new checkbox in the Appearance card applies LOESS smoothing to all PI ribbon boundaries and the median line before rendering; a Span spinbox (0.05–1.0, default 0.30) controls bandwidth — lower follows data closely, higher gives a smoother curve

v2.6.4

Sim Plot MDV filter accessibility fix.

MDV filter moved to Filters card — the "Exclude MDV=1 rows" checkbox is now in the Filters card (expanded by default) instead of the collapsed Appearance card, making it immediately visible and easy to toggle

v2.6.3

Sim Plot usability and layout fixes.

Workflow hint — a note in the Data card explains that the Sim Plot tab requires a NONMEM simulation output file with a replicate column (REP, IREP, SIM, SIMNO…), not a standard estimation sdtab
Replicate column validation — a status bar warning is shown when no recognised replicate column is found in the loaded file, preventing meaningless plots from being silently generated
Median colour default — now initialises to the current theme foreground colour instead of white (which was invisible on light backgrounds)
PI band header alignment — column labels (Vis / Lo% / Hi% / Colour / Alpha) now use exact fixed widths matching the data row widgets so they align correctly
Alpha spinbox — widened from 58 px to 72 px; values such as "0.25" no longer clip to "0"
Y-axis label overflow — replaced tight_layout with explicit subplots_adjust so the Y-axis label no longer overflows beyond the right edge of the canvas

v2.6.2

Performance and audit fixes.

Threaded table loading — the Evaluation tab now parses sdtab files in a background QThread; the Load button shows "Loading…" while parsing and the UI stays fully responsive on large files or slow network drives
IndFit row bounds guard — ragged rows (fewer columns than the header) in the Individual Fits widget no longer raise IndexError; they are silently skipped
GOF replot error logging — the silent except Exception: pass in the GOF 2×2 replot is replaced with a debug-level log entry so errors are visible with --debug without crashing

v2.6.1

Bug fixes for the Sim Plot tab and the Models tab METHOD column.

SIM method label — simulation-only runs ($SIM without $EST) now display SIM in the METHOD column of the Models tab instead of the incorrect default FO
Sim Plot layout — PI band rows redesigned: label-free compact layout with a column header row, % suffix on spinboxes, wider panel (360 px default), compact Browse/Load buttons; filter rows similarly updated

v2.6.0

New Simulation Plot tab for Monte Carlo prediction interval visualisation.

Sim Plot tab — a dedicated tab (Ctrl+6) for plotting prediction intervals from NONMEM Monte Carlo simulation output. Load any NONMEM table file or CSV (no row-count cap), configure PI bands, and generate publication-ready plots in seconds
Unlimited file loading — the table parser now accepts max_rows=None so large simulation files (50k–500k rows typical for 1 000 replicates × 500 time points) load fully without truncation
Replicate auto-detection — the tab recognises explicit replicate columns (REP, IREP, SIM, SIMNO, REP_NO, SIM_NUM, etc.) and also detects ID-cycling automatically when no explicit column is present
Configurable PI bands — up to 4 simultaneous prediction interval ribbons, each with its own percentile pair (Lo/Hi %), colour (colour picker), alpha and visibility toggle. Four presets cover the most common pharmacometric conventions (5/95 + 25/75, 2.5/97.5 + 10/90, etc.)
Multiple filters — up to 6 independent column filters (==, !=, >, <, >=, <=), ANDed together, to subset by compartment, dose group, sex, or any other column before plotting
Median line — configurable colour and line width; computed as the 50th percentile across replicates
Log/linear Y-axis — one checkbox toggles between linear and logarithmic scale, essential for PK concentration-time plots
MDV=1 exclusion — dosing-only rows filtered out by default before quantile computation
Observed data overlay — optional second file load; observed DV points are overlaid as a semi-transparent scatter on the simulated ribbons, with independent X/Y column selectors
Background computation — all quantile calculations run in a QThread so the UI stays responsive on large datasets
Save PNG — 300 DPI export via matplotlib savefig
Model context — selecting a model in the Models tab sets the browse directory for the Sim Plot file dialog, consistent with Evaluation and VPC tabs

v2.5.8

Bug fix for the ETA vs Covariate plot.

ET\d+ columns now recognised as ETAs — NONMEM truncates ETA(12) to ET12 in TABLE output. The ETA dropdown previously required the full ETA prefix, so ET12, ET13, ET14 etc. were silently placed in the covariates list and the dropdown stayed empty. Fixed by also accepting ET\d+ and PHI\d+ column names as ETAs
Residual columns excluded from covariates — NPDE, IWRES and WRES added to the covariate skip-list (alongside the existing CWRES, PRED, IPRED etc.) so they no longer appear as candidate covariates

v2.5.7

New GOF features.

NPDE distribution plot — a new "NPDE Dist" pill appears in the GOF sub-strip whenever the loaded table file contains an NPDE column. Shows a histogram with a normal density overlay and mean/SD statistics, identical in style to the CWRES Hist panel. When NPDE is absent the button is hidden automatically
PNG export on all matplotlib GOF panels — CWRES Hist, QQ Plot and NPDE Dist each now have a "Save PNG…" button that saves a 300 DPI PNG via matplotlib's savefig; the button is disabled until a plot has been rendered

v2.5.6

Bug fix for the Ron Keizer vpc backend.

Three CI bands now visible — pi_as_area was incorrectly set to TRUE, which collapsed the three separate confidence ribbons (around the 5th, 50th and 95th simulated percentiles) into a single filled slab. Changed to FALSE (the vpc package default) so a proper three-band VPC is displayed
Readr parsing warnings suppressed — NONMEM simulation files embed a TABLE NO. header row every N records; readr emits ~2000 parsing-failure warnings per VPC run (one per simulation replicate). These are harmless but were alarming. The vpc() call is now wrapped in withCallingHandlers to muffle only those specific warnings while keeping real R errors visible

v2.5.5

VPC tab overhaul — fixes implausible plots from the Ron Keizer vpc backend and removes the outdated xpose4 backend.

xpose4 backend removed — xpose4 is no longer maintained and produced implausible VPCs; the modern xpose package is a strict improvement
"Use PsN settings" mode (default on) — when checked, binning, stratification, pred-corr and LLOQ are inherited directly from the PsN output folder for both the vpc and xpose backends. Previously the tab always forced bins="auto" and explicit pred_corr/stratify args that overrode PsN's values, misaligning observations and simulated prediction intervals
Correct bins argument — when overriding manually, bins="jenks" is used instead of the invalid "auto" string
Workflow hint — a one-line note at the top of the VPC settings panel explains that a PsN vpc run must be completed first
Validation gate fix — stratification column validation is now skipped when "Use PsN settings" is checked (the column is inherited from PsN and may not appear literally in the widget)
R status bar now shows only the two current backends: vpc and xpose

v2.5.4

Bug-fix release (Tier 1 audit items + R availability check).

Python 3.9 compatibility — detached_runs.py used int | None, list[dict] and tuple[list, list] type annotations introduced in Python 3.10. Added from __future__ import annotations so the file imports cleanly on Python 3.9 (common on HPC clusters running CentOS/RHEL 8)
VPC column name sanitisation — stratification column names are now cleaned with _r_col() before embedding in the generated R script; control characters and embedded quotes that would break the R string literal are stripped. A separate _sanitize_r improvement also strips newlines and other control characters from path strings
Config directory creation — CONFIG_DIR.mkdir() is now wrapped in try/except OSError; on HPC systems with a read-only home directory the app previously raised PermissionError at import time and refused to start
R availability check at startup — if Rscript is not found on PATH, a status bar message is shown immediately on startup explaining that VPC and RStudio features are unavailable; previously the first indication was an opaque error when actually trying to use those features

v2.5.3

Bug-fix release (continued audit follow-up).

Parameter export status message — the "Parameters exported" status bar message no longer crashes when the widget tree is not in the expected shape; the hasattr(self,'parent') guard was always True and gave false safety
GOF axis column fallback — when a previously-selected X-axis column (e.g. CWRES) is absent from a newly-loaded table, the plot now falls back to the panel default (PRED or TIME) instead of silently selecting column 0 (which was typically ID or TIME at random)
GOF file-open imports — __import__('os') / __import__('subprocess') inline hacks in the "Open exported PNG?" handler replaced with normal top-level imports
History tab run I/O — _load_runs / _save_runs local duplicates removed; history tab now calls the canonical locked versions from config.py, so thread-safety fixes and future bug fixes apply consistently
Unused import removed — APP_VERSION was imported but never used in detached_runs.py
RStudio .Rproj creation — write_text() is now wrapped in a try/except OSError; read-only project directories (common on shared drives) now return a user-visible error instead of raising an unhandled exception

v2.5.2

Bug-fix release addressing findings from a thorough internal audit.

Force-kill fixed — the "Force kill (SIGKILL)" stop option in run popups now works correctly; previously it called a non-existent method and silently did nothing
Boundary warning restored — "Parameter near boundary" warnings are now correctly recorded in run history; a key-name mismatch was preventing this flag from ever being stored
Median statistics corrected — bootstrap and SIR results (bias, RSE, median parameter, dOFV median) now use a proper median calculation; the previous index-based approach produced a systematic upward bias for even-sized samples (7 call sites fixed)
Splitter layout persists — panel splitter sizes are now correctly restored on startup; an early-return in geometry restore was skipping the splitter step
Detached run reconciliation fixed (macOS) — _boot_time() previously returned 0.0 on non-Linux platforms, causing every detached run to be marked finished immediately after restart; it now returns None and the start-time cross-check is skipped when unavailable
Config write thread-safety — all config file writers (save_settings, save_bookmarks, save_runs) now hold the same lock as save_meta, preventing rare corruption from concurrent worker and main-thread writes
Subprocess session handling — RunWorker now uses start_new_session=True (was preexec_fn=os.setsid, which is unsafe with Python threads and can deadlock on macOS); import signal moved to module scope
LRT method-mismatch guard — the workbench comparison table now shows "N/A" with a tooltip instead of a p-value when the reference and candidate models used different estimation methods (e.g. FOCE vs SAEM); exported CSV emits method_mismatch in that column
Waterfall plot at OBJ=0 — subjects with an individual OBJ of exactly 0.0 were excluded from the waterfall plot because the value is falsy; corrected to is not None
ETA–covariate plot filters MDV rows — dosing records (MDV=1) are now excluded from ETA vs covariate scatter plots, consistent with all other diagnostic plots

v2.5.1

Detached runs (SSH/MobaXterm) — a new "Run detached" checkbox in the Run panel launches PsN under nohup in a new session so the job keeps running even if NMGUI2 is closed or the SSH connection drops. Automatically pre-checked when an SSH session is detected. Output is saved to a per-run .nmgui.log file in the project folder. Click the detached row in the Active & Recent Runs table to tail the log in a Watch Log window. On the next NMGUI2 startup, finished detached runs are automatically reconciled (status, timestamps, OFV) without relying on any shutdown hooks. Linux and macOS only.

v2.5.0

Concurrent popup runs — clicking Run now opens a dedicated floating window per model run; multiple models run simultaneously in independent windows, each with its own live console, iteration/OFV progress indicator, elapsed timer, and gentle/force stop controls; on completion the window title and status bar update with the termination result
Active & Recent Runs panel — the Run sub-tab now shows a persistent table of active and recent runs for the current project folder; click a live row to raise its popup window; historical rows are loaded from nmgui_run_records.json in the project directory and survive app restarts; interrupted runs are shown as "? Interrupted"
Theme overhaul — forced Fusion style across all platforms for consistent dark-mode behaviour; migrated ~20 widgets from per-widget stylesheets to object-name + global QSS so theme toggle reliably refreshes every label, separator, spin-box, combo-box and highlighter in the app
QC report — right-click any completed model → QC Report… to open a self-contained HTML report with a PASS / WARN / FAIL checklist covering termination, covariance, condition number, %RSE, parameter correlations, shrinkage, ETABAR and omega boundary checks
Model workbench — Workbench… button opens a sortable table of all completed models with ΔOFV, ΔAIC, ΔBIC, LRT p-value and reference-model selector for quick multi-model comparison
Enhanced compare dialog — the two-model comparison dialog now shows a statistics strip with ΔOFV, ΔAIC, ΔBIC, Δ parameters, LRT p-value and a significance verdict
Dataset integrity checks — at scan time, each model's data file is automatically checked for missing file, column-count mismatches, non-monotonic TIME, duplicate doses, extreme DV values and high BLQ proportion; issues appear in the Info tab's Dataset card
Collapsible layout — the Info panel uses collapsible cards (Dataset / Annotation / Notes); the Parameters tab THETA / OMEGA / SIGMA blocks collapse and expand by clicking the section header
Multi-$EST chain parsing — the .lst Output tab now renders one row per estimation step with per-step OFV, ΔOFV, runtime, significant digits and termination status
Run records — immutable audit trail for every run (UUID, SHA-256 hashes of control stream and dataset, NONMEM/PsN/NMGUI versions, duration, final OFV and status) accessible from the right-click menu
Correctness fixes — LRT p-value now correctly signed when the reference model has fewer parameters; VPC "Save PDF…" reliably produces a PDF; run record and workbench display OFV = 0.0 correctly; GitHub update-check uses numeric version comparison instead of lexicographic

Name		Name	Last commit message	Last commit date
Latest commit History 110 Commits
nmgui2		nmgui2
previous releases		previous releases
screenshots		screenshots
.gitignore		.gitignore
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
README.md		README.md
USER_GUIDE.md		USER_GUIDE.md
nmgui2.py		nmgui2.py
requirements.txt		requirements.txt

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NMGUI2

Table of contents

Features

Models tab

Model detail panel

Files tab

Ancestry tree (Tree tab)

Model Evaluation (Evaluation tab)

VPC tab

Uncertainty tab

Run History (History tab)

Run Records (audit trail)

Settings tab

Additional features

Dependencies overview

Python packages

External tools for running models

External tools for VPC generation

Quick start

Installation — macOS

1. Install Xcode Command Line Tools

2. Install Homebrew (if not already installed)

3. Install Python 3

4. Install R (required for VPC only)

5. Install RStudio (optional)

6. Install required R packages

7. Install Perl (required by PsN — usually pre-installed on macOS)

8. Install PsN

9. Clone and install NMGUI2

10. Run NMGUI2

Optional: desktop launcher

Installation — Windows

1. Install Python 3.10 or newer

2. Install R (required for VPC only)

3. Install RStudio (optional)

4. Install required R packages

5. Install Perl (required by PsN)

6. Install PsN

7. Install Git

8. Clone and install NMGUI2

9. Run NMGUI2

Optional: desktop launcher

Installation — Linux

1. Install system dependencies

2. Install Qt system libraries (required by PyQt6)

3. Install R (required for VPC only)

4. Install RStudio (optional)

5. Install required R packages

6. Install PsN

7. Clone and install NMGUI2

8. Run NMGUI2

Optional: desktop launcher

Updating NMGUI2

Previous versions

First use

Keyboard shortcuts

Configuration files

Troubleshooting

Contributing

Author

Acknowledgements

License

Changelog

v2.8.0

v2.7.9

v2.7.8

v2.7.7

v2.7.6

v2.7.5

v2.7.4

v2.7.3

v2.7.2

v2.7.1

v2.7.0

v2.6.13

v2.6.12

Packages