Disclaimer: All datasets in this repository are simulated or pseudodata generated solely for methodological demonstration purposes. No proprietary, confidential, patient-derived, or employer-affiliated data is included. This work represents independent research and educational development conducted outside of any employment context and does not reflect the proprietary methods, data, or intellectual property of any employer or collaborator.
This repository is released under the MIT License. © 2026 Bo Ma (tjmb03). Reuse with attribution.
A collection of pharmacokinetic/pharmacodynamic (PK/PD) modeling tools, interactive Shiny applications, and example scripts for Model-Informed Drug Development (MIDD).
├── MIDD_advanced_shiny/ # Advanced MIDD interactive Shiny app
├── PopPKPD_workflow_shiny/ # Population PK/PD workflow Shiny app
├── rxode2_PKPDsimulator_shiny/ # RxODE2-based PK/PD simulator Shiny app
├── .github/workflows/ # CI/CD workflows
│
├── A simple indirect response PK:PD model.R
├── Convert RxODE2 QD:BID PK:PD simulation.R
├── PBPK_modeling_example.Rmd
├── TMDD_basic.Rmd
├── Steady-state PTA
└── basic example-nlmixr2.R
| App | Description |
|---|---|
| MIDD_advanced_shiny | Advanced model-informed drug development workflows |
| PopPKPD_workflow_shiny | Interactive population PK/PD analysis and simulation |
| rxode2_PKPDsimulator_shiny | ODE-based PK/PD simulation using RxODE2 |
| File | Description |
|---|---|
A simple indirect response PK:PD model.R |
Indirect response model implementation in R |
Convert RxODE2 QD:BID PK:PD simulation.R |
Convert between once- and twice-daily dosing simulations |
PBPK_modeling_example.Rmd |
Physiologically-based PK (PBPK) modeling walkthrough |
TMDD_basic.Rmd |
Target-mediated drug disposition (TMDD) model example |
Steady-state PTA |
Probability of target attainment (PTA) at steady state |
basic example-nlmixr2.R |
Population PK fitting with nlmixr2 |
See folders for scripts and usage details.
| Framework | Purpose |
|---|---|
| RxODE2 | ODE-based PK/PD simulation in R |
| nlmixr2 | Nonlinear mixed-effects population PK/PD fitting |
| PBPK | Physiologically-based pharmacokinetic modelling |
| TMDD | Target-mediated drug disposition modelling |
| Indirect response | PD models for delayed drug effects |
| PTA | Probability of target attainment for dose optimisation |
Designed for translational scientists, pharmacometricians, and biomarker strategists.
© 2026 tjmb03. This project is provided for educational and methodological demonstration purposes.