pkpd

Physics-first, uncertainty-honest in-silico cell and drug-response simulator (Python). Validated docking/ADMET input layer (Vina, OpenFF, xTB), cell-level PK/PD modules, and a cell/colony engine under construction toward a validated interactive dish.

library of C++ functions that support applications of Stan in Pharmacometrics

Population Experimental Design (PopED) in R

Chi is an open source Python package which is designed for PKPD modelling and model-informed precision dosing (MIPD).

Open-source nonlinear mixed-effects (NLME) modeling engine for population PK/PD and pharmacometrics, with FOCEI, SAEM, analytical PK, and ODE models.

R package for using ubiquity

PySB add-on providing domain-specific macros and models for empirical and mechanistic PK/PD modeling.

Create diagrams with ggplot.

Turn any AI agent into a clinical pharmacologist and pharmacometrician. It reviews, reconciles, and prepares evidence. It never selects a dose, signs off, or submits.

Physiology-based systems pharmacology model of thyroid hormones regulation in rat and human

PK/PD simulation and fitting through Rust, Python, R, browser and MCP interfaces.

Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin

Python-first toolkit for dissolution similarity, NCA, PK/PD simulation, and pharmacometric reporting

A curated, tier-annotated dataset and simulation engine of tumor-growth-inhibition (TGI) and exposure-response models that quantifies model-selection risk in oncology drug development, exported directly into standard pharmacometric and systems-biology formats like NONMEM, SBML, and rxode2.

A Python library for automated PK/PD ODE model identification from concentration–time data. Selects the compartmental structure, estimates parameters, and flags identifiability problems; no model specification or starting values required.

How to cite: Van De Vyver, A.J., Eigenmann, M.J., Ovacik, M., Pöhl, C., Herter, S., Weinzierl, T., Fauti, T., Klein, C., Lehr, T., Bacac, M., Walz, A.-C. (2021). A novel approach for quantifying the pharmacological activity of T cell engagers utilizing in vitro time course experiments and streamlined data analysis. AAPS

ODE-based quantitative systems pharmacology model of B cell depletion and repopulation under anti-CD20 therapy (rituximab, ocrelizumab). Multi-compartment PK/PD with Bayesian parameter estimation, uncertainty quantification, and posterior predictive validation. Python · PyMC · scipy · MLflow.

Open Python Web App for Pharmcological Modeling and Analysis

An MCP server providing AI assistants with access to MATLAB SimBiology for modelling, simulating, and analyzing biological systems

PK/PD clinical trial simulator with virtual patients, adaptive randomization, external-control borrowing, and protocol optimization.