SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

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

Virtual population generation, fitting, and benchmarking.

Mechanistic Pan-Cancer Signaling Model

This repository provides the MATLAB scripts for our quantitative systems pharmacology model published in Front. Bioeng. Biotechnol., where we conduct an in silico clinical trial in breast cancer using anti-PD-1, anti-CTLA-4 antibody and an epigenetic modulator.

This repository contains the latest QSP platform for TNBC/NSCLC developed by the Popel Systems Biology Laboratory

From computationally intractable MATLAB code to ~1600x faster optimized C code

Source code for "Slow Delayed Rectifier Protects Against Arrhythmic Activity Across Multiple Species - A Computational Study"

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.

Source code for "Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions"

Schema-validated LLM extraction of QSP calibration targets from literature, via interactive MCP or batch script.

SLURM-aware orchestration and three-tier caching for QSP simulation campaigns.

SBML → C++ CVODE code generator for QSP models.

Two-stage Bayesian calibration for QSP models: literature-prior MCMC then neural posterior estimation.