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.
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"
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.
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"
Differentiable mechanistic simulation for dose-amplitude, dose-timing, and individualized regimen optimization.
Two-stage Bayesian calibration for QSP models: literature-prior MCMC then neural posterior estimation.
Schema-validated LLM extraction of QSP calibration targets from literature, via interactive MCP or batch script.
SBML → C++ CVODE code generator for QSP models.
SLURM-aware orchestration and three-tier caching for QSP simulation campaigns.
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