mechanistic-modeling

Simulation and inference of gene regulatory networks based on transcriptional bursting

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

The Dig4Bio worskhop series

Nitrogen balance model components and test procedures

PySB add-on providing utilities to add units to models and perform dimensional analysis.

This repository contains the codes for the article: Data-driven mechanistic modeling of oxygen distribution and hypoxia profile in tumor microenvironment

Parametric growth-curve modeling of a single broiler breeder hen: classical curves (Gompertz, logistic, von Bertalanffy) plus a segmented model capturing the body-weight drop at onset of lay. Includes a Streamlit app.

Open-source framework for reproducible mechanistic virtual clinical trials, combining population PBPK simulation, trial design, physiological perturbation, PK analysis, immutable provenance, and researcher-ready reporting.

This project studies causal relationship between events in the Adverse Outcome Pathway.

CDD Diffing Technique [Contrastive Decoding Diffing]

Reproducibility-first mechanistic biology research stack: CFM (SCNT feasibility), BSE (virtual PK/PD physiology), and NSCS (closed-loop equation discovery).

Mechanistic Temperature Dynamic Model - Predictive Modeling in Microbiology

Reproducible Phase 1 pipeline for mechanistic modeling and OOD trust scoring in a CiPA-28 context.

Teaching-oriented ODE epidemic mini-lab with SI, SIR, and SEIR models, parameter sweeps, and interpretable metrics.

Mechanistic models whose every number says where it came from. Describe a mechanism in plain words; get a model whose constants come from the literature (BRENDA), each with its citation.