Bayesian models for ODE models in the Systems Biology Markup Language (SBML)

LayerCake is a framework to design systems of partial differential equations (PDEs), and convert them to ordinary differential equations (ODEs) via Galerkin-type expansions.

An optimization driven ODE-based modeling pipeline for analyzing cell-signaling dynamics over time.

A Python simulation framework for studying hydrogen diffusion and trap-limited transport in multilayer semiconductor systems, motivated by degradation and defect evolution in advanced silicon solar-cell contacts.

Context-dependent pharmacology of cannabidiol: A two-pathway model linking mitochondrial VDAC gating and bioenergetic resilience to selective cytotoxicity

This repository contains simulations of drones movement according to Autonomous Drone Model.

Blender add-on to generate strange attractors.

Simulator for SAIR model proposed in Piqueira, J. R. C., Navarro, B. F., & Monteiro, L. H. A. (2005). Epidemiological models applied to viruses in computer networks. Journal of Computer and System Sciences.

A complete end-to-end pipeline for single-molecule FRET trajectory processing, 3-state kinetic modeling with bleaching, global ensemble fitting, bootstrapping, and sensitivity analysis for Hsp90 dynamics.

Soft Magnetic Materials and Ordinary Differential Equations: From Linear Circuits to Neural Network Models

This repository contains a robust and flexible Python package for solving ordinary differential equations (ODEs). It supports both Runge–Kutta schemes (explicit, DIRK) and BDF multistep methods, with adaptive time-stepping and strong support for sparse Jacobians--making it well-suited for large-scale and stiff problems.

BADDADAN is a proof of concept which builds ODE models of gene modules to study the response of A. thaliana to stress

Modeling light inducible protein interaction systems via ODEs.

Designing network motifs via ODE modeling and NSGA-II.

Vehicle dynamics with a sophisticated friction model and drive-train model that can be used to augment any multi-body simulation (such as Gazebo) involving vehicles.

MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.

Tools for numerical analysis of ODE in python

Chaotic attractors with python (Lorenz, Rossler, Rikitake etc.)

An interactive web application for exploring cell cycle models

Part of MSc Biology Project (2/2). Ordinary Differential Equations (ODE) model for modelling protein, more specifically Sfp1, translocation.