Use hypergraphs to create foodweb models which include non-trophic effects

Code for mitochondrial dynamics ODE manuscript.

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

BADDADAN is a proof of concept which combines mechanistic modelling with machine learning to study the response of A. thaliana to stress

ParameterEstimation.jl is a Julia package for estimating parameters and initial conditions of ODE models given measurement data.

A set of codes in MATLAB for ODE reconstruction using least-square method

R package for fitting kinetic models with one or more state variables to chemical degradation data

This repository provides a model of the MAPK and Akt pathways. Parameters and initial values are mainly based on biological assumptions. The model is therefore conceptual, and the purpose is to get a better understanding of the interactions between genes, that are important in some cancers.

Designing network motifs via ODE modeling and NSGA-II.

Modeling light inducible protein interaction systems via ODEs.

Python package for automatically generating Stan source code for hierarchical Bayesian ordinary differential equation models.

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.

Package for modeling glycolysis activity

A MATLAB suite of initial value problems

Modeling and Global Sensitivity Analysis of Strategies to Mitigate Covid-19 Transmission on a Structured College Campus

🔁 Analysis of a system with three species in a competitive loop.

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

Implementation of a recurrent neural network based Observer/Identifier for highly Non-Linear Dynamical Systems, using the Lorenz Attractor as a test case.

Modeling the START transition in the budding yeast cell cycle