A collection of resources regarding the interplay between differential equations, deep learning, dynamical systems, control and numerical methods.

Package for the data-driven representation of non-linear dynamics over manifolds based on a statistical distribution of local phase portrait features. Includes specific example on dynamical systems, synthetic- and real neural datasets.

Nengo library of additional extensions

Sample code for the NIPS paper "Scalable Variational Inference for Dynamical Systems"

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

Official implementation of Enhanced Gaussian Process Dynamical Modeling for Battery Health Status Forecasting.

control theory repo

Whole-cell modeling tutorials

Simulation and animation of simple passive dynamic walking models in Matlab

Example usage of the pyEXP library for dynamical discovery

The Flexible Epidemic Modeling Pipeline

ManiDyn is a MATLAB toolbox for symbolic modelling of serial-link robot Manipulators.

Kinetic modeling of glucose and acetate metabolisms in E. coli

Framework for systematically and scalably designing whole-cell models from large datasets

a gradient-based optimisation routine for highly parameterised non-linear dynamical models

JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.

`mbtransfer` is an R package for modeling microbiome dynamics. It provides functions for fitting transfer function models, simulating counterfactual trajectories, and selecting significantly perturbed taxa using mirror statistics.

A MatLab package for System Identification using linear and nonlinear auto-regresive models (N)AR, (N)ARX and (N)ARMAX models

tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Analytical & Programming exercises on linear control systems