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

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

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

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