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

Nengo library of additional extensions

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. https://agosztolai.github.io/MARBLE/

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.

Whole-cell modeling tutorials

control theory repo

Official implementation of Enhanced Gaussian process dynamical models with knowledge transfer for long-term battery degradation forecasting.

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

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.

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

`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.

Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology

Dynamical System created from mapping of curvature and torsion of image of parametric planar curve when stereographically projected to the unit sphere.

A library of hybrid N-body + test particle simulations for dynamical modeling of galaxy interactions.

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