PySINDy
PySINDy: A comprehensive Python package for robust sparse system identification - Published in JOSS (2022)
DynamicalSystems.jl
DynamicalSystems.jl: A Julia software library for chaos and nonlinear dynamics - Published in JOSS (2018)
CellPyLib
CellPyLib: A Python Library for working with Cellular Automata - Published in JOSS (2021)
TransitionsInTimeseries.jl
TransitionsInTimeseries.jl: A performant, extensible and reliable software for reproducible detection and prediction of transitions in timeseries - Published in JOSS (2024)
HarmonicBalance
A Julia package for solving nonlinear differential equations using the harmonic balance method.
complexitymeasures.jl
Estimators for probabilities, entropies, and other complexity measures derived from data in the context of nonlinear dynamics and complex systems
ModelPredictiveControl
An open source model predictive control package for Julia.
https://github.com/keichi/kedm
A high-performance implementation of Empirical Dynamic Modeling (EDM)
SMFilter
an R package implementing the filtering algorithms for the state-space models on the Stiefel manifold
modelling-saccharomyces-cerevisiae-for-the-production-of-fermented-beverages-beer-2024-
In this work, we formulate a mechanistic model consisting of three first-order Ordinary Differential Equations (ODEs) to describe ethanol production for mezcal by the Saccharomyces cerevisiae yeast using glucose and fructose as substrates.
PathSim - A System Simulation Framework
PathSim - A System Simulation Framework - Published in JOSS (2025)
NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models
NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models - Published in JOSS (2025)
saccharomyces-cerevisiae-modelling-and-nonlinear-regression-with-normalized-data
Mathematical modeling and fitting by non-linear regression to experimental data in an alcoholic fermentation by the Saccharomyces cerevisiae yeast
pyrddlgym-jax
JAX compilation of RDDL description files, and a differentiable planner in JAX.
rp_speed_test
Code to get the calculation speed for recurrence plots/ recurrence quantification analysis using MATLAB, R, Python, and Julia code.