R package for statistical inference using partially observed Markov processes

Development version of phaseR, an R package for phase plane analysis of one- and two-dimensional autonomous ODE systems

The dsmodels domain-specific-language for visualizing dynamical systems in R.

R package for dynamic bioenergetic modeling of coral-Symbiodinium symbioses

IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems

TimeCycle is a topology inspired method for the detection of cycling transcripts in circadian biology research.

Code for the paper "Identifying time lag in dynamical systems with copula entropy based transfer entropy"

Estimating route conditional travel time and its uncertainty.

Code for the paper "An empirical Bayes approach to estimating dynamic models of co-regulated gene expression" (published in Data Science in Science, 2023)

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

🌀 Illustration of the Lorenz System

🐇🦊 Illustration of Lotka–Volterra's Predator–Prey Model

🦠🤒 Illustration of the SIR Model

Code for the paper "System Identification with Copula Entropy"

Shiny apps to teach simple dynamical models in biology with an emphasis on oscillations

Introductory Tools for Phase Plane Analysis (Developed for Bowdoin College)

Nonlinear Time Series Analysis in R

Dynamical analysis of minimnal networks based on approximate majority algorithm (AM)

Enhancing Boolean networks with continuous logical operators and edge tuning: smoothing simulations

Forwards euler, backwards euler, and trapezoidal ODE solver for harmonic oscillators. Done for complexity explorer