William Gilpin

pypdb. A Python API for the RCSB Protein Data Bank (PDB)

cphy. Class materials for computational physics course

fnn. Embed strange attractors using a regularizer for autoencoders

convoca. Predict and analyze cellular automata using convolutional neural networks

shrec. Reconstructing shared causal drivers from noisy time series

portbalance. Determine optimal rebalancing of a passive stock portfolio.

cfgen. Parse a text corpus and generate sentences in the same style using context-free grammar combined with a Markov chain.

howto. How to do various tricky computer things

rice. The Riemannian Causal Embedding (RiCE) algorithm for discovering networks from time series

flowtrace_python. Python implementation of time-resolved flow tracing.

rk4. Numerically solve the Henon-Heiles problem and generate Poincare sections using a simple implementation of RK4 integration

hspmc. Monte Carlo simulation of hard sphere packing using MATLAB

diccor. A set of MATLAB routines for generating displacement vector fields from black and white time series of images.

swimpy. Utilities for working with experimental fluid mechanics datasets

lagrange2d. A Mathematica package for Lagrangian analysis of fluid flows.

fracdiff. A set of tools for simulation of fractional Brownian motion

illotka. Simulate the ill-conditioned Lotka-Volterra model

williamgilpin.github.io. HTML

chaotic_ecosystem. Mathematica code for analysis of a chaotic ecosystem model

flowtrace_imagej. ImageJ / Fiji implementation of time-resolved flow tracing.

nolds. Nonlinear measures for dynamical systems (based on one-dimensional time series)

degas. Plotting utilities for matplotlib

alveoli. Oscillating alveoli model

Data-Science-Cheatsheet. A helpful 5-page machine learning cheatsheet to assist with exam reviews, interview prep, and anything in-between.

kurep_paper. Code to create avalanches in a repulsive oscillator model.

vergas. Simulation of a Lennard-Jones gas using Verlet integration. Calculation of autocorrelation and other descriptive statistics requiring dynamical information.

flowtrace_matlab. MATLAB implementation of time-resolved flow tracing.

exrepo. An example Python repository

dynGENIE3. Semi-parametric approach for the inference of gene regulatory networks from time series of expression data

netsim. Tools for analyzing Markov models using statistical physics and graph theory