lohedges

aabbcc

Dynamic AABB trees in C++ with support for periodic systems.

slsm

A C++ implementation of a stochastic level-set method.

vmmc

A C++ library to implement the "virtual-move" Monte Carlo algorithm for approximating the dynamical evolution of systems of strongly interacting overdamped particles.

latuxit

A command-line clone of the excellent macOS program LaTeXiT.

taskfarmer

A simple task farmer for running serial tasks with mpirun, written in C.

trackr

Track reconstruction on the Graphcore IPU.

cxx-template

Manage simple C++ projects with ease.

OpenLSTO

Open Source Level Set Topology Optimization Software

proof-webui

The webUI for the PROOF project.

sander-mlmm

A simple interface to allow electostatic embedding of machine learning potentials in sander.

ash

assets

A repository to store assets (images, animations, etc.) for my GitHub projects.

biosimspace_workshop

Workshop to introduce and teach the BioSimSpace package

CAPMD

Cellular Active Particle Model - (DOME)

flux

Flux is a command-line tool that uses a Monte Carlo algorithm to converge towards a target image using a random sequence of nearest neighbor pixel swaps. Images produced by flux resemble iron filings manipulated by a magnetic field.

ipu

Example code for the IPU crash course

ising

A collection of 2d Ising model codes in various programming languages.

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

prezto

The configuration framework for Zsh

proof

Software for the identification of accessory proteins on filaments

python_and_data

Workshop that goes beyond beginner's python to give Jupyter use, intermediate python and data handling with pandas and matplotlib

rdkit

The official sources for the RDKit library

rectify

Creates ghostly, impressionistic artworks using a Monte Carlo algorithm that converges toward a target image.

sbt

An implementation of the Search by Triplet track reconstruction algorithm on the Graphcore IPU.

scikit-fmm

scikit-fmm is a Python extension module which implements the fast marching method.

siremol.org

Code for my websites

thin_filament_data

Scripts for preparing thin filament CryoEM data

unet

U-Net for PROOF project

website

A repo for my personal website.