HOOMD-blue version 3.0 A Modern, Extensible, Flexible, Object-Oriented API for Molecular Simulations. - Brandon L. Butler; Vyas Ramasubramani; Joshua A. Anderson; Sharon C. Glotzer (SciPy, 2020)

signac: Data Management and Workflows for Computational Researchers. - Bradley D. Dice; Brandon L. Butler; Vyas Ramasubramani; Alyssa Travitz; Michael M. Henry; Hardik Ojha; Kelly L. Wang; Carl S. Adorf; Eric Jankowski; Sharon C. Glotzer (SciPy, 2021)

Change point detection of events in molecular simulations using dupin. - Brandon L. Butler; Domagoj Fijan; Sharon C. Glotzer (Comput. Phys. Commun., 2024)