- HODIF: High-order derivatives, interpolations and filters for block-structured AMR. Accompanying software for Ray et al, "Using high-order methods on adaptively refined block-structured meshes – derivatives, interpolations, and filters", SIAM Journal on Scientific Computing, 2007, 29(1):139-181. BSD license.
- graphMC: a package for testing the independence of graphs generated by a Markov chain Monte Carlo method. A description of the theory is is in Ray et al, "Are we there yet? When to stop a Markov chain while generating random graphs", 9th International Workshop for Algorithms and Models for the Web Graph, A. Bonato and J. Janssen, eds, Lecture Notes in Computer Science (LNCS 7323), 2012. Download paper.
- sparse-msrf: A package for sparse modeling and estimation of fossil-fuel CO2 emission fields – MATLAB code to solve an inverse problem to estimate fossil-fuel CO2 emissions using a Multiscale Random Field model and Stagewise Orthogonal Matching Pursuit. The theory is in Sandia Technical Report.
- PRIME: A modeling framework for "real-time" characterization and forecasting of partially observed outbreak- A Python package to solve and inverse problem an infer the latent infection rate curve using Bayesian inference. The theory is in doi: 10.1007/s00466-020-01897-z.