Berkeley DB (also called libdb) is a family of embedded key-value database libraries providing scalable high-performance data management services to applications.

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

FLASH is a modular, extensible software system that consists of inter-operable modules that can be combined to generate different applications.  It has solvers for hydrodynamics, magnetohydrodynamics, equations of state, radiation transfer, diffusion, conduction, opacity, laser energy deposition, particles, nuclear burning, gravity, cosmology, magnetic resistivity, and primordial chemistry.

GDAL is a translator library for raster geospatial data formats.

GMT is Generic Mapping Tools

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

HDF is the Heirarchical Data Format library.

jq is a lightweight and flexible command-line JSON processor.