- Anki - an intelligent spaced-repetition memory training program; create flash cards
- BKchem - a free chemical drawing program
- FreeMedForms - open source electronic medical/health record
- GNU Octave - a high-level interactive language for numerical computations
- GNU PSPP - a system for statistical analysis; SPSS clone
- GPeriodic - periodic table application
- Mendeley Desktop - a free reference manager and an academic social network
- Nootka - application for learning musical score notation
- OpenEMR - open source electronic health records and medical practice management solution
- PhysMo - video motion analysis
- PyMOL - free and flexible molecular graphics and modelling package
- Reinteract - interactive Python shell
- SigViewer - viewer for biosignals such as EEG, EMG, and ECG
- Stellarium - a real-time realistic planetarium
- Qalculate - a powerful and easy to use calculator
- TiEmu - Texas Instruments calculators emulator (TI-89 and newer)
- TilEmu - Texas Instruments calculators emulator (Older TI calcs)
- (X)MedCon - medical image (DICOM, ECAT, ...) conversion tool (GUI)
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- bcd, ppt, morse - reformat input as punch cards, paper tape or morse code
- cwcp - ncurses-based Morse code tutor
- diatheke - a command-line Bible reader
- dict - DICT Protocol Client
- fortune - print a random, hopefully interesting, adage
- gperiodicASCII - a BASH script I made for using GPeriodic in the command-line
- gtypist - a typing tutor with lessons for different keyboards and languages
- medcon - medical image (DICOM, ECAT, ...) conversion tool
- pom - display the phase of the moon
- verse - displays a daily devotional verse from scripture
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