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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
A cross-platform interface for the *.mfj file format.
mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality.
"MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html.
LabJ-ng is a laboratory notebook for organic chemists. It has a client-server architecture with a web browsers interface. Data is stored on MySQL database. Chemical reactions are drawned in java applet window. See projct website for example.