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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
Dynamics of quantum systems, controlled by external fields
...With its visualization of quantum dynamics generated 'on the fly', WavePacket is suitable for teaching quantum mechanics as well as for research projects, see also the numerous demonstration examples .
The Matlab/Octave version is mature and has been used in production for decades. The C++/Python version has been superseded by https://github.com/ulflor/wavepacket.
GAST-Viz is a toolkit allowing for the creation of OpenGL atomistic simulation applications using discrete element modeling methods. A number of sample applications are included.