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I followed the instructions in https://help.ubuntu.com/community/MATLAB but still have two icons, one that starts a new matlab instance and one that refers to the running instance.

This is what my /usr/share/applications/matlab.desktop looks like:

[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Exec=matlab -desktop
Name=MATLAB
Icon=/usr/share/icons/hicolor/48x48/apps/matlab.png
Categories=Development;Math;Science
Comment=Scientific computing environment
StartupNotify=true
StartupWMClass=com-mathworks-util-PostVMInit
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