Rocs is a Graph Theory IDE for designing and analyzing graph algorithms.
Gaphor
Gaphor is a UML and SysML modeling application written in Python. It is designed to be easy to use, while still being powerful
PSPP
GNU PSPP is a program for statistical analysis of sampled data.
LabPlot
LabPlot is a free software and cross-platform computer program for interactive scientific graphing and data analysis, written for the KDE desktop.
KmPlot
KmPlot is a program to plot graphs of functions, their integrals or derivatives.