Software that may be useful for
[http://sage.math.washington.edu:9001/graph_survey graph theory]
[http://sage.math.washington.edu:9001/plot plotting/graphics]
- differential equations:
[http://www.xmds.org/ xmds] - An open-source XML based simulation package, of ordinary differential equations (ODEs) and partial differential Equations (PDEs).
scipy's collection of [http://www.scipy.org/Topical_Software#head-47d9477eccce9c3bf78260ed4d74ed3a8bdfd008 dynamical systems] programs.
- Databases/tables:
[http://www.pytables.org/ pytables]