Store properties by reference instead of name

[GoogleCodeExporter]

In the current implementation, many properties are stored by name instead of 
reference/pointer, which can lead to problems when updating a CellBlender 
model. For instance, a molecule has a name which is simply a string property. 
That same molecule name might appear in other places like reactions and release 
sites. If the original molecule name is updated, that change won't be known or 
propagated to the reactions and release sites. This illustrates a fundamental 
problem in how properties are stored, and the fix will almost certainly break 
previous CellBlender models.

Original issue reported on code.google.com by [email protected] on 7 Feb 2013 at 9:02