Dr. Penny's Ph.D. thesis is entitled "The Software Landscape: A Visual Formalism for Programming-in-the-Large".
This work ellaborates a language of nested boxes and arrows with import/export rules for describing large-scale, hierarchical software structures built atop arbitrary programming languages. At the heart of the thesis is a very large predicate that determines whether a given hierarchically-structured box and arrow "picture" is a valid landscape or not. An example of an invalid landscape, for instance, is one where a box in one sub-system uses a box in another sub-system without properly importing it.
As part of the work, Dr. Penny built a prototype implementation embedded within the Object-Oriented Turing Programming Environment. As Hausi Muller (his external thesis advisor) put it "I can personally attest to the remarkable speed of the graphical operations". You don't get a Ph.D. for nothing.