In this dissertation, I present three browsers that I have developed for the purpose
of exploring, understanding, and analyzing models, simulations, and ontologies in
biology and medicine. The first browser visualizes multidimensional simulation data
as an animation. The second browser visualizes the equations of a complex model as
a network and puts structure and organization on top of equations and variables. The
third browser is an ontology viewer and editor, directly intended for the Foundational
Model of Anatomy (FMA), but applicable to other ontologies as well. This browser
has two contributions. First, it is a lightweight deliverable that lets someone easily
dabble with the FMA. Second, it lets the user edit an ontology to create a view of
it. For the ontology browser, I also conduct user studies to refine and evaluate the
software
