Visualization for biological models, simulation, and ontologies.

摘要

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.