Andy Wu – Ph.D. Dissertation Defense

This thesis aims to explore how to physically embody and interact with computational simulations on an interactive tabletop display. To research this topic, this thesis develops an interactive tabletop application, Pathways, to support the fitting process in modeling biological systems. The application supports the concepts of Tangible User Interfaces (TUIs) and tabletop visualizations.  Pathways supports real-time simulation and provides comparisons of simulation results with experimental data on the tabletop. It also visualizes the simulation of model with animations. In addition to that, Pathways introduces a new visualization to help systems biologists quickly compare the simulation results.

The Pathways system could also change the way researchers currently think about optimization algorithms and the way they are applied in discovery. Another possible impact of Pathways is to science education by re-representing abstract problems in a way that is understandable through our own embodied experience. Pathways also can help us re-think information visualization from the perspective of embodiment and control mechanisms.

Quantitative and qualitative evaluation results are provided to substantiate the thesis claims. The results show that Pathways is more effective than the systems biologists’ current practices. The results show that, on Pathways, users achieved better fitting results and faster fitting results than the control group, which was the systems biologists’ current practice. The results also suggest that it is possible to recruit non-experts to perform the fitting tasks that are usually done by professional systems biologists.