Speaker: Stefanie Prast (Inst. 193-02)

In life sciences, a series of successive reactions within a cell are linked together to form metabolic pathways. These can be visualized as graphs and networks, but they are complex
and constantly changing. An automated visualization and layout
approach is therefore necessary. Graphical notations to describe these networks are established in life sciences, like the SBGN (System Biology Graph Notation).
Available software tools support the visual encoding of SBGN, but provide only standard means for automatic arrangement, e.g. hierarchical, circular, or tree layouts, these do not satisfy the
layout rules of SBGN. Constraint based layouts offer means to model such layout rules, but
current approaches only focus on subsets or simplifications of SBGN, e.g. compound structures are almost never taken into account during the layout process.
Providing suitable means to visualize SBGN while considering its semantics during graph layout is therefore still an open topic. In this thesis we plan to develop a multilevel layout strategy that
takes the graphical notation of life sciences into account and visualizes a metabolic pathway's data flow and compound structure, while minimizing the complexity of the network by motif simplification and semantic zooming.




10 + 10
Supervisor: Hsiang-Yun WU