Bilkent University
Department of Computer Engineering
M.S.THESIS PRESENTATION
A framework for validation and error resolution of biological pathway maps
Yusuf Ziya Özgül
Master Student
(Supervisor: Prof.Dr.Uğur Doğrusöz)
Computer Engineering Department
Bilkent University
Abstract: The exponential growth of data in the contemporary age underscores the increasing importance of visual data analysis. Consequently, the effective visualization of large-scale datasets is a major requirement for enhancing their readability and comprehensibility. Relational data, which encompasses any structure representable by a set of nodes and edges, falls within the scope of graph visualization. This technique is applicable across numerous domains, including software engineering, network systems, and computational biology. In biology, pathways and interactions are frequently modeled as graphs. The Systems Biology Graphical Notation (SBGN) is a standardized language developed by scientists to model and visualize complex biological systems using graph visualization principles. While several tools, such as Newt and SBGN-ed, exist for the visualization of SBGN pathways, a critical challenge lies in ensuring adherence to the rigorous set of validation rules mandated by the SBGN standard. SBGN-ed, for example, is capable of validating SBGN maps and detecting rule violations. This thesis presents the design and implementation of a novel framework, SyBValS. SyBValS is designed to first validate a given SBGN map to identify errors and then, critically, generate actionable suggestions for resolving each detected error. A key feature is the programmatic capability that allows a client to select and apply these suggestions, thereby transforming the erroneous map into an optimally corrected state. SyBValS represents the first comprehensive framework to integrate both map validation and automated, selective error resolution. Keywords: Information visualization, graph layout, visual analytics, compound graphs, constrained layout, spectral graph drawing
DATE: February 20, Friday @ 10:30 Place: EA 409