Bilkent University
Department of Computer Engineering
MS Thesis Presentation


Automated Layout of Process Description Maps Drawn in Systems Biology Graphical Notation


Begüm Genç
MS Student
Computer Engineering Department
Bilkent University

Evolving technology has increased the focus on genomics. The combination of today's advanced studies with decades of molecular biology research yield in huge amount of pathway data. These models can be used to improve high-throughput data analysis by linking correlation to the causation, shedding light on many complex diseases. In order to prevent ambiguity and ensure regularity of the research, a need for using a standard notation has emerged.

Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modellers and computer scientists with the intention of enabling scientists to represent networks, including models of cellular processes mentioned earlier, in a standard, unambiguous way. SBGN is formed of three languages: process, entity relationship and activity flow. This research is focused on its process diagram branch.

A graph is an abstract structure representing a set of objects linked to each other by some links. In this context, those discrete objects are represented by nodes (or vertices) and the links are represented by edges. Graphs are widely used to represent complex relational data and provides convenience for validation, effective querying and visualization.

Automated layout is commonly used to clearly visualize the information represented by graphs. Considering the fact that, biological pathways includes nested structures (e.g., nucleoplasms), we have made use of a force-directed automatic layout algorithm called Compound Spring Embedder (CoSE), which supports the compound graph structures. On top of this layout structure, we have developed a specialized layout algorithm called SBGN-PD Layout.

SBGN-PD layout enhancements mainly include properly tiling of complex members and disconnected molecules, placement of product and substrate edges on the opposite sides of a process node without disturbing the force-directed structure of the algorithm.


DATE: 23 July, 2014, Wednesday @ 14:00