Bilkent University
Department of Computer Engineering


Methods and Tools for Effective Visualization of SBGN-PD (Systems Biology Graphical Notation-Process Description) Diagrams


Mecit Sari
MSc Student
Computer Engineering Department
Bilkent University

A graph is a way of representing a set of objects (nodes) and relations (edges) between these objects. Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing, complexity management of crowded graphs are essential for efficient utilization of underlying information.

The Systems Biology Graphical Notation (SBGN) is used to standardize the graphical and visual representation of biochemical and cellular processes. It defines comprehensive sets of symbols with precise semantics, together with detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted.

The SBGN Process Description (PD) language shows the temporal courses of biochemical interactions in a network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram.

In this talk we present methods and tools to effectively visualize, manage and query SBGN-PD diagrams. Specifically, we first introduce new algorithms for proper management of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes place. Then, we discuss software components and web-based tools to visualize, manage and query SBGN-PD networks. These tools use latest web technologies and libraries.


DATE: 21 April, 2014, Monday @ 16:40