Abstract
The Systems Biology Graphical Notation (SBGN) is a standard for the visual representation of processes and networks in systems biology. Three SBGN languages (PD, ER, and AF) allow for the representation of different aspects of biological systems at different levels of detail as SBGN maps. This PhD thesis describes methods and algorithms supporting the use of SBGN maps. In particular it discusses problems such as the translation of pathway maps from the KEGG database into SBGN PD maps including automatic layout and the conversion of SBGN PD maps into SBGN AF maps. In addition, the concept of the SBGN Bricks, reusable modules which represent specific biological processes, is presented. The methods and algorithms given above as well as other techniques for creating and editing of SBGN maps have been implemented in the software SBGN-ED. Examples are presented showing the application of the developed methods and algorithms.
