High Quality Visualization of Biochemical Pathways in BioPath

Article type: Research Article

Authors: Schreiber, Falk

Affiliations: Fakultät für Mathematik und Informatik, Universität Passau, Innstraße 33, D-94030 Passau, Germany E-mail: [email protected]

Note: [] Present address: Basser department of computer science, University of Sydney, Madsen Building (F09), Sydney, NSW 2006, Australia. E-mail: [email protected]

Abstract: Biochemical reactions form large and complex networks. Comprehensible visual representations of these networks help biochemists understand the relationships between the chemical components. Typically pathway diagrams are manually produced drawings. Because of the steady progress of knowledge and the complex relationships in these networks, automatic visualizations are necessary. BioPath is a system for the exploration and automatic visualization of biochemical pathways. It has been developed to obtain an electronic version of the well-known Boehringer Biochemical Pathways poster and offers new possibilities to find information and to navigate through pathways. BioPath has a specific database containing reactions and a hierarchical clustering of reactions and reaction networks. One feature is the automatic generation of pathways from the database and their high quality visualization. This paper states the requirements for the visualization of biochemical pathways, presents a layout algorithm and shows how BioPath can be used to explore biochemical reaction networks.

Keywords: graph drawing , metabolic pathways, visualization, biochemical pathways

Journal: In Silico Biology, vol. 2, no. 2, pp. 59-73, 2002