High quality visualization of biochemical pathways in BioPath

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. Bio-Path 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.