Affiliations: Fakultät für Mathematik und Informatik,
Universität Passau, Innstraße 33, D-94030 Passau, Germany E-mail:
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.