- Article -
| In Silico Biology 2, 0006 (2002); ©2002, Bioinformation Systems e.V. |
High quality visualization of biochemical pathways in BioPath
Falk Schreiber
Universität Passau, Fakultät für Mathematik und Informatik, Innstraße 33, D-94030 Passau, Germany
E-mail: schreibe@informatik.uni-passau.de
present address:
Basser Department of Computer Science, University of Sydney, Madsen Building (F09), Sydney, NSW 2006, Australia
E-mail: falk@cs.usyd.edu.au
Edited by E. Wingender; received November 1, 2001; revised December 17, 2001, accepted January 28, 2002; published February 5, 2002
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.
Key words: biochemical pathways, metabolic pathways, visualization, graph drawing