Metabolic pathways in three dimensions

陳詰昌

                                           12/30/03

Abstract

        Today many researchers focus on representation of metabolic and gene networks. A good representation should possess the potential for expansion and self-organization to integrate separate research groups. However, there are not many papers discuss the ways to improve pathway graphic representations from the visual perception point of view. But how to represent the network in easy-understanding way ?  So this paper uses three-dimensional 'virtual reality' visualizations to represent pathway in 3D.

        The system in this paper is based on MNV ( Metabolic Network Visualizer ) language, creating description of metabolic networks using XML-compliant data model, and to visualize pathways in 3D.The 3D pathway graphs in virtual reality can have some advantages: vast information density, compromise between an overview and detail, standard GUI, Internet-readiness, and other.

Reference

1. Rojdestvenski,I. (2003) 'VRML metabolic network visualizer'. Comput. Biol. Medicine, 33, 169-182.

2. Karp,P.D. (2001) 'Pathway databases: a case study in computational symbolic theories'. Science, 293, 2040-2044

3. Bader,G.D., Betel,D. and Hogue,C.W. (2003) 'BIND: the biomolecular interaction network database'. Nucleic Acids Res.,31,248-250

http://bioinformatics.oupjournals.org/cgi/content/abstract/19/18/2436