Metabolic pathways in three dimensions

MOTIVATION Currently a substantial research effort is devoted to automated representation of metabolic and gene networks. Automatic visualization plays a significant role in such efforts, and becomes an important problem on its own. Graphical visualization of metabolic pathways has to be information dense and not 'overloaded', recognizable and unified, close to traditional and algebraically consistent. The use of three-dimensional 'virtual reality' visualizations may help to understand better the intricate topology of metabolic and regulatory networks. RESULTS A system of visualizing metabolic networks as graphs in three-dimensional space by means of Virtual Reality Modeling Language (VRML) is presented. The system is based on an XML-compliant MNV ('Metabolic Network Visualizer') language, and comprises MNV language standard and parser, MNV to VRML translator, and interactive pathway constructor, all unified by the HTML graphic user interface. AVAILABILITY The MNV can be accessed in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html SUPPLEMENTARY INFORMATION The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html