Visualizing metabolic networks in VRML

A successful data collection visualization should satisfy conflicting requirements: unification of diverse data formats, support for serendipity research, support of hierarchical structures, algorithmizability, vast information density, Internet-readiness, etc. The traditional 2D representations of metabolic pathways lack compactness and information density. Virtual reality (VR) has made significant progress in engineering, architectural design, entertainment and communication. Evident advantages of using VR for scientific visualization are subconscious orientation, compromise between overview and detail, memorizing search results, and customization. We experiment with the possibility of using immersive abstract 3D visualizations of metabolic networks. We present the trial Metabolic Network Visualizer (MNV) software, which produces graphical representation of a metabolic network as a VRML (Virtual Reality Modeling Language) world. The entities in the metabolic network are identified as "compartment", "species", "reaction" and "transporter". The properties of the above objects are described using a simple scripting language. The demonstration of the MNV software is available at http://130.239.139.41/sciencevr/mnv/indexview.html.