Automatic Layout and Visualization of Biochemical Pathway

Abstract

The main contribution of this paper is a new visualization algorithm that combines and improves well-known forced-directed layout approach and hierarchical layout approach, and can handle complex pathways composed of cycles and hierarchies. Experiment shows that our approach can clear render the global component structure of complex pathways as well as the local structure in each component. Based on our algorithm, we developed a biochemical pathway visualization system called VisualPathway, which consists of pathway category browsing , pathway layout, and pathway visualization. For category browsing, we apply fisheye visualization technique to enhance the browsing efficiency so that the user can find desired pathway more conveniently. For pathway visualization, we adopt the Petri Net as pathway representation. Users can access information behind the pathway by clicking components in the visualization.