A tool for metabolic and regulatory pathways visual analysis

The research activity in bio-informatics has now reached a new phase, called post-genomics. It aims at the description of gene products as part of global processes in cells. In this research area, the various tasks to be conducted by biologists call for methods inspired from knowledge extraction and representation, and from information visualization. We describe a system devoted to the visualization of metabolic pathways. This set of biological reactions describe product transformations in the cell. The analysis of various pathway visualization tools led us to qualitative assertions. First, it is essential that the visualization environment preserves the drawing conventions borrowed from biology. Second, it seems important to offer an environment in which the user can navigate while preserving cognitive continuity. Our system focuses on these interactive and navigational issues. It offers mechanisms such as interactive color mapping and semantic zooming of pathways through various levels of details. Our tool also aims at helping biologists in the analysis of experimental results measuring gene expression in various biological processes. Although our efforts have focused on the visualization of metabolic pathways, our system should help to visualize, analyze and discover other types of biological pathways (e.g. regulatory pathways).