PathSim visualizer: an information-rich virtual environment framework for systems biology. Increasingly, biology researchers and medical practitioners are using computational tools to model and analyze dynamic systems across scales from the macro to the cellular to the biochemical level. We are using Information-Rich Virtual Environments (IRVEs) to display the results of biological simulations, and to allow users to interact with those simulations. While simulation architectures, algorithms, and processing power have enjoyed continuous optimization to date, the user interfaces to these applications have not. The problems of designing such IRVE interfaces arise from the requirement that a variety of spatial and abstract information must be integrated into one coherent experience for the user. This paper explores the design and development issues encountered in our implementation of a bioinformatics application, PathSim (Pathogen Simulation). Specifically, we describe the information and interaction issues in building a front-end tool to visually analyze the results of an agent-based immunology simulation. Finally, we present custom scenegraph objects and consider candidate functionality for future standards components.

This software is also peer reviewed by journal TOMS.