Real-Time Volume Ray Tracing For Bioinformatics Applications

Lukas Marsalek, Stefan Nickels, Anna Dehof, Hans-Peter Lenhof, Philipp Slusallek, and Andreas Hildebrandt
Stockholm, June 2009



A large amount of invaluable information about biomolecular systems can be gained from the study of three-dimensional scalar quantities.  A prominent example are electrostatic potentials as they are used, e.g., in the study of biomolecular interactions or electron densities derived from X-Ray or microscopy experiments. Visualizing this data in a way that allows to effectively extract the desired information is a particularly hard problem. In computer graphics, volume ray tracing has been accepted as the method of choice for the visualization of such datasets, but this has rarely been used in bioinformatics contexts, despite its image quality and information visualization potential. In particular, ray tracing has traditionally been deemed much too slow a technique for interactive applications. The wide availability of extremely parallel processing units on modern graphics adapters, however, now allows to harness the power of volume raytracing  also for interactive, real-time visualization.

In this work,  we show a GPU-based volume raytracing application particularly adapted to biomolecular data sets. It offers real-time, high-quality visualization, while also giving a fine-grained control over the mapping of scalar values to colors by specifying so-called transfer functions in an intuitive GUI. It is integrated into the molecular viewer and modelling tool BALLView and hence has access to a wide variety of data sources and formats, like the Viper database for viral hull structures or computed electrostatic potentials.