Platform independent real-time x3d shaders and their applications in bioinformatics visualization

Since the introduction of programmable Graphics Processing Units (GPUs) and procedural shaders, hardware vendors have each developed their own individual real-time shading language standard. None of these shading languages is fully platform independent. Although this real-time programmable shader technology could be developed into 3D application on a single system, this platform dependent limitation keeps the shader technology away from 3D Internet applications. The primary purpose of this dissertation is to design a framework for translating different shader formats to platform independent shaders and embed them into the eXtensible 3D (X3D) scene for 3D web applications. This framework includes a back-end core shader converter, which translates shaders among different shading languages with a middle XML layer. Also included is a shader library containing a basic set of shaders that developers can load and add shaders to. This framework will then be applied to some applications in Biomolecular Visualization. We first defined a minimal set of shaders for common elements in protein molecules such as "Carbon", "Nitrogen", "Oxygen", "Hydrogen", "Phosphorus", "Sulphur", and "Other", which is used for all undefined elements. Then 3D molecule data sets are converted in a pipeline from PDB to CML to X31). During the conversion from CML to X3D, we automatically add predefined shaders to each of the elements. At the end of this pipeline, a high quality real-time shaded molecular structure is created and ready for use on the Web. Considering the usability, a set of functions for improving the user manipulation and optimizing the real-time interactive performance has been designed. A Multi-Users Shared Envirnment has been set up for sharing dynamic shaders on Web3D application.