Development of the Core Visualization Infrastructure
Through Genetic Disease Data 4D Visualization

Led by Dr. Christoph W. Sensen

Using the CAVE Automated Virtual Environment (CAVE) and related visualization software as the basic tool kit, Dr. Sensen's team is developing a system to integrate diverse information on genetic diseases.

The outcome of the 4D Project will be a software system for visual data analysis that addresses two core areas:

• Exploration of the effects of genotype variation on phenotype outcomes.
  
• Creation of standard mechanisms of cross-associations between diverse data types.
  

The Project supports three main types of biomedical information:

• Medical imaging data such as those derived from functional Magnetic Resonance Imaging (fMRI), Computed Tomography (CT), Positron Emission Tomography (PET), and microscopy.
  
• Anatomical organ reconstructions in the form of 3D surface-based models and digital atlases of the organism's anatomy.
  
• Time-varying biochemical concentration data such as those from gene expression microarrays, proteomic studies, pharmaco-kinetic studies, and metabolomic experiments.
  

Data is supplied by collaborating teams on the 4D Project. Biomedical experts from these teams also provide usability expertise to Dr. Sensen's team to guarantee that interactions with visual models of disease-related data in the 4D environment correctly reflect needs of biomedical research.

Dr. Sensen's team at The Center of Excellence for Visual Genomics (COE) is expanding their ongoing research and development activities to form the foundation for this Project.

The team is completing acquisition of Java 3D anatomical atlases for mapping genomics, proteomics, and imaging data from other subprojects. It will then create a tool kit for virtual reality-based exploration of genomic, proteomic, and metabolomic data on a molecular scale, and link this tool kit visually to the models on anatomical scale.

The team will also continue development of visual techniques suitable for bioinformatics. For example, the Project requires implementation of portability features for the 4D software across a number of visualization environments including the CAVE, portable 3D visualization displays, and desktops to preserve maximum functionality. Advanced level of detail management features and data skeletonization will be developed to enable massive amounts of data to be loaded into the visual model on demand, in a scalable fashion.

Eventually, the efforts of the Sensen team will culminate in a system that enables complex visual information-retrieval queries and biomedically relevant data mining strategies.