Project:
Visualization for Genome Data
using Virtual Reality Technology

>>Japanese

Visualizaton for Genome Data using VR Technology

Summary

In genome science, human genome sequence has been decoded and microarray technology has enabled the simultaneous measurement of the gene expression level of more than 30,000 genes. Gene expression level is proportional to the number of mRNAs transcribed from genes, thus it indicates the activity of genes in a cell. It is expected that gene expression data and other biological data will provide information on the gene function, the mechanisms of disease progression, and assist in drug discovery. Computer science and information technology can be expected to help these analyses. Thus, a research area called "Bioinformatics" or "Information Biology" has been emerged.

We focus on the visualization of genome data for genome researchers to easy to understand the data intuitively. We think that virtual reality technology can help in the improvement of the effectivity of genome data analysis by enabling interactive visualization and providing a three-dimensional virtual environment. We has developed visualization systems for genome analysis using virtual reality technology, collaborated with Laboratory for Systems Biology and Medicine (LSBM), the Department of Genome Science, and the Department of Molecular Medicine, in the Research Center for Advanced Science and Technology (RCAST), the University of Tokyo. In our research, visualization of the genome data using an immersive projection technology is expected to be effective to grasp the whole data because it is possible to present huge information at a time with the immersive projection display.

Current Situation

Gene expression data are able to measure as numeric using the microarray technology. We use the data obtained from Gene Chip by Affymetrix. We have developed systems for the data analysis, evaluation of the data, and visualization of the data. We are developing the virtual environment using immesive projection technology, named VEGAS, Virtual Environment for Genome Analysis and Simulation.

vegas

VEGAS (Virtual Environment for Genome Analysis and Simulation) is now specific for the gene expression analysis using an immersive projection display. It uses CABIN systems and uses the software library for CABIN system, named CABINlib. We are developing VEGAS not only to analyze the gene expression data but also to analyze many kind of biological information, biological simulation, visualization, and exhibition.

Photos are followings: the immersive projection display, named CABIN, the virtual environment for some specific gene selection using gene expression data, the computer graphic of a cell in the virtual environment, and the expression imbalance map (EIM).

Immersive Projection Display : CABIN

The Virtual Environment for Specific Gene Selection using Gene Expression Data with VEGAS

Computer Graphics of a Cell in the Virtual Environment

Expression Imbalance Map

 

References

  • Kunihiro Nishimura, Koji Abe, Shumpei Ishikawa, Shuichi Tsutsumi, Hiroyuki Aburatani, Koichi Hirota, and Michitaka Hirose, "Virtual Environment Design Guidelines for Gene Expression Analysis: The Utility of a Lab Bench Metaphor and a Road Metaphor", IEEE Virtual Reality Conference 2004, pp.247-248, Chicago, USA, 2004.3.

  • Makoto Kano, Kunihiro Nishimura, Shuichi Tsutsumi, Hiroyuki Aburatani, Koichi Hirota and Michitaka Hirose, "Cluster Overlap Distribution Map: Visualization for Gene Expression Analysis Using Immersive Projection Technology", Presence: Teleoperators and Virtual Environments, Vol.12, Issue.1, pp.96-109, 2003.

  • Makoto Kano, Kunihiro Nishimura, Shumpei Ishikawa, Shuichi Tsutsumi, Koichi Hirota, Michitaka Hirose and Hiroyuki Aburatani, "Expression Imbalance Map: A New Visualization Method for Detection of mRNA Expression Imbalance Regions", Physiol. Genomics, Vol.13, pp.31-46, 2003.

Immersive Projection Display : CABIN

CABIN (Computer Augmented Booth for Image Navigation) is an immersive multi-screen display with five screens. CABIN's features include the use of tempered glass as a floor screen and the capability to render both CG and real images. The five-screen-configuration is expected to provide a wider field of view and broader work space in observing virtual space. The distortion of the virtual space displayed in CABIN has also been investigated, and was prove to be very small. CABIN is at IML (Intelligent Modeling Laboratory) in the Hongo campus. We also developed SCABIN that consists of three screens (two walls and floor) at RCAST (Research Center for Advanced Science and Technology) in Komaba-Research campus.

Reference

  • Michitaka Hirose, Tetsuro Ogi, Shohei Ishiwata, Toshio Yamada, "Development and evaluation of the CABIN immersive multiscreen display", Systems and Computers in Japan, Vol.30(1), pp.13-22, 1999.

Applications of CABIN

We developed many applications using CABIN. Some applications are simulations of theory of relativity, molecular vibration, and fluid dynamics. Other applications are visualization of genome data, biological information, network information, and software. We also developed techniques to make a realistic virtual world, such as using IBR (Image Based Rendering). We have developed virtual marunouchi, and the earth. You can see the earth seamlessly from moon to the ground with our application. We also have developped the way to make live stereo video avatar. We have integrated sound and haptics into CABIN. This way, you can touch the visualized objects and hear sounds from 3-dimensional directions.

Last Updated on May. 4th, 2004.