Visual data mining of genomic databases by immersive graph-based exploration

ABSTRACT

Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process for biologists, using usually data mining approaches. However, it is difficult to deals with these genomic information using actual bioinformatics data mining tools, because data are heterogeneous, huge in quantity and geographically distributed. In this paper, we present a new approach between data mining and virtual reality visualization, called visual data mining. Indeed Virtual Reality becomes ripe, with efficient display devices and intuitive interaction in an immersive context. Moreover, biologists use to work with 3D representation of their molecules, but in a desktop context. We present a software solution, Genome3DExplorer, which addresses the problem of genomic data visualization, of scene management and interaction. This solution is based on a well-adapted graphical and interaction paradigm, where local and global topological characteristics of data are easily visible, on the contrary to traditional genomic database browsers, always focused on the zoom and details level.

REFERENCES

• 1: Damien Touraine , Patrick Bourdot , Yacine Bellik , Laurence Bolot, A framework to manage multimodal fusion of events for advanced interactions within virtual environments, Proceedings of the workshop on Virtual environments 2002, May 30-31, 2002, Barcelona, Spain
• 2: J. Hérisson , P. E. Gros , N. Férey , O. Magneau , R. Gherbi, DNA in Virtuo visualization and exploration of 3D genomic structures, Proceedings of the 3rd international conference on Computer graphics, virtual reality, visualisation and interaction in Africa, November 03-05, 2004, Stellenbosch, South Africa [doi>10.1145/1029949.1029955]
• 3: Greg Humphreys , Mike Houston , Ren Ng , Randall Frank , Sean Ahern , Peter D. Kirchner , James T. Klosowski, Chromium: a stream-processing framework for interactive rendering on clusters, Proceedings of the 29th annual conference on Computer graphics and interactive techniques, July 23-26, 2002, San Antonio, Texas
• 4: Eisen, M. B. Spellman, P. T. Brown, P. O. and Botstein, D. 1998. Cluster Analysis and Display of Genome-wide Expression Patterns. In proceedings of the National Academy of Sciences, of the USA, 95, 14863--14868.
• 5: Makoto Kano , Shuichi Tsutsumi , Kunihiro Nishimura , Hiroyuki Aburatani , Koichi Hirota , Michitaka Hirose, Visualization for Genome Function Analysis Using Immersive Projection Technology, Proceedings of the IEEE Virtual Reality Conference 2002, p.224, March 24-28, 2002
• 6: Ashish Sharma , Xinlian Liu , Paul Miller , Aiichiro Nakano , Rajiv K. Kalia , Priya Vashishta , Wei Zhao , Timothy J. Campbell , Andy Haas, Immersive and Interactive Exploration of Billion-Atom Systems, Proceedings of the IEEE Virtual Reality Conference 2002, p.217, March 24-28, 2002
• 7: I. Rojdestvenski , F. Pettersson , D. Modjeska, Sequence World: A Genetics Database in Virtual Reality, Proceedings of the International Conference on Information Visualisation, p.513, July 19-21, 2000
• 8: Eades, P. 1984. A Heuristic for Graph Drawing. Congressus Nutnerantiunt, 42, 149--160.
• 9: Thomas M. J. Fruchterman , Edward M. Reingold, Graph drawing by force-directed placement, Software—Practice & Experience, v.21 n.11, p.1129-1164, Nov. 1991 [doi>10.1002/spe.4380211102]

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.5 INFORMATION INTERFACES AND PRESENTATION (I.7)
      H.5.1 Multimedia Information Systems
          Subjects: Artificial, augmented, and virtual realities

Additional Classification:
  I. Computing Methodologies
  I.3 COMPUTER GRAPHICS
      I.3.7 Three-Dimensional Graphics and Realism
          Subjects: Virtual reality

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES

Keywords:
genomic data, graph-based visualization, human-computer interaction, immersive exploration, virtual reality