Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes

  • Ham, Sung-Il (Department of Architectural Engineering, Yonsei University) ;
  • Song, Eun-Ha (Department of Computer Science, Ewha Womans University) ;
  • Yang, San-Duk (Department of Computer Science, Ewha Womans University) ;
  • Thong, Chin-Ting (Department of Computer Science, Ewha Womans University) ;
  • Rhie, Arang (Department of Computer Science, Ewha Womans University) ;
  • Galbadrakh, Bulgan (Department of Computer Science, Ewha Womans University) ;
  • Lee, Kyung-Eun (Department of Computer Science, Ewha Womans University) ;
  • Park, Hyun-Seok (Department of Computer Science, Ewha Womans University) ;
  • Lee, San-Ho (Department of Computer Science, Ewha Womans University)
  • Published : 2009.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in two- and a-half dimensions (2.5D) as an alternative to three-dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.

Keywords

References

  1. Baur, M., Brandes, U., Gaertler, M., and Wagner, D. (2004). Drawing the as graph in 2.5 dimensions, proceeding of graph drawing. Lecture Notes in Computer Science 3383, 43-48
  2. Song, E.H., Ham, S.I., Yang, S.D., Rhie, A., Park, H.S., and Lee, S.H. (2008). J2dPathway: A global metabolic pathway viewer with node abstracting features. Genomics Inform. 6, 68-71 https://doi.org/10.5808/GI.2008.6.2.068
  3. Song, E.H. (2009). 2.5D metabolic pathway drawing modules based on 2-layered layout (in Korean). Journal of KIISE: Computer Systems and Theory (to be submitted)
  4. Iragne, F., Nikolski, M., Mathieu. B., Auber, D., and Sherman, D. (2005). ProViz: protein interaction visualization and exploration. Bioinform. 21, 272-274 https://doi.org/10.1093/bioinformatics/bth494
  5. Rojdestvenski, I. (2003). VRML metabolic network visualizer. Comp. Bio. Med . 33, 169-182 https://doi.org/10.1016/S0010-4825(02)00062-8
  6. Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P.A., Weing, W., Wilbur, W.J., Hatzivassiloglou, V., and Friedman, C. (2004). GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Informat . 37, 43-53 https://doi.org/10.1016/j.jbi.2003.10.001
  7. Yang, Y., Engin, L., Wurtele, E.S., Cruz-Neira, C., and Dickerson, J.A. (2005). Integration of metabolic networks and gene expression in virtual reality. Bioinform . 21, 3645-3650 https://doi.org/10.1093/bioinformatics/bti581
  8. Wiese, R., Iglsperger, M., and Schabert, P. (2000). They Files graph library: documentation and code. http://www-pr.informatik.uni-tuebingen.de/yfiles