A Novel Grid-Based Visualization Approach for Metabolic Networks with Advanced Focus&Context View

  • Markus Rohrschneider
  • Christian Heine
  • André Reichenbach
  • Andreas Kerren
  • Gerik Scheuermann
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5849)

Abstract

The universe of biochemical reactions in metabolic pathways can be modeled as a complex network structure augmented with domain specific annotations. Based on the functional properties of the involved reactions, metabolic networks are often clustered into so-called pathways inferred from expert knowledge. To support the domain expert in the exploration and analysis process, we follow the well-known Table Lens metaphor with the possibility to select multiple foci.

In this paper, we introduce a novel approach to generate an interactive layout of such a metabolic network taking its hierarchical structure into account and present methods for navigation and exploration that preserve the mental map. The layout places the network nodes on a fixed rectilinear grid and routes the edges orthogonally between the node positions. Our approach supports bundled edge routes heuristically minimizing a given cost function based on the number of bends, the number of edge crossings and the density of edges within a bundle.

References

  1. 1.
    Misue, K., Eades, P., Lai, W., Sugiyama, K.: Layout Adjustment and the Mental Map. Journal of Visual Languages and Computing 6(2), 183–210 (1995)CrossRefGoogle Scholar
  2. 2.
    Rao, R., Card, S.K.: The table lens: merging graphical and symbolic representations in an interactive focus + context visualization for tabular information. In: Proceedings of the SIGCHI conference on Human factors in computing systems, pp. 318–322. ACM, New York (1994)Google Scholar
  3. 3.
    Karp, P.D., Paley, S.M., Romero, P.: The Pathway Tools software. Bioinformatics 18, 225–232 (2002)Google Scholar
  4. 4.
    Hu, Z., Mellor, J., Wu, J., DeLisi, C.: VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 5(1), e17 (2004)CrossRefGoogle Scholar
  5. 5.
    Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Gen. Res. 13(11), 2498–2504 (2003)CrossRefGoogle Scholar
  6. 6.
    Schreiber, F.: High Quality Visualization of Biochemical Pathways in BioPath. In Silico Biology 2(2), 59–73 (2002)Google Scholar
  7. 7.
    Karp, P.D., Ouzounis, C.A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahren, D., Tsoka, S., Darzentas, N., Kunin, V., Lopez-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 33(19), 6083–6089 (2005)CrossRefGoogle Scholar
  8. 8.
    DiBattista, G., Eades, P., Tamassia, R., Tollis, I.G.: Graph Drawing: Algorithms for the Visualization of Graphs. Prentice Hall, New Jersey (1999)Google Scholar
  9. 9.
    Nicholson, D.E.: Metabolic Pathways Map (Poster). Sigma Chemical Co., St. Louis (1997)Google Scholar
  10. 10.
    Lungu, M., Xu, K.: Biomedical Information Visualization. In: Kerren, A., Ebert, A., Meyer, J. (eds.) GI-Dagstuhl Research Seminar 2007. LNCS, vol. 4417, pp. 311–342. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  11. 11.
    Kerren, A., Ebert, A., Meyer, J.: Human-Centered Visualization Environments. In: Kerren, A., Ebert, A., Meyer, J. (eds.) GI-Dagstuhl Research Seminar 2007. LNCS, vol. 4417, pp. 1–9. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  12. 12.
    Kerren, A.: Interactive Visualization and Automatic Analysis of Metabolic Networks – A Project Idea. Technical Report, Institute of Computer Graphics and Algorithms, Vienna University of Technology, Austria (2003)Google Scholar
  13. 13.
    Albrecht, M., Kerren, A., Klein, K., Kohlbacher, O., Mutzel, P., Paul, W., Schreiber, F., Wybrow, M.: On Open Problems in Biological Network Visualization. In: Proc. of the 17th International Symposium on Graph Drawing, Chicago, USA. Springer, Heidelberg (2009) (to appear)Google Scholar
  14. 14.
    Albrecht, M., Kerren, A., Klein, K., Kohlbacher, O., Mutzel, P., Paul, W., Schreiber, F., Wybrow, M.: A Graph-drawing Perspective to Some Open Problems in Molecular Biology. Technical report TR08-01-003, Lehrstuhl XI für Algorithm Engineering, Fakultät für Informatik, TU Dortmund, Germany (2008)Google Scholar
  15. 15.
    Brandes, U., Dwyer, T., Schreiber, F.: Visualizing Related Metabolic Pathways in Two and a Half Dimensions. In: Liotta, G. (ed.) GD 2003. LNCS, vol. 2912, pp. 111–122. Springer, Heidelberg (2004)Google Scholar
  16. 16.
    Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/kegg/
  17. 17.
    Klukas, C., Schreiber, F.: Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 23(3), 344–350 (2007)CrossRefGoogle Scholar
  18. 18.
    Michal, G.: Biochemical Pathways: Biochemie-Atlas. Spektrum Akademischer Verlag, Heidelberg (1999)Google Scholar
  19. 19.
    Saraiya, P., North, C., Duca, K.: Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Information Visualization 4(3), 191–205 (2005)CrossRefGoogle Scholar
  20. 20.
    Shneiderman, B.: The Eyes Have It: A Task by Data Type Taxonomy for Information Visualizations. In: VL, pp. 336–343 (1996)Google Scholar
  21. 21.
    Streit, M., Kalkusch, M., Kashofer, K., Schmalstieg, D.: Navigation and Exploration of Interconnected Pathways. Eurographics / IEEE-VGTC Symposium on Visualization 27(3) (2008)Google Scholar
  22. 22.
    Kamada, T., Kawai, S.: An algorithm for drawing general undirected graphs. Inf. Process. Lett. 31(1), 7–15 (1989)MATHCrossRefMathSciNetGoogle Scholar
  23. 23.
    Kirkpatrick, S., Gelatt, C.D., Vecchi, M.P.: Optimization by simulated annealing. Science 220, 671–680 (1983)CrossRefMathSciNetGoogle Scholar
  24. 24.
    Hart, P.E., Nilsson, N.J., Raphael, B.: A Formal Basis for the Heuristic Determination of Minimum Cost Paths. IEEE Transactions on Systems Science and Cybernetics 4(2), 100–107 (1968)CrossRefGoogle Scholar
  25. 25.
    Batini, C., Nardelli, E., Tamassia, R.: A Layout Algorithm for Data Flow Diagrams. IEEE Trans. Software Eng. 12(4), 538–546 (1986)Google Scholar
  26. 26.
    Kaufmann, M., Wagner, D. (eds.): Drawing Graphs. LNCS, vol. 2025. Springer, Heidelberg (2001)MATHGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Markus Rohrschneider
    • 1
  • Christian Heine
    • 1
  • André Reichenbach
    • 1
  • Andreas Kerren
    • 2
  • Gerik Scheuermann
    • 1
  1. 1.Department of Computer ScienceUniversity of LeipzigGermany
  2. 2.School of Mathematics and Systems EngineeringVäxjö UniversitySweden

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