A Compound Graph Layout Algorithm for Biological Pathways

  • Ugur Dogrusoz
  • Erhan Giral
  • Ahmet Cetintas
  • Ali Civril
  • Emek Demir
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3383)


We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented within Patika, a pathway analysis tool for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and pathway abstractions. Experimental results show that execution times and quality of the produced drawings with respect to commonly accepted layout criteria and pathway drawing conventions are quite satisfactory.


  1. 1.
    Becker, M.Y., Rojas, I.: A graph layout algorithm for drawing metabolic pathways. Bioinformatics 17, 461–467 (2001)CrossRefGoogle Scholar
  2. 2.
    Bertault, F.: Force-directed algorithm that preserves edge crossing properties. In: Kratochvil, J. (ed.) GD 1999. LNCS, vol. 1731, pp. 351–358. Springer, Heidelberg (1999)CrossRefGoogle Scholar
  3. 3.
    Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Ayaz, A., Gulesir, G., Nisanci, G., Cetin-Atalay, R.: An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics 20(3), 349–356 (2002)CrossRefGoogle Scholar
  4. 4.
    Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R., Ozturk, M.: PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 18(7), 996–1003 (2002)CrossRefGoogle Scholar
  5. 5.
    Di Battista, G., Eades, P., Tamassia, R., Tollis, I.G.: Graph Drawing, Algorithms for the Visualization of Graphs. Prentice-Hall, Englewood Cliffs (1999)MATHGoogle Scholar
  6. 6.
    Eades, P., Feng, Q., Lin, X.: Straight-line drawing algorithms for hierarchical graphs and clustered graphs. In: North, S. (ed.) GD 1996. LNCS, vol. 1190, pp. 113–128. Springer, Heidelberg (1997)Google Scholar
  7. 7.
    Fruchterman, T.M.J., Reingold, E.M.: Graph drawing by force-directed placement. Software Practice and Experience 21(11), 1129–1164 (1991)CrossRefGoogle Scholar
  8. 8.
    Fukuda, K., Takagi, T.: Knowledge representation of signal transduction pathways. Bioinformatics 17(9), 829–837 (2001)CrossRefGoogle Scholar
  9. 9.
    Genc, B., Dogrusoz, U.: A constrained, force-directed layout algorithm for biological pathways. In: Liotta, G. (ed.) GD 2003. LNCS, vol. 2912, pp. 349–356. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  10. 10.
    Sugiyama, K., Misue, K.: A Generic Compound Graph Visualizer/Manipulator: D-ABDUCTOR. In: Brandenburg, F.J. (ed.) GD 1995. LNCS, vol. 1027, pp. 500–503. Springer, Heidelberg (1996)CrossRefGoogle Scholar
  11. 11.
    Karp, P.D., Paley, S.: Automated drawing of metabolic pathways. In: Third International Conference on Bioinformatics and Genome Research, Tallahassee, Florida, June 1994, pp. 225–238 (1994)Google Scholar
  12. 12.
    Sander, G.: Layout of compound directed graphs. Technical Report A/03/96, University of Saarlandes, CS Dept., Saarbrücken, Germany (1996)Google Scholar
  13. 13.
    Schreiber, F.: High quality visualization of biochemical pathways in BioPath. Silico Biology 2(2), 59–73 (2002)Google Scholar
  14. 14.
    Sugiyama, K., Misue, K.: Visualization of structural information: Automatic drawing of compound digraphs. IEEE Transactions on Systems, Man and Cybernetics 21(4), 876–892 (1991)CrossRefMathSciNetGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Ugur Dogrusoz
    • 1
    • 2
  • Erhan Giral
    • 1
  • Ahmet Cetintas
    • 1
  • Ali Civril
    • 1
  • Emek Demir
    • 1
  1. 1.Center for BioinformaticsBilkent UniversityAnkaraTurkey
  2. 2.Tom Sawyer SoftwareOaklandUSA

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