A Constrained, Force-Directed Layout Algorithm for Biological Pathways

  • Burkay Genc
  • Ugur Dogrusoz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2912)

Abstract

We present a new elegant algorithm for layout of biological signaling pathways. It uses a force-directed layout scheme, taking into account directional and regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA and results with respect to computational complexity and quality of the layout have been found satisfactory.

References

  1. 1.
    Becker, M.Y., Rojas, I.: A graph layout algorithm for drawing metabolic pathways. Bioinformatics 17, 461–467 (2001)CrossRefGoogle Scholar
  2. 2.
    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. To appear in Bioinformatics (2003)Google Scholar
  3. 3.
    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
  4. 4.
    Dogrusoz, U., Feng, Q., Madden, B., Doorley, M., Frick, A.: Graph visualization toolkits. IEEE Computer Graphics and Applications 22(1), 30–37 (2002)CrossRefGoogle Scholar
  5. 5.
    Fruchterman, T.M.J., Reingold, E.M.: Graph drawing by force-directed placement. Software Practice and Experience 21(11), 1129–1164 (1991)CrossRefGoogle Scholar
  6. 6.
    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
  7. 7.
    Sugiyama, K., Misue, K.: A simle and unified method for drawing graphs: Magnetic-spring algorithm. In: Tamassia, R., Tollis, I.G. (eds.) GD 1994. LNCS, vol. 894, pp. 364–375. Springer, Heidelberg (1995)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Burkay Genc
    • 1
  • Ugur Dogrusoz
    • 1
  1. 1.Computer Engineering Department and Center for BioinformaticsBilkent UnivAnkaraTurkey

Personalised recommendations