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)


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.


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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

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