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.


Spring Force Repulsion Force Layout Algorithm Force Versus Pathway Integration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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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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