A constrained, force-directed layout algorithm for biological pathways

Genc B., Dogrusoz U.

GRAPH DRAWING, vol.2912, pp.314-319, 2004 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Volume: 2912
  • Publication Date: 2004
  • Journal Name: GRAPH DRAWING
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED)
  • Page Numbers: pp.314-319
  • Hacettepe University Affiliated: No


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.