A constrained, force-directed layout algorithm for biological pathways

Genc B. , Dogrusoz U.

GRAPH DRAWING, cilt.2912, ss.314-319, 2004 (SCI İndekslerine Giren Dergi) identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 2912
  • Basım Tarihi: 2004
  • Dergi Adı: GRAPH DRAWING
  • Sayfa Sayıları: ss.314-319


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.