A compound graph layout algorithm for biological pathways

Ugur Dogrusoz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Research output: Contribution to journalConference articlepeer-review

27 Scopus citations


We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented within PATIKA, a pathway analysis tool for drawing complicated biological pathways with compartimental constraints and arbitrary nesting relations to represent molecular complexes and pathway abstractions. Experimental results show that execution times and quality of the produced drawings with respect to commonly accepted layout criteria and pathway drawing conventions are quite satisfactory.

Original languageEnglish (US)
Pages (from-to)442-447
Number of pages6
JournalLecture Notes in Computer Science
StatePublished - 2004
Externally publishedYes
Event12th International Symposium on Graph Drawing, GD 2004 - New York, NY, United States
Duration: Sep 29 2004Oct 2 2004

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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