A compound graph layout algorithm for biological pathways

Authors:
Ugur Dogrusoz;Erhan Giral;Ahmet Cetintas;Ali Civril;Emek Demir
Affiliations:
Center for Bioinformatics, Bilkent University, Ankara, Turkey;Center for Bioinformatics, Bilkent University, Ankara, Turkey;Center for Bioinformatics, Bilkent University, Ankara, Turkey;Center for Bioinformatics, Bilkent University, Ankara, Turkey;Center for Bioinformatics, Bilkent University, Ankara, Turkey
Venue:
GD'04 Proceedings of the 12th international conference on Graph Drawing
Year:
2004

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Abstract

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 compartmental 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.