A Compound Graph Layout Algorithm for Biological Pathways
Dogrusoz, Ugur and Giral, Erhan and Cetintas, Ahmet and Civril, Ali and Demir, Emek (2004) A Compound Graph Layout Algorithm for Biological Pathways. In: Graph Drawing 12th International Symposium, GD 2004, September 29-October 2, 2004, New York, NY, USA , pp. 442-447 (Official URL: http://dx.doi.org/10.1007/978-3-540-31843-9_45).
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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.
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