Logo

Login

A Constrained, Force-Directed Layout Algorithm for Biological Pathways

Genc, Burkay and Dogrusoz, Ugur (2004) A Constrained, Force-Directed Layout Algorithm for Biological Pathways. [Conference Paper]

Full text not available from this repository.

Abstract

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.

Item Type:Conference Paper
Classifications:S Software and Systems > S.120 Visualization
ID Code:461
Deposited By:Selbach, Anna
Deposited On:09 Dec 2004
Last Modified:25 Jan 2010 11:16
Alternative Locations:http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2912&spage=314

Repository Staff Only: item control page

References

M. Y. Becker and I. Rojas. A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17:461-467, 2001.

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, and R. Cetin-Atalay. An ontology for colaborative cinstruction and analysis of cellular pathways. To appear in Bioinformatics, 2003.

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay and M. Ozturk. PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics, 18(7):996-1003, 2002.

U. Dogrusoz, Q. Feng, B. Madden, M. Doorley, and A. Frick. Graph visualizationk toolkits. IEEE Computer Graphics and Applications, 22(1):30-37, January/February 2002.

T. M. J. Fruchterman and E. M. Reingold. Graph drawing by force-directed placement. Software Practice and Experience, 21(11):1164, 1991.

P. D. Karp and S. Paley. Automated drawing of metabolic pathways. In Third International Conference on Bioinformatics and Genome Research, pages 225-238, Tallahassee, Florida, June 1994.

K. Sugiyama and K. Misue. A simple and unified method for drawing graphs: Magnetic-spring algorithm. In R. Tamassia and I. Tollis, editors, Graph Drawing (proc. GD '94), volume 894 of Lecture Notes in Computer Science, pages 364-375. Springer-Verlag, 1995.

GDEA is powered by EPrints 3 which is developed by the School of Electronics and Computer Science at the University of Southampton. More information and software credits.