A Constrained, Force-Directed Layout Algorithm for Biological Pathways
Genc, Burkay and Dogrusoz, Ugur (2004) A Constrained, Force-Directed Layout Algorithm for Biological Pathways. In: Graph Drawing 11th International Symposium, GD 2003, September 21-24, 2003, Perugia, Italy , pp. 314-319 (Official URL: http://dx.doi.org/10.1007/978-3-540-24595-7_29).
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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.
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