Graph drawing by force-directed placement
Software—Practice & Experience
Graph Drawing: Algorithms for the Visualization of Graphs
Graph Drawing: Algorithms for the Visualization of Graphs
Constraint-Based Spring-Model Algorithm for Graph Layout
GD '95 Proceedings of the Symposium on Graph Drawing
GD '95 Proceedings of the Symposium on Graph Drawing
GD '96 Proceedings of the Symposium on Graph Drawing
Integration of Declarative and Algorithmic Approaches for Layout Creation
GD '94 Proceedings of the DIMACS International Workshop on Graph Drawing
A Simple and Unified Method for Drawing Graphs: Magnetic-Spring Algorithm
GD '94 Proceedings of the DIMACS International Workshop on Graph Drawing
IEEE Computer Graphics and Applications
A new algorithm for removing node overlapping in graph visualization
Information Sciences: an International Journal
Mental map preserving graph drawing using simulated annealing
Information Sciences: an International Journal
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Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular 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 visualization and analysis toolkit named Patika, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. Patika version 1.0 beta is available upon request at http://www.patika.org.