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Genomics Inform > Volume 7(3); 2009 > Article
J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes.
Sung Il Ham, Eun Ha Song, San Duk Yang, Chin Ting Thong, Arang Rhie, Bulgan Galbadrakh, Kyung Eun Lee, Hyun Seok Park, San Ho Lee
1Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea.
2Department of Architectural Engineering, Yonsei University, Seoul 120-749, Korea.
The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in twoand- a-half dimensions (2.5D) as an alternative to three dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.
Keywords: metabolic pathways; pathway editor; visualization
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