J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes.

Ham,  Sung Il; Song,  Eun Ha; Yang,  San Duk; Thong,  Chin Ting; Rhie,  Arang; Galbadrakh,  Bulgan; Lee,  Kyung Eun; Park,  Hyun Seok; Lee,  San Ho

doi:2009.7.3.171

Genomics Inform > Volume 7(3); 2009 > Article

Note

Genomics & Informatics 2009;7(3): 171-174.

DOI: https://doi.org/10.5808/gi.2009.7.3.171

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. neo@ewha.ac.kr
²Department of Architectural Engineering, Yonsei University, Seoul 120-749, Korea.

Abstract

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