• Journal of KIISE:Software and Applications
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• v.34 no.5
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• pp.389-396
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• 2007

The comparison of metabolic pathway in different species is important in detecting a missing gene. There are many visualizations for metabolic pathway. However, Biologists need not only a simple path but also a visualization for comparison. K-Viz is a tool for visualization of metabolic pathway based on KEGG. To compare pathways in different species, K-Viz uses different color for path such as PathComp in KEGG and shows the table of path in pathway. K-Viz helps biologists to understand the comparison of metabolic pathways in different species.

• Journal of the Korea Society of Computer and Information
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• v.18 no.5
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• pp.95-102
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• 2013

In metabolomics, metabolic pathway is represented by well-displayed graph. Metabolic pathways, especially, have a complex binding structure, which makes the graphical representation hard to visualize. There is a problem that edge crossings exponentially increase as the number of nodes grows. To apply automatic graph layout techniques to the genome-scale metabolic flow of metabolism domains, it is very important to reduce unnecessary edge crossing on a metabolic pathway layout. we proposed a metabolic pathway layout algorithm based on 2-layer layout. Our algorithm searches any meaningful component existing in a pathway, such as circular components, highly connected nodes, and the components are drawn in upper layer. Then the remaining subgraphs except meaningful components are drawn in lower layer by utilizing a new radial layout algorithm. It reduces ultimately reduced the number of edge crossings. This algorithm is the basis of flexible analysis for metabolic pathways.

• Genomics & Informatics
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• v.2 no.4
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• pp.191-194
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• 2004

Exponentially increasing biopathway data in recent years provide us with means to elucidate the large-scale modular organization of the cell. Given the existing information on metabolic and regulatory networks, inferring biopathway information through scientific reasoning or data mining of large scale array data or proteomics data get great attention. Naturally, there is a need for a user-friendly system allowing the user to combine large and diverse pathway data sets from different resources. We built a data warehouse - BIOWAY - for analyzing and visualizing biological pathways, by integrating and customizing resources. We have collected many different types of data in regards to pathway information, including metabolic pathway data from KEGG/LIGAND, signaling pathway data from BIND, and protein information data from SWISS-PROT. In addition to providing general data retrieval mechanism, a successful user interface should provide convenient visualization mechanism since biological pathway data is difficult to conceptualize without graphical representations. Still, the visual interface in the previous systems, at best, uses static images only for the specific categorized pathways. Thus, it is difficult to cope with more complex pathways. In the BIOWAY system, all the pathway data can be displayed in computer generated graphical networks, rather than manually drawn image data. Furthermore, it is designed in such a way that all the pathway maps can be expanded or shrinked, by introducing the concept of super node. A subtle graphic layout algorithm has been applied to best display the pathway data.

• Genomics & Informatics
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• v.7 no.3
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• pp.171-174
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• 2009

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 two- and 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.

• Journal of the Korea Society of Computer and Information
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• v.18 no.6
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• pp.71-79
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• 2013

Metabolic pathway, represented by well-displayed graph, have a complex binding structure, which makes the graphical representation hard to visualize. To apply automatic graph layout techniques to the genome-scale metabolic flow of metabolism domains, it is very important to reduce unnecessary edge crossing on a metabolic pathway layout. we proposed a metabolic pathway layout algorithm based on 3-layer layout. Our algorithm searches any meaningful component existing in a pathway, such as circular components, highly connected nodes, and the components are drawn in middle layer. Then the remaining subgraphs except meaningful components are drawn in upper and lower layer by utilizing a new radial layout algorithm. It reduces ultimately reduced the number of edge crossings. Our algorithm solve the problem that edge crossings exponentially increase as the number of nodes grows.

• Genomics & Informatics
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• v.6 no.3
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• pp.147-152
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• 2008

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.

• Genomics & Informatics
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• v.7 no.3
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• pp.168-170
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• 2009

The explosion in biological data resulting from high-throughput experiments requires new software tools to manipulate and display pathways in a way that can integrate disparate sources of information. A visual Java-based CAD tool for drawing and annotating biological pathways with semiautomatic image-processing features is described in this paper. The result of the image-editing process is an XML file for the appropriate links. This tool integrates the pathway images and XML file sources. The system has facilities for linking graphical objects to external databases and is capable of reproducing existing visual representations of pathway maps.