Visual network analysis of dynamic metabolic pathways
ISVC'10 Proceedings of the 6th international conference on Advances in visual computing - Volume Part I
CarGene: Characterisation of sets of genes based on metabolic pathways analysis
International Journal of Data Mining and Bioinformatics
A novel grid-based visualization approach for metabolic networks with advanced focus&context view
GD'09 Proceedings of the 17th international conference on Graph Drawing
Visual analysis of bipartite biological networks
EG VCBM'08 Proceedings of the First Eurographics conference on Visual Computing for Biomedicine
Visualizing genome expression and regulatory network dynamics in genomic and metabolic context
EuroVis'08 Proceedings of the 10th Joint Eurographics / IEEE - VGTC conference on Visualization
Navigation and exploration of interconnected pathways
EuroVis'08 Proceedings of the 10th Joint Eurographics / IEEE - VGTC conference on Visualization
Toward the role of interaction in visual analytics
Proceedings of the Winter Simulation Conference
Guiding the interactive exploration of metabolic pathway interconnections
Information Visualization
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Motivation: The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database is a very valuable information resource for researchers in the fields of life sciences. It contains metabolic and regulatory processes in the form of wiring diagrams, which can be used for browsing and information retrieval as well as a base for modeling and simulation. Thus it helps in understanding biological processes and higher-order functions of biological systems. Currently the KEGG website uses semi-static visualizations for the presentation and navigation of its pathway information. While this visualization style offers a good pathway presentation and navigation, it does not provide some of the possibilities related to dynamic visualizations, most importantly, the creation and visualization of user-specific pathways. Results: This paper presents methods for the dynamic visualization, interactive navigation and editing of KEGG pathway diagrams. These diagrams, given as KEGG Markup Language (KGML) files, can be visually explored using novel approaches combining semi-static and dynamic visualization, but also edited or even newly created and then exported into KGML files. Availability: KGML-ED, a program implementing the presented methods, is available free of charge to the scientific community at http://kgml-ed.ipk-gatersleben.de Contact: schreibe@ipk-gatersleben.de