Christian Klukas1, Falk Schreiber. 1. Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany.
Abstract
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.
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.
Authors: Alexander Lex; Christian Partl; Denis Kalkofen; Marc Streit; Samuel Gratzl; Anne Mai Wassermann; Dieter Schmalstieg; Hanspeter Pfister Journal: IEEE Trans Vis Comput Graph Date: 2013-12 Impact factor: 4.579
Authors: Hendrik Rohn; Astrid Junker; Anja Hartmann; Eva Grafahrend-Belau; Hendrik Treutler; Matthias Klapperstück; Tobias Czauderna; Christian Klukas; Falk Schreiber Journal: BMC Syst Biol Date: 2012-11-10
Authors: Ghia M Euskirchen; Raymond K Auerbach; Eugene Davidov; Tara A Gianoulis; Guoneng Zhong; Joel Rozowsky; Nitin Bhardwaj; Mark B Gerstein; Michael Snyder Journal: PLoS Genet Date: 2011-03-03 Impact factor: 5.917