Bioinformatics Visualization and Integration with Open Standards: The Bluejay Genomic Browser

Issue title: DAGSTUHL SEMINAR "INTEGRATIVE BIOINFORMATICS"

Article type: Research Article

Authors: Turinsky, Andrei L. | Ah-Seng, Andrew C. | Gordon, Paul M.K. | Stromer, Julie N. | Taschuk, Morgan L. | Xu, Emily W. | Sensen, Christoph W.

Affiliations: University of Calgary, Faculty of Medicine, Sun Center of Excellence for Visual Genomics, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1

Note: [] Corresponding author. E-mail: [email protected]

Abstract: We have created a new Java™-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs; an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet; and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a local stand-alone application, with or without connection to the Internet. It is available free of charge and as open source via http://bluejay.ucalgary.ca.

Keywords: bioinformatics, visualization, open standards, eXtensible Markup Language (XML), Scalable Vector Graphics (SVG), Java™, BioMOBY web services, Bluejay

Journal: In Silico Biology, vol. 5, no. 2, pp. 187-198, 2005