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In Silico Biology 5, 0018 (2004); ©2004, Bioinformation Systems e.V.  

Bioinformatics visualization and integration with open standards: The Bluejay genomic browser

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

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

* Corresponding author; Email:

Edited by E. Wingender; received October 07, 2004; revised and accepted November 18, 2004; published November 27, 2004


We have created a new JavaTM-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

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