Abstract
BackgroundThe Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.ResultsBluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.ConclusionBluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.
Highlights
The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research
This allows the user to seamlessly link from the visualized data, internally represented as a Document Object Model (DOM) [4], to Moby-compliant Web services by embedding the Seahawk Moby client [5]
Bluejay comes with a bookmark that lets the user access genome data annotated using the MAGPIE system, which uses Gene Ontology (GO) [14] as the gene classification system
Summary
Bluejay supports Moby [3], a protocol consisting of a common XML object ontology for biological entities and a standardized request/response mechanism for automating Web-based analysis. This allows the user to seamlessly link from the visualized data, internally represented as a Document Object Model (DOM) [4], to Moby-compliant Web services by embedding the Seahawk Moby client [5]. The TIGR MultiExperiment Viewer (MeV) [6] is integrated into Bluejay such that it functions as a fully embedded module (see Additional file 1) Through this integration, Bluejay can show gene expression values in a genomic context, enabling biologists to draw additional inferences from gene expression analyses (e.g., operon structures). If an XML file with a large amount of data is requested, the proxy performs data skeletonization on-the-fly, using an eXtensible Stylesheet Language Transformation (XSLT) [7], which allows Bluejay to run on a memory-limited computing environment (and as an applet)
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