Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Soh, Jung; Gordon, Paul M.; Taschuk, Morgan; Dong, Anguo; Ah-Seng, Andrew C.; Turinsky, Andrei L.; Sensen, Christoph Wilhelm

doi:10.1186/1471-2105-9-450

Cited by 9 publications

(6 citation statements)

References 20 publications

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“…This system is currently in beta test and may be accessed through http://nif.nih.gov. In the same way, Sho and colleagues [13] developed XML-based genomic information and provided scalable vector graphics output named Blujay for genome annotation. They incorporated the gene expression information, comparative analysis with an unlimited number of other genomes in the same view, numerous display customization features, GPS-style waypoints for marking multiple points of interest on a genome and user relevance feedback of annotated genes or textual items.…”

Section: Recent Prospectus Using Xmlmentioning

confidence: 99%

“…They incorporated the gene expression information, comparative analysis with an unlimited number of other genomes in the same view, numerous display customization features, GPS-style waypoints for marking multiple points of interest on a genome and user relevance feedback of annotated genes or textual items. [13] They have also developed a user friendly system based on XML that enables end-users who use a quality labeled software package, to automatically produce all the legally necessary documents concerning the registry of physiotherapy electronic healthcare records. Gil-Redondo R [14] developed the user-configurable XML virtual screening data management on an integrated platform that stores ligand information, modular and pluggable architecture.…”

Section: Recent Prospectus Using Xmlmentioning

confidence: 99%

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Techniques for integrating -omics data

Akula¹,

Miriyala²,

Thota³

et al. 2009

Bioinformation

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Abstract:The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.

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Section: Recent Prospectus Using Xmlmentioning

confidence: 99%

Section: Recent Prospectus Using Xmlmentioning

confidence: 99%

Techniques for integrating -omics data

Akula¹,

Miriyala²,

Thota³

et al. 2009

Bioinformation

View full text Add to dashboard Cite

show abstract

“…Bluejay is a stand‐alone genome browser, which can be used to visualize genome annotation with abundant features for customized visualization, intuitive navigation, and data integration (Turinsky et al, ; Soh et al, ). Unlike the UCSC Genome Browser (Fujita et al, ; UNIT here), Ensembl Genome Browser (Flicek et al, ; UNIT here), or the NCBI Map Viewer (Feolo et al, ; UNIT here), Bluejay can be locally installed on personal computers (Windows PC and Macintosh) or servers as a stand‐alone application.…”

Section: Introductionmentioning

confidence: 99%

The Bluejay Genome Browser

Soh

Gordon

Sensen

2012

CP in Bioinformatics

Self Cite

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The Bluejay genome browser is a stand‐alone visualization tool for the multi‐scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication‐quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context‐sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in‐depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform‐independent and is freely available from http://bluejay.ucalgary.ca. Curr. Protoc. Bioinform. 37:10.9.1‐10.9.23. © 2012 by John Wiley & Sons, Inc.

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“…The diversity of tools available for visualizing and browsing genomic data has increased dramatically over the last years: Bluejay [ 1 ], GenoMap [ 2 ], GenomeComp [ 3 ], GenomeViz [ 4 ], DiProGB [ 5 ] to cite but a few. Projects aiming at supplanting or complementing current genomes browsers (GBs) are blooming as well.…”

Section: Introductionmentioning

confidence: 99%

CompaGB: An open framework for genome browsers comparison

et al. 2011

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BackgroundTools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.FindingsTo assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...ConclusionsThe framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.

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Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Cited by 9 publications

References 20 publications

Techniques for integrating -omics data

Techniques for integrating -omics data

The Bluejay Genome Browser

CompaGB: An open framework for genome browsers comparison

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