JBrowse: a next-generation genome browser.

By Mitchell Skinner, A. Uzilov, Lincoln D. Stein, C. Mungall, I. Holmes. Genome Research, 2009

700 citations recorded by the source corpus.

We describe an open source, portable, JavaScript-based genome browser, JBrowse, that can be used to navigate genome annotations over the web. JBrowse helps preserve the user's sense of location by avoiding discontinuous transitions, instead offering smoothly animated panning, zooming, navigation, and track selection. Unlike most existing genome browsers, where the genome is rendered into images on the webserver and the role of the client is restricted to displaying those images, JBrowse distributes work between the server and client and therefore uses significantly less server overhead than previous genome browsers. We report benchmark results empirically comparing server- and client-side rendering strategies, review the architecture and design considerations of JBrowse, and describe a simple wiki plug-in that allows users to upload and share annotation tracks.

Subfields: Artificial Intelligence, Information Systems, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/693f00e6dab7b4b289640df6cf96eae872f3cf0f

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Citations in the corpus

A beginner's guide to eukaryotic genome annotation (2012, methodology): “They can also directly edit the gene models using the Apollo genome browser and JBROWSE.”
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, background): “Three-dimensional objects are often used for representing protein structures [1, 2], one-dimensional tracks for genome sequences [3, 4], force-directed graphs for interaction networks [5], trees for phylogenetic relationships [6, 7].”
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data (2016, methodology): “To visualize our various ChIP-seq datasets, we used Jbrowse (38), which was a fast and embeddable genome browser built completely with JavaScript and HTML5, to construct the ChIPBase genome browser.”
The Sol Genomics Network (SGN)—from genotype to phenotype to breeding (2014, methodology): “SGN has provided this functionality in the past using the GBrowse system (26), but recently added the newer JBrowse (27), which offers a more modern and fluid user experience.”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, methodology): “File 1 can be used to export the annotation results to any GFF3-compatible software tools, such as Chado [27], GBrowse [28], JBrowse [29], Apollo [30], and etc. for storage, presentation and editing.”
seqMINER: an integrated ChIP-seq data interpretation platform (2010, background): “…that allow: annotation of genomic features present in the neighbourhood of the relevant enrichment signals (5–7), detection and de novo deﬁnition of consensus DNA motifs (6), cross and compare information from distinct datasets (8) and comprehensive visualization of the obtained GW results (9–11).”
JBrowse: a dynamic web platform for genome visualization and analysis (2016, methodology): “The earliest version of JBrowse was a dynamic HTML application with a JavaScript client, reliant on server-side Bioperl components that were largely inherited from GBrowse [1].”
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants (2018, background): “Furthermore, Peak Browse helps users restrict their genomic regions of interest, and each binding sites with gene structures can be visualized in the JBrowse genome browser (Figure 1E) (35).”
SNP-Seek database of SNPs derived from 3000 rice genomes (2014, methodology): “To browse and visualize genes and SNPs in the rice genome, we integrated the JBrowse genome browser (11) as a feature of our site.”
The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies (2017, positive): “and embedded in the JBrowse genome browser (Skinner et al., 2009) to visualize the mutations.”
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data (2016, methodology): “Recently, to provide access to the growing number of datasets from experiments that use highthroughput sequencing technologies, we have deployed the JBrowse genome browser (35).”
Mouse Genome Database (MGD) 2019 (2018, background): “org/), a JavaScriptbased interactive genome browser with multiple features for navigation and track selection (14).”
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species (2011, methodology): “1, box 1) provides the compiled genomes (closed and incomplete, chromosomal and plasmid) for a given taxon, with statistics for all three different annotation methods and direct links to an interactive genome browser based on JBrowse (37, 38).”
The Genome 10K Project: A Way Forward (2015, neutral): “JBrowse: a next-generation genome browser.”
Rice SNP-seek database update: new SNPs, indels, and queries (2016, background): “This is a significant update to the JBrowse genome browser (22) since our first release.”