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Draft:JBrowse

From Wikipedia, the free encyclopedia

JBrowse
DeveloperGeneric Model Organism Database project
Release2009; 17 years ago (2009)
Stable release
JBrowse 2 (see GitHub)
Operating systemCross-platform (web; desktop via Electron)
PlatformJavaScript, HTML5; TypeScript and React (JBrowse 2)
TypeGenome browser
LicenseApache License 2.0 (JBrowse 2); LGPL / Artistic License (JBrowse 1)
Websitejbrowse.org

JBrowse is a free and open-source genome annotation browser associated with the Generic Model Organism Database (GMOD) project. It is a JavaScript-based application that performs layout and rendering on the client, in contrast to earlier web-facing genome browsers such as GBrowse and the UCSC Genome Browser that ran on a web server and relied primarily on the Common Gateway Interface.[1][2] JBrowse and its successor JBrowse 2 are used by many model organism databases and other genomics resources to display genome annotations, read alignments, variants, and other genome-mapped data on the web.[3][4]

The original JBrowse application was introduced in 2009[1] as a JavaScript-based alternative to existing server-rendered genome browsers, with the goal of reducing server load and providing a more fluid user experience than existing CGI-based browsers. The second version of the software, JBrowse 2, was released in 2023 as a complete React-based rewrite, adding support for comparative genomics views (e.g. synteny and dot plots), structural variation inspection, and other view types.[4]

JBrowse is identified by the Alliance of Genome Resources as one of the core components of web-facing infrastructure for the eight model-organism knowledgebases maintained by the consortium.[3]

History

[edit]

Background and predecessors

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The Generic Model Organism Database project was established to develop open-source informatics tools that could be shared across model organism databases. An early genome browser produced by the project, GBrowse, was a Perl-based CGI application that has been described as the first portable web-based genome browser to achieve widespread adoption.[5][4]

JBrowse 1 (2009–2023)

[edit]

JBrowse was first described in a 2009 article by Skinner et al in Genome Research. The authors proposed a JavaScript genome browser that performed rendering on the web client rather than the server in order to reduce server resource requirements and to enable smoother animated transitions during panning and zooming.[1]. Subsequent articles described support for multimodal integration of next-generation sequencing and other genomics data formats including BAM, Wiggle, BigWig, VCF, and GFF3.[6][7][2][8]

A 2016 article in Genome Biology described JBrowse as a mature platform with support for plugins and faceted track navigation. By the time of that publication, JBrowse was reportedly in use by major model-organism resources including WormBase, Phytozome, the Sol Genomics Network, the Genome Database for Rosaceae, and Araport, and was used as a visualization layer by tools including Apollo, SeqWare, Maker, and GenSAS.[2]

JBrowse 2 (2023–present)

[edit]

In 2023 Diesh, Buels, and colleagues described JBrowse 2 in Genome Biology as a ground-up rewrite of the original application, motivated by constraints in JBrowse 1 — such as the assumption that only one genome would ever be displayed at a time — that the authors stated had become difficult to extend.[4] The new version of JBrowse addressed performance more systematically than its predecessor, e.g. developing statistical metrics of frame rate consistency as a quantitative benchmark of user interface responsiveness during visualizations that involve navigating through large (genome-scale) datasets[4].

JBrowse 2 introduced several new view types, including a circular view inspired by Circos,[9] a dot plot view, a linear synteny view, a tabular view, an "SV inspector" composite view that combines tabular and circular views for prioritizing structural variants, and a "breakpoint split view" for examining gene fusions and translocations.[4] The JBrowse project has released a number of JavaScript and TypeScript components for handling standard bioinformatics data formats, such as CRAM-JS, a JavaScript implementation of CRAM reference-based decompression that is also used by the Integrative Genomics Viewer (igv.js).[10]

Subsequent articles described use of JBrowse 2 for setting up genome browsers in general,[11] for visualizing synteny using whole-genome alignments,[12] and for integrating protein structures, multiple sequence alignments, and phylogenetic trees alongside nucleotide-level data.[13]

Funding

[edit]

JBrowse development has been supported primarily by grants from the NIH[2][4]. Apollo, a downstream genome annotation editor that uses JBrowse for visualization, has also been supported by NIH funding.[14]

Architecture

[edit]

JBrowse is designed for static-site deployment: data parsing and rendering occur on the client, and the web server need only serve files via HTTP. This allows hosting on services such as Amazon S3 or GitHub Pages without server-side code.[2][4] The original prototype was motivated directly by Google Maps, and utilized the same strategy as the early Google Maps (viz. pre-rendered image tiles). Later versions dispensed with pre-rendered images and placed annotation glyphs directly into the Document Object Model.[1]

JBrowse 2 is implemented in TypeScript and uses React for the user interface and the mobx-state-tree library for state management; web workers are used to keep data parsing and time-consuming rendering operations off the main thread. The software uses a plugin architecture via which third parties can implement new track types, view types, data adapters, renderers, and authentication mechanisms. Plugins can be installed from within the application using an in-app plugin store.[4]

Variants and integrations

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Several products are derived from the JBrowse 2 codebase:[4]

  • JBrowse Web — the standard web application
  • JBrowse Desktop — a cross-platform desktop application built using Electron
  • JBrowse CLI — a command-line administrative tool, used to load assemblies, tracks, and indices for searching by feature name[11]
  • JBrowse Embedded Components — React components published on npm for embedding views in other web applications
  • JBrowseR — an R package distributed via CRAN that embeds JBrowse 2 in Shiny applications and R Markdown documents[15]
  • JBrowse Jupyter — a Python package distributed via PyPI that embeds JBrowse 2 in Jupyter notebooks[16]

Apollo, a separate genome annotation editor developed within the GMOD project, uses JBrowse to display annotations during interactive curation.[17][14]

Adoption

[edit]

In a 2024 article in Genetics the Alliance of Genome Resources consortium described JBrowse as one of the genome-browsing components of its central infrastructure.[3] The Alliance comprises eight knowledgebases — the Saccharomyces Genome Database, WormBase, FlyBase, the Mouse Genome Database, the Zebrafish Information Network, the Rat Genome Database, Xenbase, and the Gene Ontology Consortium — and was recognized in 2022 as a Core Global Biodata Resource by the Global Biodata Coalition.[3]

JBrowse has been used by other biological databases including Phytozome,[18] the Sol Genomics Network,[19] the Genome Database for Rosaceae,[20] Araport,[21] the SNP-Seek rice variation database,[22] the i5k Workspace for arthropod genomes,[23] GrainGenes,[24] and Echinobase.[25] Disease- and pathogen-related databases that have used JBrowse include COSMIC,[26] the PATRIC bacterial bioinformatics database,[27] the VEuPathDB database of eukaryotic pathogens and their vectors,[28] NIAGADS for Alzheimer's disease genetics,[29] and the LANL HIV Sequence Database.[30]

A common pattern for bioinformatics tools that perform genome-scale analyses is to release their results via a genome browser. Due to its static site capabilities, which enable secure low-cost sharing of results, JBrowse has become a popular choice for this form of web-based publication. Examples include the CNVpytor copy-number variation tool,[31] the RNAStructuromeDB RNA structure database,[32] and the Treenome Browser for visualizing phylogenies containing millions of coronavirus genomes.[33]

Educational use

[edit]

JBrowse has been used in educational settings. The G-OnRamp project, described by Sargent and colleagues in 2020, is a Galaxy-based pipeline that produces JBrowse instances for use in undergraduate-driven collaborative genome annotation; it has been used by educators across multiple institutions in collaboration with the Howard Hughes Medical Institute's Genomics Education Partnership.[34] The JBrowse-based Apollo tool was used by the UK-based Genome Decoders project to engage students from 60 schools in the UK in annotation of the genes in the DNA of the human whipworm parasite Trichuris trichiura.

Reception

[edit]

A 2009 article in Nature Biotechnology described the software as "a next-generation genome browser uniquely defined by its ability to offload much of the computation-intensive work of data visualization to a user's web browser".[35]

A 2013 review of web-based genome browsers by Wang and colleagues at Peking University, published in Briefings in Bioinformatics, placed JBrowse among the mainstream web-based genome browsers, in a survey that also covered the UCSC Genome Browser, Ensembl, GBrowse, ABrowse, SViewer, and Anno-J. The review identified JBrowse and Anno-J as the two browsers in the survey that performed rendering on the client rather than the server, and presented a comparison of features across the surveyed browsers.[36]

See also

[edit]

References

[edit]
  1. ^ a b c d Skinner, Mitchell E.; Uzilov, Andrew V.; Stein, Lincoln D.; Mungall, Christopher J.; Holmes, Ian H. (September 2009). "JBrowse: a next-generation genome browser". Genome Research. 19 (9): 1630–1638. doi:10.1101/gr.094607.109. PMC 2752129. PMID 19570905.
  2. ^ a b c d e Buels, Robert; Yao, Eric; Diesh, Colin M.; Hayes, Richard D.; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M.; Elsik, Christine G.; Lewis, Suzanna E.; Stein, Lincoln; Holmes, Ian H. (12 April 2016). "JBrowse: a dynamic web platform for genome visualization and analysis". Genome Biology. 17 (1) 66. Bibcode:2016GenBi..17...66B. doi:10.1186/s13059-016-0924-1. PMC 4830250. PMID 27072794.
  3. ^ a b c d Alliance of Genome Resources Consortium (May 2024). "Updates to the Alliance of Genome Resources central infrastructure". Genetics. 227 (1) iyae049. doi:10.1093/genetics/iyae049. PMC 11075556. PMID 38552170.
  4. ^ a b c d e f g h i j Diesh, Colin; Stevens, Garrett J.; Xie, Peter; De Jesus Martinez, Teresa; Hershberg, Elliot A.; Leung, Angel; Guo, Emma; Dider, Shihab; Zhang, Junjun; Bridge, Caroline; Hogue, Gregory; Duncan, Andrew; Morgan, Matthew; Flores, Tia; Bimber, Benjamin N.; Haw, Robin; Cain, Scott; Buels, Robert M.; Stein, Lincoln D.; Holmes, Ian H. (17 April 2023). "JBrowse 2: a modular genome browser with views of synteny and structural variation". Genome Biology. 24 (1): 74. doi:10.1186/s13059-023-02914-z. PMC 10111719. PMID 37069644.
  5. ^ Stein, Lincoln D.; Mungall, Christopher; Shu, ShengQiang; Caudy, Michael; Mangone, Marco; Day, Allen; Nickerson, Elizabeth; Stajich, Jason E.; Harris, Todd W.; Arva, Adrian; Lewis, Suzanna (October 2002). "The generic genome browser: a building block for a model organism system database". Genome Research. 12 (10): 1599–1610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
  6. ^ Skinner, Mitchell E.; Holmes, Ian H. (December 2010). "Setting up the JBrowse genome browser". Current Protocols in Bioinformatics. Chapter 9: Unit 9.13. doi:10.1002/0471250953.bi0913s32. PMID 21154708.
  7. ^ Westesson, Oscar; Skinner, Mitchell; Holmes, Ian (March 2013). "Visualizing next-generation sequencing data with JBrowse". Briefings in Bioinformatics. 14 (2): 172–177. doi:10.1093/bib/bbr078. PMC 3603212. PMID 22253280.
  8. ^ Yao, Eric; Buels, Robert; Sen, Taner Z.; Stein, Lincoln; Holmes, Ian (11 May 2020). "JBrowse Connect: A server API to connect JBrowse instances and users". PLOS Computational Biology. 16 (5) e1007261. Bibcode:2020PLSCB..16E7261Y. doi:10.1371/journal.pcbi.1007261. PMC 7241844. PMID 32392213.
  9. ^ Krzywinski, Martin; Schein, Jacqueline; Birol, İnanç; Connors, Joseph; Gascoyne, Randy; Horsman, Doug; Jones, Steven J.; Marra, Marco A. (September 2009). "Circos: an information aesthetic for comparative genomics". Genome Research. 19 (9): 1639–1645. doi:10.1101/gr.092759.109. PMC 2752132. PMID 19541911.
  10. ^ Buels, Robert; Dider, Shihab; Diesh, Colin; Robinson, James; Holmes, Ian (1 November 2019). "Cram-JS: reference-based decompression in node and the browser". Bioinformatics. 35 (21): 4451–4452. doi:10.1093/bioinformatics/btz411. PMID 31099382.
  11. ^ a b Diesh, Colin; Buels, Robert; Stevens, Garrett; Bridge, Caroline; Cain, Scott; Stein, Lincoln; Holmes, Ian (August 2024). "Setting up the JBrowse 2 genome browser". Current Protocols. 4 (8): 24250–24256. doi:10.1002/cpz1.1120. PMC 11378282. PMID 39167047.
  12. ^ Diesh, Colin; Stevens, Garrett; Cain, Scott; Stein, Lincoln; Holmes, Ian (December 2025). "Setting up JBrowse 2 for visualizing genome synteny". Current Protocols. 5 (12) e70236. doi:10.1002/cpz1.70236. PMC 12679896. PMID 41347761.
  13. ^ Diesh, Colin; Stevens, Garrett; Bridge, Caroline; Hogue, Gregory; Buels, Robert; Cain, Scott; Stein, Lincoln; Holmes, Ian (2026). "Proteins in the genome browser: integration of phylogenies, alignments, and structures with nucleotide-level evidence in JBrowse 2". Journal of Molecular Biology. 438 (18) 169645. doi:10.1016/j.jmb.2026.169645. PMID 41565000.
  14. ^ a b Dunn, Nathan A.; Unni, Deepak R.; Diesh, Colin; Munoz-Torres, Monica; Harris, Nomi L.; Yao, Eric; Rasche, Helena; Holmes, Ian H.; Elsik, Christine G.; Lewis, Suzanna E. (February 2019). "Apollo: democratizing genome annotation". PLOS Computational Biology. 15 (2) e1006790. Bibcode:2019PLSCB..15E6790D. doi:10.1371/journal.pcbi.1006790. PMC 6380598. PMID 30726205.
  15. ^ Hershberg, Elliot A.; Stevens, Garrett; Diesh, Colin; Xie, Peter; De Jesus Martinez, Teresa; Buels, Robert; Stein, Lincoln; Holmes, Ian (4 November 2021). "JBrowseR: an R interface to the JBrowse 2 genome browser". Bioinformatics. 37 (21): 3914–3915. doi:10.1093/bioinformatics/btab459. PMC 8570810. PMID 34213545.
  16. ^ De Jesus Martinez, Teresa; Hershberg, Elliot A.; Guo, Emma; Stevens, Garrett J.; Diesh, Colin; Xie, Peter; Bridge, Caroline; Cain, Scott; Haw, Robin; Buels, Robert M.; Stein, Lincoln D.; Holmes, Ian H. (1 January 2023). "JBrowse Jupyter: a Python interface to JBrowse 2". Bioinformatics. 39 (1) btad032. doi:10.1093/bioinformatics/btad032. PMC 9913041. PMID 36648331.
  17. ^ Lee, Eduardo; Helt, Gregg A.; Reese, Justin T.; Munoz-Torres, Monica C.; Childers, Christopher P.; Buels, Robert M.; Stein, Lincoln; Holmes, Ian H.; Elsik, Christine G.; Lewis, Suzanna E. (10 September 2013). "Web Apollo: a web-based genomic annotation editing platform". Genome Biology. 14 (8): R93. doi:10.1186/gb-2013-14-8-r93. PMC 4014802. PMID 24000942.
  18. ^ Goodstein, David M.; Shu, Shengqiang; Howson, Russell; Neupane, Rochak; Hayes, Richard D.; Fazo, Joni; Mitros, Therese; Dirks, William; Hellsten, Uffe; Putnam, Nicholas; Rokhsar, Daniel S. (January 2012). "Phytozome: a comparative platform for green plant genomics". Nucleic Acids Research. 40 (Database issue): D1178–D1186. doi:10.1093/nar/gkr944. PMC 3245001. PMID 22110026.
  19. ^ Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.; Saha, Surya; Tecle, Isaak Y.; Strickler, Susan R.; Bombarely, Aureliano; Fisher-York, Thomas; Pujar, Anuradha; Foerster, Hartmut; Mueller, Lukas A. (January 2015). "The Sol Genomics Network (SGN)—from genotype to phenotype to breeding". Nucleic Acids Research. 43 (Database issue): D1036–D1041. doi:10.1093/nar/gku1195. PMC 4383986. PMID 25428362.
  20. ^ Jung, Sook; Ficklin, Stephen P.; Lee, Taein; Cheng, Chun-Huai; Blenda, Anna; Zheng, Ping; Yu, Jing; Bombarely, Aureliano; Cho, Ilhyung; Ru, Sushan; Main, Dorrie (January 2014). "The Genome Database for Rosaceae (GDR): year 10 update". Nucleic Acids Research. 42 (Database issue): D1237–D1244. doi:10.1093/nar/gkt1012. PMC 3965020. PMID 24225320.
  21. ^ Krishnakumar, Vivek; Hanlon, Matthew R.; Contrino, Sergio; Ferlanti, Erik S.; Karamycheva, Svetlana; Kim, Maria; Rosen, Benjamin D.; Cheng, Chia-Yi; Moreira, Walter; Mock, Stephen A. (January 2015). "Araport: the Arabidopsis information portal". Nucleic Acids Research. 43 (Database issue): D1003–D1009. doi:10.1093/nar/gku1200. PMC 4383980. PMID 25414324.
  22. ^ Alexandrov, Nickolai; Tai, Shuaishuai; Wang, Wensheng; Mansueto, Locedie; Palis, Kevin; Fuentes, Roven Rommel; Ulat, Victor Jun; Chebotarov, Dmytro; Zhang, Gengyun; Li, Zhikang; Mauleon, Ramil; Hamilton, Ruaraidh Sackville; McNally, Kenneth L. (January 2015). "SNP-Seek database of SNPs derived from 3000 rice genomes". Nucleic Acids Research. 43 (Database issue): D1023–D1027. doi:10.1093/nar/gku1039. PMC 4384024. PMID 25429973.
  23. ^ Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin (January 2015). "The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes". Nucleic Acids Research. 43 (Database issue): D714–D719. doi:10.1093/nar/gku983. PMC 4383916. PMID 25332403.
  24. ^ Yao, Eric; Blake, Victoria C.; Cooper, Laurel; Wight, Charlene P.; Michel, Steven; Cagirici, H. Busra; Lazo, Gerard R.; Birkett, Clay L.; Waring, David J.; Jannink, Jean-Luc; Holmes, Ian; Waters, Amanda J.; Eickholt, David P.; Sen, Taner Z. (2022). "GrainGenes: a data-rich repository for small grains genetics and genomics". Database. 2022 (1) baac034. doi:10.1093/database/baac034. PMC 9216568. PMID 35552411.
  25. ^ Cary, Gregory A.; Cameron, R. Andrew; Hinman, Veronica F. (2018). "EchinoBase: tools for echinoderm genome analyses". Eukaryotic Genomic Databases. Methods in Molecular Biology. Vol. 1757. pp. 349–369. doi:10.1007/978-1-4939-7737-6_12. ISBN 978-1-4939-7736-9. PMC 6314195. PMID 29761465.
  26. ^ Forbes, Simon A.; Beare, David; Gunasekaran, Prasad; Leung, Kenric; Bindal, Nidhi; Boutselakis, Harry; Ding, Minjie; Bamford, Sally; Cole, Charlotte; Ward, Sari; Kok, Chai Yin; Jia, Mingming; De, Tisham; Teague, Jon W.; Stratton, Michael R.; McDermott, Ultan; Campbell, Peter J. (January 2015). "COSMIC: exploring the world's knowledge of somatic mutations in human cancer". Nucleic Acids Research. 43 (Database issue): D805–D811. doi:10.1093/nar/gku1075. PMC 4383913. PMID 25355519.
  27. ^ Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Tim; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J. C.; Yoo, Hyunseung Seol; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W. (January 2014). "PATRIC, the bacterial bioinformatics database and analysis resource". Nucleic Acids Research. 42 (Database issue): D581–D591. doi:10.1093/nar/gkt1099. PMC 3965095. PMID 24225323.
  28. ^ Amos, Beatrice; Aurrecoechea, Cristina; Barba, Matthieu; Barreto, Ana; Basenko, Evelina Y.; Bażant, Wojciech; Belnap, Robert; Blevins, Ann S.; Böhme, Ulrike; Brestelli, John (7 January 2022). "VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center". Nucleic Acids Research. 50 (D1): D898–D911. doi:10.1093/nar/gkab929. PMC 8728164. PMID 34718728.
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  31. ^ Suvakov, Milovan; Panda, Arijit; Diesh, Colin; Holmes, Ian; Abyzov, Alexej (10 November 2021). "CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing". GigaScience. 10 (11) giab074. doi:10.1093/gigascience/giab074. PMC 8612021. PMID 34817058.
  32. ^ Andrews, Ryan J.; Baber, Levi; Moss, Walter N. (2017). "RNAStructuromeDB: A genome-wide database for RNA structural inference". Scientific Reports. 7 (1): 17269. Bibcode:2017NatSR...717269A. doi:10.1038/s41598-017-17510-y. PMC 5722888. PMID 29222504.
  33. ^ Kramer, Alexander M.; Sanderson, Theo; Corbett-Detig, Russell (2023). "Treenome Browser: co-visualization of enormous phylogenies and millions of genomes". Bioinformatics. 39 (1) btac772. doi:10.1093/bioinformatics/btac772. PMC 9805588. PMID 36453872.
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[edit]

Category:Bioinformatics software Category:Free bioinformatics software Category:Free science software Category:Free software programmed in JavaScript Category:Free software programmed in TypeScript Category:Genome browsers Category:Software using the Apache license Category:2009 software

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