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BioJS

BioJS is an open-source project for bioinformatics data on the web.[1] Its goal is to develop an open-source library of JavaScript components to visualise biological data.[2] BioJS develops and maintains small building blocks (components) which can be reused by others. For a discovery of available components, BioJS maintains a registry Archived 2018-03-13 at the Wayback Machine.

BioJS
Initial release2012
Repository
Written inJavaScript
TypeBioinformatics
LicenseApache 2
Websitebiojs.net

History

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The first version of BioJS was released in 2012 by John Gomez Carvajal. It was developed as a JavaScript library of web components to represent biological data in web applications. Version 2.0 included a complete redesign of the library and was released in 2014 as a Google Summer of Code project led by Manuel Corpas and developed by David Dao and Sebastian Wilzbach. Since then over 100 people contributed to the project. Currently more than 150 components are available in the BioJS registry.

Selected list of published components

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  • DAG Viewer[3]
  • DNA Content Viewer[4]
  • FeatureViewer[5]
  • HeatMapViewer[6]
  • Intermine analysis[7]
  • Intermine endpoints[8]
  • KEGGViewer[9]
  • PPI-Interactions[10]
  • PsicquicGraph[11]
  • Sequence[12]
  • wigExplorer[13]
  • treeWidget[14]

Institutions using BioJS

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See also

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References

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  1. ^ Corpas; Jimenez, Rafael; Carbon, Seth J; García, Alex; Garcia, Leyla; Goldberg, Tatyana; Gomez, John; Kalderimis, Alexis; Lewis, Suzanna E; Mulvany, Ian; Pawlik, Aleksandra; Rowland, Francis; Salazar, Gustavo; Schreiber, Fabian; Sillitoe, Ian; Spooner, William H; Thanki, Anil; Villaveces, José M; Yachdav, Guy; Hermjakob, Henning (2014). "BioJS: an open source standard for biological visualisation – its status in 2014". F1000Research. 3: 55. doi:10.12688/f1000research.3-55.v1. ISSN 2046-1402. PMC 4103492. PMID 25075290.
  2. ^ "BioJS Vision and Mission". BioJS. Archived from the original on 10 August 2014. Retrieved 29 August 2014.
  3. ^ Kalderimis, Alexis; Stepan, Radek; Sullivan, Julie; Lyne, Rachel; Lyne, Michael; Micklem, Gos (2014). "BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs". F1000Research. 3: 51. doi:10.12688/f1000research.3-51.v1. ISSN 2046-1402. PMC 3945768. PMID 24627804.
  4. ^ Thanki, Anil S.; Caim, Shabhonam; Corpas, Manuel; Davey, Robert P. (2014). "DNAContentViewer a BioJS component to visualise GC/AT Content". F1000Research. 3: 54. doi:10.12688/f1000research.3-54.v1. ISSN 2046-1402.
  5. ^ Garcia, Leyla; Yachdav, Guy; Martin, Maria-Jesus (2014). "FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences". F1000Research. 3: 47. doi:10.12688/f1000research.3-47.v2. ISSN 2046-1402. PMC 3983936. PMID 24741440.
  6. ^ Yachdav, Guy; Hecht, Maximilian; Pasmanik-Chor, Metsada; Yeheskel, Adva; Rost, Burkhard (2014). "HeatMapViewer: interactive display of 2D data in biology". F1000Research. 3: 48. doi:10.12688/f1000research.3-48.v1. ISSN 2046-1402. PMC 4023661. PMID 24860644.
  7. ^ Kalderimis, Alexis; Stepan, Radek; Sullivan, Julie; Lyne, Rachel; Lyne, Michael; Micklem, Gos (2014). "BioJS InterMine List Analysis: A BioJS component for displaying graphical or statistical analysis of collections of items from InterMine endpoints". F1000Research. 3: 45. doi:10.12688/f1000research.3-45.v1. ISSN 2046-1402.
  8. ^ Kalderimis, Alexis; Stepan, Radek; Sullivan, Julie; Lyne, Rachel; Lyne, Michael; Micklem, Gos (2014). "BioJS InterMineTable Component: A BioJS component for displaying data from InterMine compatible webservice endpoints". F1000Research. 3: 46. doi:10.12688/f1000research.3-46.v1. ISSN 2046-1402.
  9. ^ Villaveces, Jose M.; Jimenez, Rafael C.; Habermann, Bianca H. (2014). "KEGGViewer, a BioJS component to visualize KEGG Pathways". F1000Research. 3: 43. doi:10.12688/f1000research.3-43.v1. ISSN 2046-1402. PMC 3954160. PMID 24715980.
  10. ^ Salazar, Gustavo A.; Meintjes, Ayton; Mulder, Nicola (2014). "PPI layouts: BioJS components for the display of Protein-Protein Interactions". F1000Research. 3: 50. doi:10.12688/f1000research.3-50.v1. ISSN 2046-1402. PMC 4103490. PMID 25075288.
  11. ^ Villaveces, Jose M.; Jimenez, Rafael C.; Habermann, Bianca H. (2014). "PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers". F1000Research. 3: 44. doi:10.12688/f1000research.3-44.v1. ISSN 2046-1402. PMC 4097353. PMID 25075287.
  12. ^ Gomez, John; Jimenez, Rafael (2014). "Sequence, a BioJS component for visualising sequences". F1000Research. 3: 52. doi:10.12688/f1000research.3-52.v1. ISSN 2046-1402. PMC 4103491. PMID 25075289.
  13. ^ Thanki, Anil S.; Jimenez, Rafael C.; Kaithakottil, Gemy G.; Corpas, Manuel; Davey, Robert P. (2014). "wigExplorer, a BioJS component to visualise wig data". F1000Research. 3: 53. doi:10.12688/f1000research.3-53.v2. ISSN 2046-1402. PMC 5054804. PMID 27781080.
  14. ^ Schreiber, Fabian (2014). "treeWidget: a BioJS component to visualise phylogenetic trees". F1000Research. 3: 49. doi:10.12688/f1000research.3-49.v1. ISSN 2046-1402.
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