BioJS
{{Infobox Software
|name = BioJS
|logo = BioJS Logo.svg
|released = 2012
|programming language = JavaScript
|genre = Bioinformatics
|license = Apache 2
|website = {{URL|biojs.net}}
}}
BioJS is an open-source project for bioinformatics data on the web.{{Cite journal |last1=Corpas |authorlink1 = Manuel Corpas (Scientist)|last2=Jimenez |first2=Rafael |last3=Carbon |first3=Seth J |last4=García |first4=Alex |last5=Garcia |first5=Leyla |last6=Goldberg |first6=Tatyana |last7=Gomez |first7=John |last8=Kalderimis |first8=Alexis |last9=Lewis |first9=Suzanna E |year=2014 |title=BioJS: an open source standard for biological visualisation – its status in 2014 |journal=F1000Research | pmid=25075290 | doi=10.12688/f1000research.3-55.v1 |issn=2046-1402 |last10=Mulvany |first10=Ian |last11=Pawlik |first11=Aleksandra |last12=Rowland |first12=Francis |last13=Salazar |first13=Gustavo |last14=Schreiber |first14=Fabian |last15=Sillitoe |first15=Ian |last16=Spooner |first16=William H |last17=Thanki |first17=Anil |last18=Villaveces |first18=José M |last19=Yachdav |first19=Guy |last20=Hermjakob |first20=Henning| volume=3 | page=55 |pmc=4103492 | doi-access=free }} Its goal is to develop an open-source library of JavaScript components to visualise biological data.{{Cite web |url=http://biojs.net/our_mission.html |title=BioJS Vision and Mission |publisher=BioJS |archive-url=https://web.archive.org/web/20140810063209/http://biojs.net/our_mission.html |archive-date=10 August 2014 |url-status=dead |access-date=29 August 2014}} BioJS develops and maintains small building blocks (components) which can be reused by others. For a discovery of available components, BioJS maintains a [https://biojs.net/#/components registry] {{Webarchive|url=https://web.archive.org/web/20180313202921/http://biojs.net/#/components |date=2018-03-13 }}.
History
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
- DAG Viewer{{cite journal|last1=Kalderimis|first1=Alexis|last2=Stepan|first2=Radek|last3=Sullivan|first3=Julie|last4=Lyne|first4=Rachel|last5=Lyne|first5=Michael|last6=Micklem|first6=Gos|title=BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs|journal=F1000Research|year=2014|volume=3 |page=51 |issn=2046-1402|pmid=24627804 | doi=10.12688/f1000research.3-51.v1|pmc=3945768 |doi-access=free }}
- DNA Content Viewer{{cite journal|last1=Thanki|first1=Anil S.|last2=Caim|first2=Shabhonam|last3=Corpas|first3=Manuel|authorlink3 = Manuel Corpas (Scientist)|last4=Davey|first4=Robert P.|title=DNAContentViewer a BioJS component to visualise GC/AT Content|journal=F1000Research|year=2014|volume=3 |page=54 |issn=2046-1402|doi=10.12688/f1000research.3-54.v1|doi-access=free}}
- FeatureViewer{{cite journal|last1=Garcia|first1=Leyla|last2=Yachdav|first2=Guy|last3=Martin|first3=Maria-Jesus|title=FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences|journal=F1000Research|year=2014|volume=3 |page=47 |issn=2046-1402|pmid=24741440 |doi=10.12688/f1000research.3-47.v2| pmc=3983936 |doi-access=free}}
- HeatMapViewer{{cite journal|last1=Yachdav|first1=Guy|last2=Hecht|first2=Maximilian|last3=Pasmanik-Chor|first3=Metsada|last4=Yeheskel|first4=Adva|last5=Rost|first5=Burkhard|title=HeatMapViewer: interactive display of 2D data in biology|journal=F1000Research|year=2014|volume=3 |page=48 |issn=2046-1402| pmid=24860644|doi=10.12688/f1000research.3-48.v1 | pmc=4023661|doi-access=free}}
- Intermine analysis{{cite journal|last1=Kalderimis|first1=Alexis|last2=Stepan|first2=Radek|last3=Sullivan|first3=Julie|last4=Lyne|first4=Rachel|last5=Lyne|first5=Michael|last6=Micklem|first6=Gos|title=BioJS InterMine List Analysis: A BioJS component for displaying graphical or statistical analysis of collections of items from InterMine endpoints|journal=F1000Research|year=2014|volume=3 |page=45 |issn=2046-1402|doi=10.12688/f1000research.3-45.v1|doi-access=free}}
- Intermine endpoints{{cite journal|last1=Kalderimis|first1=Alexis|last2=Stepan|first2=Radek|last3=Sullivan|first3=Julie|last4=Lyne|first4=Rachel|last5=Lyne|first5=Michael|last6=Micklem|first6=Gos|title=BioJS InterMineTable Component: A BioJS component for displaying data from InterMine compatible webservice endpoints|journal=F1000Research|year=2014|volume=3 |page=46 |issn=2046-1402|doi=10.12688/f1000research.3-46.v1|doi-access=free}}
- KEGGViewer{{cite journal|last1=Villaveces|first1=Jose M.|last2=Jimenez|first2=Rafael C.|last3=Habermann|first3=Bianca H.|title=KEGGViewer, a BioJS component to visualize KEGG Pathways|journal=F1000Research|year=2014|volume=3 |page=43 |issn=2046-1402|pmid=24715980| doi=10.12688/f1000research.3-43.v1|pmc=3954160 |doi-access=free}}
- PPI-Interactions{{cite journal|last1=Salazar|first1=Gustavo A.|last2=Meintjes|first2=Ayton|last3=Mulder|first3=Nicola|title=PPI layouts: BioJS components for the display of Protein-Protein Interactions|journal=F1000Research|year=2014|volume=3 |page=50 |issn=2046-1402|pmid=25075288 |doi=10.12688/f1000research.3-50.v1 | pmc=4103490 |doi-access=free}}
- PsicquicGraph{{cite journal|last1=Villaveces|first1=Jose M.|last2=Jimenez|first2=Rafael C.|last3=Habermann|first3=Bianca H.|title=PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers|journal=F1000Research|year=2014|volume=3 |page=44 |issn=2046-1402|pmid=25075287 | doi=10.12688/f1000research.3-44.v1|pmc=4097353|doi-access=free}}
- Sequence{{cite journal|last1=Gomez|first1=John|last2=Jimenez|first2=Rafael|title=Sequence, a BioJS component for visualising sequences|journal=F1000Research|year=2014|volume=3 |page=52 |issn=2046-1402|pmid=25075289| doi=10.12688/f1000research.3-52.v1| pmc=4103491|doi-access=free}}
- wigExplorer{{cite journal|last1=Thanki|first1=Anil S.|last2=Jimenez|first2=Rafael C.|last3=Kaithakottil|first3=Gemy G.|last4=Corpas|first4=Manuel|authorlink4 = Manuel Corpas (Scientist)|last5=Davey|first5=Robert P.|title=wigExplorer, a BioJS component to visualise wig data|journal=F1000Research|year=2014|volume=3 |page=53 |issn=2046-1402|doi=10.12688/f1000research.3-53.v2|pmid=27781080 |pmc=5054804 |doi-access=free}}
- treeWidget{{cite journal|last1=Schreiber|first1=Fabian|title=treeWidget: a BioJS component to visualise phylogenetic trees|journal=F1000Research|year=2014|volume=3 |page=49 |issn=2046-1402|doi=10.12688/f1000research.3-49.v1|doi-access=free}}
Institutions using BioJS
- EBI
- ELife
- InterMine
- Berkeley Lab
- OpenPHACTS
- [http://www.rostlab.org/ Rostlab]
- TGAC
See also
{{Portal|Free and open-source software|Biology}}
References
{{reflist}}
External links
- {{Official website|biojs.net}}
- {{Github|biojs}}
{{JavaScript}}