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BioJS: an open source standard for biological visualisation – its status in 2014

Journal Article · · F1000Research
 [1];  [2];  [3];  [4];  [2];  [5];  [2];  [6];  [3];  [7];  [8];  [2];  [9];  [10];  [11];  [12];  [13];  [14];  [15];  [2]
  1. The Genome Analysis Centre, Norwich (United Kingdom); DOE/OSTI
  2. European Molecular Biology Lab. (EMBL), Hinxton (United Kingdom). European Bioinforatics Inst. (EBI)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Florida State Univ., Tallahassee, FL (United States). School of Library and Information Science
  5. Technische Univ., Munich (Germany). Dept. of Informatics, Bioinformatics & Computational Biology
  6. Univ. of Cambridge (United Kingdom). Cambridge Systems Biology Centre. Dept. of Genetics
  7. eLife, Cambridge (United Kingdom)
  8. Open Univ., Milton Keynes (United Kingdom). Faculty of Mathematics, Computing and Technology
  9. Univ. of Cape Town (South Africa). Computational Biology Group
  10. European Molecular Biology Lab. (EMBL), Hinxton (United Kingdom). European Bioinforatics Inst. (EBI); The Wellcome Trust Sanger Institute, Hinxton, Cambridge (United Kingdom)
  11. Univ. College London (United Kingdom). Dept. of Biochemistry. Biomolecular Structure and Modelling Group
  12. Eagle Genomics Ltd, Cambridge (United Kingdom)
  13. The Genome Analysis Centre, Norwich (United Kingdom)
  14. Max Planck Inst. of Biochemistry (Germany)
  15. Technische Univ., Munich (Germany). Dept. of Informatics, Bioinformatics & Computational Biology; Technische Univ., Munich (Germany). Graduate School of Information Science in Health (GSISH); Biosof LLC, New York, NY (United States)
+ Show Author Affiliations
BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI ID:
1629553
Journal Information:
F1000Research, Journal Name: F1000Research Vol. 3; ISSN 2046-1402
Publisher:
F1000ResearchCopyright Statement
Country of Publication:
United States
Language:
English

References (6)

BioJava: an open-source framework for bioinformatics in 2012 journal August 2012
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains journal November 2012
The Bioperl Toolkit: Perl Modules for the Life Sciences journal October 2002
BioRuby: bioinformatics software for the Ruby programming language journal August 2010
Reactome: a database of reactions, pathways and biological processes journal November 2010
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments journal December 2013

Cited By (14)

MSAViewer: interactive JavaScript visualization of multiple sequence alignments journal July 2016
ProtVista: visualization of protein sequence annotations journal March 2017
BioCIDER: a Contextualisation InDEx for biological Resources discovery journal April 2017
TogoGenome/TogoStanza: modularized Semantic Web genome database journal January 2019
The complex portal - an encyclopaedia of macromolecular complexes journal October 2014
Tools and data services registry: a community effort to document bioinformatics resources journal November 2015
GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens journal October 2016
Ten Simple Rules for Developing Public Biological Databases journal November 2016
BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results journal October 2018
Additional file 1 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools dataset January 2023
Additional file 2 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools dataset January 2023
Anatomy of BioJS, an open source community for the life sciences journal July 2015
Four simple recommendations to encourage best practices in research software journal January 2017
AliTV—interactive visualization of whole genome comparisons journal January 2017

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES