BioRuby

BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biology and other bioinformatics tasks.[1] BioRuby is released under the GNU GPL version 2 or Ruby licence[2] and is one of a number of Bio* projects, designed to reduce code duplication.[3]

BioRuby
Stable release
2.0.2 / 31 December 2020 (2020-12-31)
Repository
Written inRuby
TypeBioinformatics
LicenseGPL
Websitebioruby.open-bio.org

In 2011, the BioRuby project introduced the Biogem software plugin system,[4] with two or three new plugins added every month.

BioRuby is managed via the BioRuby website and GitHub repository.[5][6]

History

BioRuby

The BioRuby project was first started in 2000 by Toshiaki Katayama as a Ruby implementation of similar bioinformatics packages such as BioPerl and BioPython. The initial release of version 0.1 was frequently updated by contributors both informally and at organised “hackathon” events; in June 2005, BioRuby was funded by IPA as an Exploratory Software Project,[7] culminating with the release of version 1.0.0 in February 2006.[8] Between 2009 and 2012, BioRuby was the focus of a number of Google Summer of Code projects to improve the codebase.[9] BioRuby Version 2.0.0 was released in 2019.[6]

Biogem

Biogem provides a set of tools for bioinformaticians who want to code an application or library that uses or extends BioRuby's core library, as well as share the code as a gem on rubygems.org.[10] Any gem published via the Biogem framework is also listed at biogems.info.[11]

The aim of Biogem is to promote a modular approach to the BioRuby package and simplify the creation of modules by automating process of setting up directory/file scaffolding, a git repository and releasing online package databases.[12]

#BiogemDescriptionVersion
1bioBioinformatics Library1.4.3.0001
2biodiversityParser of scientific names3.1.5
3Simple Spreadsheet extractorBasic spreadsheet content extraction using Apache poi0.13.3
4Bio gemSoftware generator for Ruby1.36
5Bio samtoolsBinder of samtools for Ruby2.1.0
6t2 serverSupport for interacting with the taverna 2 server1.1.0
7bio ucsc apiThe Ruby ucsc api0.6.2
8entrezhttp request to entrez e-utilities0.5.8.1
9bio gadgetGadget for bioinformatics0.4.8
10sequenceserverBlast search made easy!0.8.7

See also

References
  1. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (October 2010). "BioRuby: bioinformatics software for the Ruby programming language". Bioinformatics. 26 (20): 2617–9. doi:10.1093/bioinformatics/btq475. PMC 2951089. PMID 20739307.
  2. "bioruby/README.rdoc at master · bioruby/bioruby". 2014-05-08. Retrieved 2014-11-09.
  3. Mangalam H (2002). "The Bio* toolkits--a brief overview". Brief Bioinform. 3 (3): 296–302. doi:10.1093/bib/3.3.296. PMID 12230038.
  4. Bonnal R, Aerts J, Githinji G, Goto N, MacLean D, Miller C, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom T, Woodcroft B, Katayama T, Prins P (April 2012). "Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics". Bioinformatics. 28 (7): 1035–7. doi:10.1093/bioinformatics/bts080. PMC 3315718. PMID 22332238.
  5. "bioruby/bioruby". BioRuby Project. 2021-05-15. Retrieved 25 May 2021.
  6. "BioRuby". bioruby.org. Retrieved 25 May 2021.
  7. "IPA Information-technology Promotion Agency, Japan : IPA:Exploratory IT Human Resources Project (The MITOH Program)".
  8. "[BioRuby] BioRuby 1.0.0 released". 2006-02-27. Retrieved 2014-09-10.
  9. "bioruby/documents". GitHub. Retrieved 25 May 2021.
  10. "RubyGems.org | your community gem host". rubygems.org. Retrieved 25 May 2021.
  11. "biogems.info - gems for bioinformatics". biogems.info. Retrieved 25 May 2021.
  12. "Plugins - BioRuby".
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