BioRuby
{{Infobox software
| name = BioRuby
| logo = Bioruby_package_logo.png
| screenshot = Bioruby shell on rails.png
| caption = A BioRuby shell on Rails
| latest release version = 2.0.2
| latest release date = {{Release date and age|2020|12|31|df=yes}}
| programming language = Ruby
| genre = Bioinformatics
| license = GPL
| website = {{URL|http://bioruby.open-bio.org/}}
}}
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.{{cite journal |vauthors=Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T |title=BioRuby: bioinformatics software for the Ruby programming language |journal=Bioinformatics |volume=26 |issue=20 |pages=2617–9 |date=October 2010 |pmid=20739307 |pmc=2951089 |doi=10.1093/bioinformatics/btq475 }} BioRuby is released under the GNU GPL version 2 or Ruby licence{{Cite web|url = https://github.com/bioruby/bioruby/blob/master/README.rdoc|title = bioruby/README.rdoc at master · bioruby/bioruby|date = 2014-05-08|access-date = 2014-11-09}} and is one of a number of Bio* projects, designed to reduce code duplication.{{cite journal| author=Mangalam H| title=The Bio* toolkits--a brief overview. | journal=Brief Bioinform | year= 2002 | volume= 3 | issue= 3 | pages= 296–302 | pmid=12230038 | doi= 10.1093/bib/3.3.296| doi-access= free }}
In 2011, the BioRuby project introduced the Biogem software plugin system,{{cite journal |vauthors=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 |title=Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |journal=Bioinformatics |volume=28 |issue=7 |pages=1035–7 |date=April 2012 |pmid=22332238 |pmc=3315718 |doi=10.1093/bioinformatics/bts080 |url=}} with two or three new plugins added every month.
BioRuby is managed via the BioRuby website and GitHub repository.{{cite web |title=bioruby/bioruby |url=https://github.com/bioruby/bioruby |publisher=BioRuby Project |access-date=25 May 2021 |date=2021-05-15}}{{cite web |title=BioRuby |url=http://bioruby.org/ |website=bioruby.org |access-date=25 May 2021}}
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,{{Cite web|url = https://www.ipa.go.jp/english/humandev/third.html|title = IPA Information-technology Promotion Agency, Japan : IPA:Exploratory IT Human Resources Project (The MITOH Program)}} culminating with the release of version 1.0.0 in February 2006.{{Cite web|url = http://mailman.open-bio.org/pipermail/bioruby/2006-February/002683.html|title = [BioRuby] BioRuby 1.0.0 released|date = 2006-02-27|access-date = 2014-09-10}} Between 2009 and 2012, BioRuby was the focus of a number of Google Summer of Code projects to improve the codebase.{{cite web |title=bioruby/documents |url=https://github.com/bioruby/documents/wiki/Google_Summer_of_Code |website=GitHub |access-date=25 May 2021 |language=en}} BioRuby Version 2.0.0 was released in 2019.
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.{{cite web |title=RubyGems.org {{!}} your community gem host |url=https://rubygems.org/ |website=rubygems.org |access-date=25 May 2021}} Any gem published via the Biogem framework is also listed at biogems.info.{{cite web |title=biogems.info - gems for bioinformatics |url=http://biogems.info |website=biogems.info |access-date=25 May 2021}}
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.{{Cite web|url = http://bioruby.open-bio.org/wiki/Plugins|title = Plugins - BioRuby}}
= Popular Biogems =
| class="wikitable" | |||
| Biogem | Description | Version | |
|---|---|---|---|
| 1 | [http://rubygems.org/gems/bio bio] | Bioinformatics Library | 1.4.3.0001 |
| 2 | [http://rubygems.org/gems/biodiversity biodiversity] | Parser of scientific names | 3.1.5 |
| 3 | [http://rubygems.org/gems/simple-spreadsheet-extractor Simple Spreadsheet extractor] | Basic spreadsheet content extraction using Apache poi | 0.13.3 |
| 4 | [http://rubygems.org/gems/bio-gem Bio gem] | Software generator for Ruby | 1.36 |
| 5 | [http://rubygems.org/gems/bio-samtools Bio samtools] | Binder of samtools for Ruby | 2.1.0 |
| 6 | [http://rubygems.org/gems/t2-server t2 server] | Support for interacting with the taverna 2 server | 1.1.0 |
| 7 | [http://rubygems.org/gems/bio-ucsc-api bio ucsc api] | The Ruby ucsc api | 0.6.2 |
| 8 | [http://rubygems.org/gems/entrez entrez] | http request to entrez e-utilities | 0.5.8.1 |
| 9 | [http://rubygems.org/gems/bio-gadget bio gadget] | Gadget for bioinformatics | 0.4.8 |
| 10 | [http://rubygems.org/gems/sequenceserver sequenceserver] | Blast search made easy! | 0.8.7 |
See also
References
{{Reflist}}
External links
- {{Official website|http://bioruby.org}}
Category:Free bioinformatics software