BioRuby - Revision history

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2025-12-23T19:22:19Z

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	\| programming language = [[Ruby (programming language)\|Ruby]]		\| programming language = [[Ruby (programming language)\|Ruby]]
	\| genre = [[Bioinformatics]]		\| genre = [[Bioinformatics]]
	\| license = [[~~GPL~~]]		\| license = [[BSD licenses#2-clause license ("Simplified BSD License" or "FreeBSD License")\|BSD 2-clause license]]
	\| website = {{URL\|http://bioruby.open-bio.org/}}		\| website = {{URL\|http://bioruby.open-bio.org/}}
	}}		}}
	'''BioRuby '''is a collection of [[open-source software\|open-source]] [[Ruby (programming language)\|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.<ref name="pmid20739307">{{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 }}</ref> BioRuby is released under the [[~~GNU GPL~~]] ~~version 2~~ or [[Ruby License\|Ruby licence]]<ref>{{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}}</ref> and is one of a number of Bio* projects, designed to reduce code duplication.<ref name="pmid12230038">{{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 }}</ref>		'''BioRuby '''is a collection of [[open-source software\|open-source]] [[Ruby (programming language)\|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.<ref name="pmid20739307">{{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 }}</ref> BioRuby is released under the [[BSD licenses#2-clause license ("Simplified BSD License" or "FreeBSD License")\|BSD 2-clause license]] or [[Ruby License\|Ruby licence]]<ref>{{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}}</ref> and is one of a number of Bio* projects, designed to reduce code duplication.<ref name="pmid12230038">{{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 }}</ref>

	In 2011, the BioRuby project introduced the Biogem software plugin system,<ref name="pmid22332238">{{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=}}</ref> with two or three new plugins added every month.		In 2011, the BioRuby project introduced the Biogem software plugin system,<ref name="pmid22332238">{{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=}}</ref> with two or three new plugins added every month.
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	[[Category:Free bioinformatics software]]		[[Category:Free bioinformatics software]]
	[[Category:~~Perl~~ software]]		[[Category:Free software programmed in Ruby]]
	[[Category:Computational science]]		[[Category:Computational science]]
	[[Category:Bioinformatics software]]		[[Category:Bioinformatics software]]
			[[Category:Software using the BSD license]]

imported>Wikideas1: /* See also */ Earth BioGenome Project

2025-03-10T13:30:13Z

See also: Earth BioGenome Project

New page

{{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 (programming language)|Ruby]]
| genre = [[Bioinformatics]]
| license = [[GPL]]
| website = {{URL|http://bioruby.open-bio.org/}}
}}
'''BioRuby '''is a collection of [[open-source software|open-source]] [[Ruby (programming language)|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.<ref name="pmid20739307">{{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 }}</ref> BioRuby is released under the [[GNU GPL]] version 2 or [[Ruby License|Ruby licence]]<ref>{{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}}</ref> and is one of a number of Bio* projects, designed to reduce code duplication.<ref name="pmid12230038">{{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 }}</ref>

In 2011, the BioRuby project introduced the Biogem software plugin system,<ref name="pmid22332238">{{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=}}</ref> with two or three new plugins added every month.

BioRuby is managed via the BioRuby website and [[GitHub]] repository.<ref name="github">{{cite web |title=bioruby/bioruby |url=https://github.com/bioruby/bioruby |publisher=BioRuby Project |access-date=25 May 2021 |date=2021-05-15}}</ref><ref name="home">{{cite web |title=BioRuby |url=http://bioruby.org/ |website=bioruby.org |access-date=25 May 2021}}</ref>

==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|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,<ref>{{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)}}</ref> culminating with the release of version 1.0.0 in February 2006.<ref>{{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}}</ref> Between 2009 and 2012, BioRuby was the focus of a number of [[Google Summer of Code]] projects to improve the codebase.<ref name="github-gsoc">{{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}}</ref> BioRuby Version 2.0.0 was released in 2019.<ref name="home" />

== 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.<ref name="rubygems-home">{{cite web |title=RubyGems.org {{!}} your community gem host |url=https://rubygems.org/ |website=rubygems.org |access-date=25 May 2021}}</ref> Any gem published via the Biogem framework is also listed at biogems.info.<ref name="biogems-home">{{cite web |title=biogems.info - gems for bioinformatics |url=http://biogems.info |website=biogems.info |access-date=25 May 2021}}</ref>

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.<ref>{{Cite web|url = http://bioruby.open-bio.org/wiki/Plugins|title = Plugins - BioRuby}}</ref>

=== Popular Biogems ===
{| class="wikitable"
|-
! <nowiki>#</nowiki> !! 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==
* [[Open Bioinformatics Foundation]]
* [[BioPerl]]
* [[BioPython]]
* [[BioJava]]
* [[BioJS]]
* [[Earth BioGenome Project]]

==References==
{{Reflist}}

==External links==
* {{Official website|http://bioruby.org}}

[[Category:Free bioinformatics software]]
[[Category:Perl software]]
[[Category:Computational science]]
[[Category:Bioinformatics software]]