BioRuby: Difference between revisions
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| programming language = [[Ruby (programming language)|Ruby]] | | programming language = [[Ruby (programming language)|Ruby]] | ||
| genre = [[Bioinformatics]] | | genre = [[Bioinformatics]] | ||
| license = [[ | | 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 [[ | '''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: | [[Category:Free software programmed in Ruby]] | ||
[[Category:Computational science]] | [[Category:Computational science]] | ||
[[Category:Bioinformatics software]] | [[Category:Bioinformatics software]] | ||
[[Category:Software using the BSD license]] | |||
Latest revision as of 19:22, 23 December 2025
Script error: No such module "Infobox".Template:Template other Script error: No such module "Check for unknown parameters".Script error: No such module "Check for conflicting parameters". 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 BSD 2-clause license or Ruby licence[2] and is one of a number of Bio* projects, designed to reduce code duplication.[3]
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]
Popular Biogems
| # | Biogem | Description | Version |
|---|---|---|---|
| 1 | bio | Bioinformatics Library | 1.4.3.0001 |
| 2 | biodiversity | Parser of scientific names | 3.1.5 |
| 3 | Simple Spreadsheet extractor | Basic spreadsheet content extraction using Apache poi | 0.13.3 |
| 4 | Bio gem | Software generator for Ruby | 1.36 |
| 5 | Bio samtools | Binder of samtools for Ruby | 2.1.0 |
| 6 | t2 server | Support for interacting with the taverna 2 server | 1.1.0 |
| 7 | bio ucsc api | The Ruby ucsc api | 0.6.2 |
| 8 | entrez | http request to entrez e-utilities | 0.5.8.1 |
| 9 | bio gadget | Gadget for bioinformatics | 0.4.8 |
| 10 | sequenceserver | Blast search made easy! | 0.8.7 |
See also
References
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External links
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