BioRuby
{{#invoke:Infobox|infobox}}Template:Template other{{#invoke:Check for unknown parameters | check | showblankpositional=1 | unknown = Template:Main other | preview = Page using Template:Infobox software with unknown parameter "_VALUE_"|ignoreblank=y | AsOf | author | background | bodystyle | caption | collapsetext | collapsible | developer | discontinued | engine | engines | genre | included with | language | language count | language footnote | latest preview date | latest preview version | latest release date | latest release version | latest_preview_date | latest_preview_version | latest_release_date | latest_release_version | licence | license | logo | logo alt | logo caption | logo upright | logo size | logo title | logo_alt | logo_caption | logo_upright | logo_size | logo_title | middleware | module | name | operating system | operating_system | other_names | platform | programming language | programming_language | released | replaced_by | replaces | repo | screenshot | screenshot alt | screenshot upright | screenshot size | screenshot title | screenshot_alt | screenshot_upright | screenshot_size | screenshot_title | service_name | size | standard | title | ver layout | website | qid }}Template:Main other 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.<ref name="pmid20739307">Template:Cite journal</ref> BioRuby is released under the GNU GPL version 2 or Ruby licence<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> and is one of a number of Bio* projects, designed to reduce code duplication.<ref name="pmid12230038">Template:Cite journal</ref>
In 2011, the BioRuby project introduced the Biogem software plugin system,<ref name="pmid22332238">Template:Cite journal</ref> with two or three new plugins added every month.
BioRuby is managed via the BioRuby website and GitHub repository.<ref name="github">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref><ref name="home">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>
HistoryEdit
BioRubyEdit
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,<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> culminating with the release of version 1.0.0 in February 2006.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</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">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> BioRuby Version 2.0.0 was released in 2019.<ref name="home" />
BiogemEdit
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">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> Any gem published via the Biogem framework is also listed at biogems.info.<ref name="biogems-home">{{#invoke:citation/CS1|citation |CitationClass=web }}</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>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>
Popular BiogemsEdit
| # | 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 |