BioRuby is a collection of

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

Ruby Ruby is a pinkish-red-to-blood-red-colored gemstone, a variety of the mineral corundum ( aluminium oxide). Ruby is one of the most popular traditional jewelry gems and is very durable. Other varieties of gem-quality corundum are called sapph ...

code, comprising classes for computational

molecular biology Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

and

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

. It contains classes for DNA and protein

sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome ...

sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...

, biological database parsing,

structural biology Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries we ...

and other bioinformatics tasks. BioRuby is released under the

GNU GPL The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first ...

version 2 or Ruby licence and is one of a number of Bio* projects, designed to reduce code duplication. In 2011, the BioRuby project introduced the Biogem software plugin system, with two or three new plugins added every month. BioRuby is managed via the BioRuby website and

GitHub GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...

repository.

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 is an Open-source software, open-source collection of non-commercial Python (programming language), Python tools for computational biology and bioinformatics.Refer to the Biopython website for othepapers describing Biopython and a list ...

. 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, culminating with the release of version 1.0.0 in February 2006. Between 2009 and 2012, BioRuby was the focus of a number of

Google Summer of Code The Google Summer of Code, often abbreviated to GSoC, is an international annual program in which Google awards stipends to contributors who successfully complete a free and open-source software coding project during the summer. , the program is ...

projects to improve the codebase. 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. Any gem published via the Biogem framework is also listed at biogems.info. 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.

Popular Biogems

References

External links