BioRuby

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 has been frequently updated by contributors both informally and at organised “hackathon” events, with the most recent release of version 1.4.3.0001 in May 2013.

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.

BioRuby has been the focus of a number of Google Summer of Code projects, including;

Version history

The above list of releases is abbreviated; the full list can be found here.

Installation

BioRuby is able to be installed onto any instance of Ruby; as Ruby is a highly cross platform language, BioRuby is available on most modern operating systems.

It is required that Ruby be installed prior to BioRuby installation.

Mac OS X/Unix/Linux

Mac OS X has Ruby and RubyGems installed by default and for Unix/Linux installation of RubyGems is recommended.

If Ruby and RubyGems are installed, BioRuby can be installed using this command via the terminal;

If you need to install from the source code distribution, obtain the latest package from the archive and in the bioruby source directory, run the following commands;

Windows

Installation via RubyGems is highly recommended; this requires Ruby and RubyGems be installed, then the following command run at the command prompt;

Usage

BioRuby can be accessed via the terminal, Ruby IDEs or via a BioRubyOnRails implementation. Instructions for the installation and use of BioRubyOnRails can be found at bioruby.open-bio.org/wiki/BioRubyOnRails.

Basic Syntax

The following are examples of basic sequence manipulations using BioRuby. You can find more syntax examples at bioruby.open-bio.org/wiki/SampleCodes#.

String to Bio::Sequence object

Parsing a string into Bio::Sequence object.

Bio::Sequence object to String

This an example that showcases the simplicity of BioRuby. It does not require any method call to convert the sequence object to a string.

Parsing a sequence object into a string.

Translating a DNA or RNA Sequence or SymbolList to Protein

There is no need to convert DNA sequence to RNA sequence or vice versa before its translation in BioRuby. You can simply call a translate method for Bio::Sequence::NA object.

Translating a single codon to a single amino acid

The general translation example shows how to use the translate method of Bio::Sequence::NA object but most of what goes on is hidden behind the convenience method. If you only want to translate a single codon into a single amino acid you get exposed to a bit more of the gory detail but you also get a chance to figure out more of what is going on under the hood.

Another way to do this is the following

Writing Sequences in Fasta format

To print out any Bio::Sequence object in FASTA format, All you need is to call is "puts objectName.is_fasta()"

Reading in a Fasta file

This program opens FASTA format file for reading and iterates on each sequence in the file.

This program automatically detects and reads FASTA format files given as its arguments.

Similar but specify FASTA format explicitly.

See more syntax examples on SampleCodes

Major Classes

The below classes have been identified by a group of major code contributors as major classes.

Basic Data Structure

These classes allow you to natively store complicated biological data structure effectively.

Databases and sequence file formats

Accesses online biological databases and reads from common file-formats.

Wrapper and parsers for bioinformatics tool

These classes allow for easy access to commonly used bioinformatics tools.

File, network and database I/O

A full list of classes and modules can be found at bioruby.org/rdoc/.

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.

Biogem makes use of github.com and rubygems.org and requires the setup of unique accounts on these websites.

Plugins

BioRuby will have a completed plugin system at the 1.5 release.