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Copyright

Copyright © 2001-2007 Toshiaki Katayama <k@bioruby.org>, Copyright © 2008 Jan Aerts <jandot@bioruby.org> Copyright © 2011-2019 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

• The above statement is limited to this file. See below about BioRuby’s copyright and license.

++

Copyright © 2001-2019 Toshiaki Katayama <k@bioruby.org>

BioRuby is an open source Ruby library for developing bioinformatics software. Object oriented scripting language Ruby has many features suitable for bioinformatics research, for example, clear syntax to express complex objects, regular expressions for text handling as powerful as Perl’s, a wide variety of libraries including web service etc. As the syntax of the Ruby language is simple and very clean, we believe that it is easy to learn for beginners, easy to use for biologists, and also powerful enough for the software developers.

In BioRuby, you can retrieve biological database entries from flat files, internet web servers and local relational databases. These database entries can be parsed to extract information you need. Biological sequences can be treated with the fulfilling methods of the Ruby’s String class and with regular expressions. Daily tools like Blast, Fasta, Hmmer and many other software packages for biological analysis can be executed within the BioRuby script, and the results can be fully parsed to extract the portion you need. BioRuby supports major biological database formats and provides many ways for accessing them through flatfile indexing, web services etc. Various web services can be easily utilized by BioRuby.

See RELEASE_NOTES.rdoc for news and important changes in this version.

README.rdoc

This file. General information and installation procedure.

RELEASE_NOTES.rdoc

News and important changes in this release.

KNOWN_ISSUES.rdoc

Known issues and bugs in BioRuby.

doc/RELEASE_NOTES-*.rdoc

Release notes for old versions.

doc/Changes-1.3.rdoc

News and incompatible changes from 1.2.1 to 1.3.0.

doc/Changes-0.7.rd

News and incompatible changes from 0.6.4 to 1.2.1.

doc/Tutorial.rd

BioRuby Tutorial.

doc/Tutorial.rd.html

HTML version of Tutorial.rd.

ChangeLog

History of changes.

doc/ChangeLog-*

ChangeLog for old versions.

doc/ChangeLog-before-1.4.2

changes before 1.4.2.

doc/ChangeLog-before-1.3.1

changes before 1.3.1.

README_DEV.rdoc

Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.

doc/Tutorial.rd.ja

BioRuby Tutorial written in Japanese.

doc/Tutorial.rd.ja.html

HTML version of Tutorial.rd.ja.

In sample/, There are many sample codes and demo scripts.

BioRuby’s official website is at bioruby.org/. You will find links to related resources including downloads, mailing lists, Wiki documentation etc. in the top page.

• bioruby.org/

Mirror site is available, hosted on Open Bioinformatics Foundation (OBF).

• bioruby.open-bio.org/

The stable release is freely available from the BioRuby website.

• bioruby.org/archive/

RubyGems (packaging system for Ruby) version of the BioRuby package is also available for easy installation.

• rubygems.org/gems/bio

If you need the latest development version, this is provided at

• github.com/bioruby/bioruby

and can be obtained by the following procedure:

% git clone git://github.com/bioruby/bioruby.git

• Ruby 2.0.0 or later – www.ruby-lang.org/

  • Ruby 2.7.8, 3.0.6, 3.1.4, 3.2.2 or later is recommended.

  • See KNOWN_ISSUES.rdoc for Ruby version specific problems.

Some optional libraries can be utilized to extend BioRuby’s functionality. If your needs meets the following conditions, install them by using RubyGems, or download and install from the following web sites.

Creating faster flatfile index using Berkley DB:

• GitHub:ruby-bdb (which took over bdb) (No RubyGems available)

  • Oracle Berkeley DB and C compiler will be required.

If you are using RubyGems, just type

% gem install bio

Alternatively, manually download bio-X.X.X.gem from bioruby.org/archive/ and install it by using gems command.

To check if bioruby works fine on a machine, self-test codes are bundled. Note that some tests may need internet connection.

To run tests,

% ruby test/runner.rb

For those familiar with Rake,

% rake test

also works.

Before reporting test failure, please check KNOWN_ISSUES.rdoc about known platform-dependent issues. We are happy if you write patches to solve the issues.

If you want to use the OBDA (Open Bio Database Access) to obtain database entries, copy a sample configuration file in the BioRuby distribution

bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini

to

/etc/bioinformatics/seqdatabase.ini	(system wide configuration)

or

~/.bioinformatics/seqdatabase.ini	(personal configuration)

and change the contents according to your preference. For more information on the OBDA, see obda.open-bio.org/ .

You can load all BioRuby classes just by requiring ‘bio.rb’. All the BioRuby classes and modules are located under the module name ‘Bio’ to separate the name space.

#!/usr/bin/env ruby
require 'bio'

You can also read other documentation in the ‘doc’ directory.

bioruby-x.x.x/doc/

Many plugins (called Biogem) are now available. See biogems.info/ for list of plugins and related software utilizing BioRuby.

• biogems.info/

Plugins (Biogems) listed below had been included in BioRuby in former days, and were split to separate packages to reduce complexity and external dependencies.

• bio-shell

• bio-executables

• bio-blast-xmlparser

• bioruby-phyloxml

  • NOTE: Please uninstall bio-phyloxml, that have been created as a preliminary trial of splitting a module in 2012 and have not been maintained after that.

• bio-biosql

Plugins (Biogems) listed below may be useful for running existing codes.

• bio-old-biofetch-emulator – Emulates deprecated BioRuby’s BioFetch server by using other existing web services.

To develop your own plugin, see “Plugins” pages of BioRuby Wiki.

• bioruby.open-bio.org/wiki/Plugins

For existing BioRuby users, it is recommended to install the following gems:

bio-shell

If you use the BioRuby Shell.

bio-executables

If you use br_bio* commands.

bio-old-biofetch-emulator

If you run existing codes using BioFetch, including sample and demo codes in sample/.

bio-blast-xmlparser

If you treat BLAST XML result files and Expat XML parser (with development files) is installed in your system.

bioruby-phyloxml

If you use Bio::PhyloXML and Libxml2 (with developemnt files) is installed in your system.

Note that it is NOT recommended to install bio-biosql unless you have really used Bio::SQL, because it depends on older version of ActiveRecords and ActiveSupport that may not be run on recent Ruby versions.

BioRuby can be freely distributed under the same terms as Ruby. See the file COPYING (or COPYING.ja written in Japanese).

As written in the file COPYING, see the file LEGAL for files distributed under different license.

If you use BioRuby in academic research, please consider citing the following publication.

• BioRuby: Bioinformatics software for the Ruby programming language. Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama. Bioinformatics (2010) 26(20): 2617-2619.

  • doi: 10.1093/bioinformatics/btq475

  • PMID: 20739307

Current staff of the BioRuby project can be reached by sending e-mail to <staff@bioruby.org>.