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= BioRuby BioRuby project aims to implement integrated environment for Bioinformatics. Object oriented scripting language Ruby has many good points suitable for bioinfomatics research. Powerful regular expressions like Perl, purely object oriented, simple and very clean syntax -- easy to learn for beginners, easy to use for biologists, powerful enough for 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 any information you need. Biological sequences are treated with Ruby's powerful string methods and regular expressions. Daily tools like Blast, Fasta and Hmmer programs can be executed and the results are fully parsed to extract scores and/or alignments. BioRuby also supports some databases and web services developed in Japan such as KEGG, AAindex, and DBGET etc. == WHERE TO GET * WWW -- ((<URL:http://bioruby.org/>)) * FTP -- ((<URL:ftp://ftp.bioruby.org/bioruby/>)) * CVS -- ((<URL:http://cvs.bioruby.org/>)) % cvs -d :pserver:firstname.lastname@example.org:/export/cvs login CVS password: (no password is required, just push return) % cvs -d :pserver:email@example.com:/export/cvs co bioruby == REQUIREMENTS * Ruby 1.6.6 or newer -- ((<URL:http://www.ruby-lang.org/>)) == OPTIONAL REQUIREMENTS * Ruby library -- ((<URL:http://raa.ruby-lang.org/>)) * [RAA:strscan] for parsing Blast default output. * [RAA:rexml] for parsing Blast XML output and using DAS. * [RAA:xmlparser] can be used for faster Blast XML parsing. * [RAA:ruby-dbi] and at least one driver from [RAA:mysql-ruby], [RAA:postgres], [RAA:oracle] to use with BioSQL. * [RAA:bdb] for faster flat file indexing. * [RAA:pp] for pretty print in debug. * [RAA:soap4r] (version >= 22.214.171.124) for KEGG API. Note that libraries which SOAP4R depends such as [RAA:date2], [RAA:devel-logger], [RAA:http-access] (version >= j) with one of [RAA:xmlscan], [RAA:rexml], [RAA:rexml-stable], [RAA:xmlparser], [RAA:nqxml] are also needed. Note that 'strscan', 'rexml', 'pp', 'date2' and 'xmlscan' are included in the Ruby 1.8.0 distibution (you don't need to install them by yourself). * External applications can be used if installed * Blast (version >= 2.2.5) for blast execution on local computer * FASTA for fasta, ssearch execution on local computer * HMMER for hmmsearch, hmmpfam execution on local computer == INSTALL In the bioruby source directory (such as bioruby-x.x.x/), run install.rb as follows: % ruby install.rb config % ruby install.rb setup % su # ruby install.rb install If you are using Mac OS X, you should use 'sudo' command instead of 'su'. % ruby install.rb config % ruby install.rb setup % sudo ruby install.rb install You can try % ruby install.rb --help for more details. If you want to use the OBDA (Open Bio Database Access) to obtain database entries, copy a sample config file etc/bioinformatics/seqdatabase.ini to /etc/bioinformatics/seqdatabase.ini (system wide configuration) or ~/.bioinformatics/seqdatabase.ini (personal configuration) and chage the contens according to your preference. For more informations on the OBDA, see ((<URL:http://obda.open-bio.org/>)). == USAGE You can load all BioRuby classes just by require 'bio' and all the BioRuby classes are defined under the module Bio for the name space. See the documentation for each class. #!/usr/bin/env ruby require 'bio' == LICENCE GPL for applications, LGPL for libraries. Note that, install.rb included in the BioRuby package comes from [RAA:setup] by Minero Aoki. == AUTHORS * KATAYAMA Toshiaki <firstname.lastname@example.org>, project leader * Yoshinori K. Okuji <email@example.com> * Mitsuteru C. Nakao <firstname.lastname@example.org> * KAWASHIMA Shuichi <email@example.com> * GOTO Naohisa <firstname.lastname@example.org> * and many others on the Internet...