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Machine Learning"],"readme":"--\n= README.rdoc - README for BioRuby\nCopyright:: Copyright (C) 2001-2007 Toshiaki Katayama \u003ck@bioruby.org\u003e,\n            Copyright (C) 2008      Jan Aerts \u003cjandot@bioruby.org\u003e\n            Copyright (C) 2011-2019 Naohisa Goto \u003cng@bioruby.org\u003e\nLicense::   The Ruby License\n* The above statement is limited to this file. See below about BioRuby's\n  copyright and license.\n++\n\n= BioRuby\n\nCopyright (C) 2001-2019 Toshiaki Katayama \u003ck@bioruby.org\u003e\n\nBioRuby is an open source Ruby library for developing bioinformatics\nsoftware.  Object oriented scripting language Ruby has many features\nsuitable for bioinformatics research, for example, clear syntax to\nexpress complex objects, regular expressions for text handling as\npowerful as Perl's, a wide variety of libraries including web service\netc.  As the syntax of the Ruby language is simple and very clean, we\nbelieve that it is easy to learn for beginners, easy to use for\nbiologists, and also powerful enough for the software developers.\n\nIn BioRuby, you can retrieve biological database entries from flat\nfiles, internet web servers and local relational databases.  These\ndatabase entries can be parsed to extract information you need.\nBiological sequences can be treated with the fulfilling methods of the\nRuby's String class and with regular expressions.  Daily tools like\nBlast, Fasta, Hmmer and many other software packages for biological\nanalysis can be executed within the BioRuby script, and the results\ncan be fully parsed to extract the portion you need.  BioRuby supports\nmajor biological database formats and provides many ways for accessing\nthem through flatfile indexing, web services etc.  Various web\nservices can be easily utilized by BioRuby.\n\n\n== FOR MORE INFORMATION\n\nSee RELEASE_NOTES.rdoc for news and important changes in this version.\n\n=== Documents in this distribution\n\n==== Release notes, important changes and issues\n\nREADME.rdoc:: This file. General information and installation procedure.\nRELEASE_NOTES.rdoc:: News and important changes in this release.\nKNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.\ndoc/RELEASE_NOTES-*.rdoc:: Release notes for old versions.\ndoc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.\ndoc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.\n\n==== Tutorials and other useful information\n\ndoc/Tutorial.rd:: BioRuby Tutorial.\ndoc/Tutorial.rd.html:: HTML version of Tutorial.rd.\n\n==== BioRuby development\n\nChangeLog:: History of changes.\ndoc/ChangeLog-*:: ChangeLog for old versions.\ndoc/ChangeLog-before-1.4.2:: changes before 1.4.2.\ndoc/ChangeLog-before-1.3.1:: changes before 1.3.1.\nREADME_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.\n\n==== Documents written in Japanese\n\ndoc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.\ndoc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.\n\n==== Sample codes\n\nIn sample/, There are many sample codes and demo scripts.\n\n=== WWW\n\nBioRuby's official website is at http://bioruby.org/.\nYou will find links to related resources including downloads,\nmailing lists, Wiki documentation etc. in the top page.\n\n* http://bioruby.org/\n\nMirror site is available, hosted on Open Bioinformatics Foundation (OBF).\n\n* http://bioruby.open-bio.org/\n\n== WHERE TO OBTAIN\n\n=== WWW\n\nThe stable release is freely available from the BioRuby website.\n\n* http://bioruby.org/archive/\n\n=== RubyGems\n\n{RubyGems (packaging system for Ruby)}[http://rubygems.org/] version of\nthe BioRuby package is also available for easy installation.\n\n* https://rubygems.org/gems/bio\n\n=== git\n\nIf you need the latest development version, this is provided at\n\n* https://github.com/bioruby/bioruby\n\nand can be obtained by the following procedure:\n\n  % git clone git://github.com/bioruby/bioruby.git\n\n\n== REQUIREMENTS\n\n* Ruby 2.0.0 or later -- http://www.ruby-lang.org/\n  * Ruby 2.7.8, 3.0.7, 3.1.6, 3.2.7, 3.3.7, 3.4.2 or later is recommended.\n  * See KNOWN_ISSUES.rdoc for Ruby version specific problems.\n\n\n== OPTIONAL REQUIREMENTS\n\nSome optional libraries can be utilized to extend BioRuby's functionality.\nIf your needs meets the following conditions, install them by using RubyGems,\nor download and install from the following web sites.\n\nCreating faster flatfile index using Berkley DB:\n\n* {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]\n  (which took over {bdb}[https://github.com/ruby-bdb/bdb])\n  (No RubyGems available)\n  * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.\n\n\n== INSTALL\n\n=== INSTALL by using RubyGems (recommended)\n\nIf you are using RubyGems, just type\n\n  % gem install bio\n\nAlternatively, manually download bio-X.X.X.gem from \nhttp://bioruby.org/archive/ and install it by using gems command.\n\n\n=== Running self-test\n\nTo check if bioruby works fine on a machine, self-test codes are bundled.\nNote that some tests may need internet connection.\n\nTo run tests,\n\n % ruby test/runner.rb\n\nFor those familiar with Rake,\n\n % rake test\n\nalso works.\n\nBefore reporting test failure, please check KNOWN_ISSUES.rdoc about known\nplatform-dependent issues.  We are happy if you write patches to solve the\nissues.\n\n\n== SETUP\n\nIf you want to use the OBDA (Open Bio Database Access) to obtain database\nentries, copy a sample configuration file in the BioRuby distribution\n\n  bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini\n\nto\n\n  /etc/bioinformatics/seqdatabase.ini\t(system wide configuration)\n\nor\n\n  ~/.bioinformatics/seqdatabase.ini\t(personal configuration)\n\nand change the contents according to your preference.  For more\ninformation on the OBDA, see http://obda.open-bio.org/ .\n\n\n== USAGE\n\nYou can load all BioRuby classes just by requiring 'bio.rb'.  All the\nBioRuby classes and modules are located under the module name 'Bio' to\nseparate the name space.\n\n  #!/usr/bin/env ruby\n  require 'bio'\n\nYou can also read other documentation in the 'doc' directory.\n\n  bioruby-x.x.x/doc/\n\n\n== PLUGIN (Biogem)\n\nMany plugins (called Biogem) are now available. See http://biogems.info/\nfor list of plugins and related software utilizing BioRuby.\n\n* http://biogems.info/\n\nPlugins (Biogems) listed below had been included in BioRuby in former days,\nand were split to separate packages to reduce complexity and external\ndependencies.\n\n* {bio-shell}[https://rubygems.org/gems/bio-shell]\n* {bio-executables}[https://rubygems.org/gems/bio-executables]\n* {bio-blast-xmlparser}[https://rubygems.org/gems/bio-blast-xmlparser]\n* {bioruby-phyloxml}[https://rubygems.org/gems/bioruby-phyloxml]\n  * NOTE: Please uninstall bio-phyloxml, that have been created as a\n    preliminary trial of splitting a module in 2012 and have not been\n    maintained after that.\n* {bio-biosql}[https://rubygems.org/gems/bio-biosql]\n\nPlugins (Biogems) listed below may be useful for running existing codes.\n\n* {bio-old-biofetch-emulator}[https://rubygems.org/gems/bio-old-biofetch-emulator] -- Emulates deprecated BioRuby's BioFetch server by using other existing web services.\n\nTo develop your own plugin, see \"Plugins\" pages of BioRuby Wiki.\n\n* http://bioruby.open-bio.org/wiki/Plugins\n\n=== Recommended Plugins (gems)\n\nFor existing BioRuby users, it is recommended to install the following gems:\n\nbio-shell :: If you use the BioRuby Shell.\nbio-executables :: If you use br_bio* commands.\nbio-old-biofetch-emulator :: If you run existing codes using BioFetch, including sample and demo codes in sample/.\nbio-blast-xmlparser :: If you treat BLAST XML result files and Expat XML parser (with development files) is installed in your system.\nbioruby-phyloxml :: If you use Bio::PhyloXML and Libxml2 (with developemnt files) is installed in your system.\n\nNote that it is NOT recommended to install bio-biosql unless you have\nreally used Bio::SQL, because it depends on older version of ActiveRecords\nand ActiveSupport that may not be run on recent Ruby versions.\n\n\n== LICENSE\n\nBioRuby can be freely distributed under the same terms as Ruby.\nSee the file COPYING (or COPYING.ja written in Japanese).\n\nAs written in the file COPYING, see the file LEGAL for files distributed\nunder different license.\n\n== REFERENCE\n\nIf you use BioRuby in academic research, please consider citing the following\npublication.\n\n* BioRuby: Bioinformatics software for the Ruby programming language.\n  Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and \n  Toshiaki Katayama.\n  Bioinformatics (2010) 26(20): 2617-2619.\n  * {doi: 10.1093/bioinformatics/btq475}[http://bioinformatics.oxfordjournals.org/content/26/20/2617]\n  * {PMID: 20739307}[http://www.ncbi.nlm.nih.gov/pubmed/20739307]\n\n\n== CONTACT\n\nCurrent staff of the BioRuby project can be reached by sending e-mail\nto \u003cstaff@bioruby.org\u003e.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioruby%2Fbioruby","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioruby%2Fbioruby","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioruby%2Fbioruby/lists"}