ngoto-bio 1.2.9.9001

data/ChangeLog

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+2008-07-30  BioHackathon2008 participants from BioRuby project
+
+	* Branch 'biohackathon2008' is merged.
+	  See doc/Changes-1.3.rd for incompatible changes.
+
+	* lib/bio/sequence.rb, lib/bio/sequence/
+	* lib/bio/db/embl/
+	* lib/bio/db/genbank/
+	* lib/bio/db/fasta.rb, lib/bio/db/fasta/
+
+	  A new method #to_biosequence is added to Bio::EMBL, Bio::GenBank
+	  and Bio::FastaFormat. Bio::FastaFormat#to_seq is now an alias of
+	  the #to_biosequence method.
+
+	  Bio::Sequence#output is added to output formatted text.
+	  Supported formats are: EMBL, GenBank, Fasta, or raw.
+
+	  Written by Naohisa Goto and Jan Aerts.
+	
+	* lib/bio/db/biosql/
+	* lib/bio/io/sql.rb, lib/bio/io/biosql/
+
+	  New BioSQL implementation by Raoul Jean Pierre Bonnal.
+
+	* lib/bio/reference.rb
+	* lib/bio/feature.rb
+
+	  Bio::References and Bio::Features are obsoleted.
+	  For more information, see doc/Changes-1.3.rd.
+
+	* (Many changes are not listed here. See git log for details.)
+
+2008-07-30  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
+
+	  Branch 'test-gff3' in git://github.com/ngoto/bioruby is merged.
+	  Fixed gff3 attribute bug, and many improvements are added.
+	  See doc/Changes-1.3.rd for incompatible changes.
+	  Thanks to Ben Woodcroft who reported the bug and contributed codes.
+
+2008-07-29  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Bug fix: fixed ScanError when bit score is in exponential notation
+	  such as 1.234e+5. Regular expressions for numerics including
+	  exponential notations are changed to get correct values.
+
+2008-07-18  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/hmmer.rb
+
+	  Bug fix: ArgumentError caused by misspelling of a variable name.
+
+2008-06-23  Jan Aerts <jan.aerts@gmail.com>
+
+	* README.rdoc
+	* README_DEV.rdoc
+	* gemspec.rb
+	
+	  Renamed README files to RDoc gets parsed on github website.
+	  (commit 34b7693f74de2358759e955d8ce36cfe15e64b54)
+	  Edited README.rdoc and README_DEV.rdoc to reflect move from CVS
+	  to git.
+	  (commit a61b16163d3ca74f3f7c8d8e8f03f5f8c68dee60)
+
+2008-06-13  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/reference.rb
+	* test/unit/bio/test_reference.rb
+
+	  * New method Bio::Reference#pubmed_url added (renamed the url method
+	    in CVS revision 1.25).
+	  * Bio::Reference#endnote is changed not to overwrite url if url is
+	    already given by user.
+	  * Improvement of Bio::Reference#bibtex method. (Idea to improve
+	    bibtex method is originally made by Pjotr Prins.)
+
+	* test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
+	  "require 'bio/sequence'" is needed to run the tests in this file.
+	  (commit 735e3563b723645afa65f0e4213a7c92152f68ec)
+
+2008-05-19  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* sample/fastasort.rb
+
+	  Simple example for sorting a flatfile
+	  (commit 677ac7c0707860f0478e75f72f23faa05b29dc6d)
+
+	* doc/Tutorial.rd
+	* sample/fastagrep.rb
+	* sample/fastasort.rb
+
+	  Piping FASTA files (examples and doc)
+	  (commit ecd5e04477246dcf6cac84a6fbd21fb59efa3cf0)
+
+2008-05-14  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Bug fix: Possibly because of the output format changes of PHI-BLAST,
+	  Bio::Blast::Default::Report::Iteration#eff_space (and the shortcut
+	  method in the Report class) failed for PHI-BLAST (blastpgp) results,
+	  and Iteration#pattern and #pattern_positions (and the
+	  shortcut methods in the Report class) returned incorrect values.
+
+2008-05-12  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/xmlparser.rb, lib/bio/appl/blast/rexml.rb
+
+	  Bug fix: unit test sometime fails due to improper treatment of some
+	  Blast parameters and difference between rexml and xmlparser.
+	  To fix the bug, types of some parameters may be changed, e.g.
+	  Bio::Blast::Report#expect is changed to return Float or nil.
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Bug fix: Bio::Blast::Default::Report#eff_space returns wrong value 
+	  ("Effective length of database"). It should return the value of
+	  "Effective search space".
+
+	* test/unit/bio/appl/blast/test_xmlparser.rb
+
+	  Bug fix: tests in test/unit/bio/appl/blast/test_report.rb were
+	  ignored because of conflicts of the names of test classes.
+	  Class name in test_xmlparser.rb is changed to fix the bug.
+
+2008-04-23  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/embl/common.rb
+
+	  Bug fix: Bio::EMBL#references failed to parse journal name,
+	  volume, issue, pages, and year. In addition, it might failed
+	  to parse PubMed ID.
+	  (commit c715f51729b115309a78cf29fdce7fef992da875)
+
+2008-04-18  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/embl/sptr.rb
+
+	  Bug fix: Bio::SPTR#references raises NoMethodError since
+	  lib/bio/db/embl/sptr.rb CVS version 1.34.
+	  (commit 1b3e484e19c9c547cecfe53858a646b525685e0d)
+
+2008-04-15  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/rpsblast.rb
+
+	  Newly added RPS-Blast default (-m 0) output parser.
+
+2008-04-01  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Fixed a bug: Failed to parse database name in some cases.
+	  Thanks to Tomoaki Nishiyama who reported the bug and sent patches
+	  ([BioRuby-ja] BLAST format0 parser fails header parsing output
+	  of specific databases).
+
+	* lib/bio/db/pdb/chain.rb, lib/bio/db/pdb/pdb.rb
+
+	  Fixed bugs: Bio::PDB::Chain#aaseq failed for nucleotide chain;
+	  Failed to parse chains for some entries (e.g. 1B2M).
+	  Thanks to Semin Lee who reported the bugs and sent patches
+	  ([BioRuby] Bio::PDB parsing problem (1B2M)).
+
+2008-02-19  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/ncbirest.rb
+	* lib/bio/io/pubmed.rb
+
+	  NCBI E-Utilities (REST) functionality is separated to ncbirest.rb
+	  and pubmed.rb is changed to utilize the Bio::NCBI::REST class for
+	  esearch and efetch. You can now search and retrieve any database
+	  in any format that NCBI supports by E-Utilities through the
+	  Bio::NCBI::REST interface (currently, only esearch and efetch methods
+	  are implemented).
+	  (commit 0677bb69044cf6cfba453420bc1bbeb422f691c1)
+	  (commit f60e9f8153efacff0c97d12fb5c0830ebeb02edd)
+	  (commit 6e4670ab5e67ca596788f4c26a95a9687d36ce84)
+
+2008-02-13  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* doc/Tutorial.rd
+	  (commit d7ee01d86d6982f6b8aa19eba9adac95bebb08e8)
+
+2008-02-12  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Fixed bugs: Failed to parse query length for long query
+	  (>= 10000 letters) as comma is inserted for digit separator
+	  by blastall; Failed to parse e-value for some BLASTX results.
+	  Thanks to Shuji Shigenobu who reported the bugs and sent patches.
+
+2008-02-11  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* doc/Tutorial.rd
+
+	  Expanding on the Tutorial
+	  (bdc1d14f497909041fa761f659a74d98702a335a)
+	  Minor adjustments to Tutorial
+	  (72b5f4f0667a3a0c44ca31b0ab8228381e37919c)
+
+2008-02-06  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* sample/na2aa.rb
+
+	  Simple example to translate any NA to AA fasta
+	  (commit 433f974219cf04342935c1760464af24a5696c49)
+
+2008-02-05  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* sample/gb2fasta.rb
+
+	  Fixed broken require in gb2fasta example
+	  (commit b55daed0d6cff2e45155be01ef2a946925c972cf)
+
+2008-02-05  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* doc/Tutorial.rd
+
+	  Minor tweak to Tutorial.rd
+	  (commit 75416d780f99de24498a47fd22703d74f9a22329)
+
+2008-02-03  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* doc/Tutorial.rd
+
+	  More doctests in Tutorial.rd
+	  (commit 39d182bb67977956c0f22631ac596d65ccce74ff)
+
+2008-02-02  Pjotr Prins <pjotr.prins@wur.nl>
+
+	* doc/Tutorial.rd
+
+	  Tabs in the Tutorial broke the rd parser - the Wiki will be fixed
+	  now.
+	  (commit 49078a5dea4f16f44add1882c60bf75df67ea19b)
+	  Updating tutorial.
+	  (commit f2f2005c3964f37e2d65afef0d52e63950d6bcb7)
+	  (commit d2b05581953712d0ac67ba0de1aa43853ed4e27f)
+
+2008-02-02  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/rails/vendor/plugins/
+
+	  The 'generators' directory is moved under the 'bioruby' subdirectory
+	  so that 'bioruby --rails' command can work with Rails 2.x series
+	  in addition to the Rails 1.2.x series.
+
+2008-01-30  Mitsuteru Nakao <n@bioruby.org>
+
+	* lib/bio/appl/blast.rb
+
+	  Fixed the bug at building the blastall command line options ('-m 0').
+	  (commit 61443d177847825505103488573186dfc4e7568e)
+
+2008-01-10  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/emboss.rb
+
+	  Added a method Bio::EMBOSS.run(program, arguments...)
+	  and Bio::EMBOSS.new is obsoleted.
+	  (commit fa04d97b073aefe05edc34a84498ba0a57ff98d2)
+
+2008-01-10  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/hinv.rb
+
+	  Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
+	  web service in REST mode is added.
+
+2007-12-30  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 1.2.1 released
+
+	  This version is not Ruby 1.9 (released few days ago) compliant yet.
+
+2007-12-28  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/report/format0.rb
+
+	  Fixed parse error when compisition-based statistics were enabled.
+	  In addition, Bio::Blast::Default::Report#references and
+	  Bio::Blast::Default::Report::HSP#stat_method methods are added.
+	  In NCBI BLAST 2.2.17, default option of composition-based
+	  statistics for blastp or tblastn are changed to be enabled
+	  by default.
+
+	* lib/bio/appl/blast/report/wublast.rb
+
+	  Changed to follow the above changes in format0.rb.
+
+	* lib/bio/sequence/common.rb
+
+	  Ruby 1.9 compliant: in window_search method, a local variable name
+	  outside the iterator loop is changed not to be shadowed by the
+	  iterator variable.
+
+	* lib/bio/db/pdb/pdb.rb
+
+	  Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
+	  argument passing of super from method defined by define_method()
+	  is not supported. Specify all arguments explicitly." error.
+
+	  Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
+	  Bio::PDB::Record.create_definition_hash (Note: they should only
+	  be internally used by PDB parser and users should not call them)
+	  are changed to follow the change of Module#constants which
+	  returns an array of Symbol instead of String.
+
+2007-12-26  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/alignment.rb
+
+	  Ruby 1.9 compliant: in EnumerableExtension#each_window and
+	  OriginalAlignment#index methods, local variable names outside the
+	  iterator loops are changed not to be shadowed by iterator
+	  variables.
+	  
+	  Warning messages for uninitialized instance variables of
+	  @gap_regexp, @gap_char, @missing_char, and @seqclass
+	  are suppressed.
+
+	* test/unit/bio/test_alignment.rb
+
+	  Ruby 1.9 compliant: Ruby 1.9 compliant: The last comma in Array.[]
+	  is no longer allowed. (For example,
+	    class A < Array; end; A[ 1, 2, 3, ]
+	  raises syntax error in Ruby 1.9.)
+
+2007-12-21  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db/medline.rb
+
+	  Added doi and pii methods to extract DOI and PII number from AID field
+
+2007-12-18  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/pdb/pdb.rb
+
+	  Bio::PDB#inspect is added to prevent memory exhaust problem.
+	  ([BioRuby] Parse big PDB use up all memory)
+
+	* lib/bio/db/pdb/model.rb
+
+	  Bio::PDB::Model#inspect is added.
+
+	* lib/bio/db/pdb/chain.rb
+
+	  Bio::PDB::Chain#inspect is added.
+
+	* lib/bio/db/pdb/residue.rb
+
+	  Bio::PDB::Residue#inspect is added.
+	  This also affects Bio::PDB::Heterogen#inspect.
+
+2007-12-15  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 1.2.0 released
+
+	  * BioRuby shell is improved
+	    * file save functionality is fixed
+	    * deprecated require_gem is changed to gem to suppress warnings
+	    * deprecated end_form_tag is rewrited to suppress warnings
+	    * images for Rails shell are separated to the bioruby directory
+	    * spinner is shown during the evaluation
+	    * background image in the textarea is removed for the visibility
+	  * Bio::Blast is fixed to parse -m 8 formatted result correctly
+	  * Bio::PubMed is rewrited to enhance its functionality
+	    * e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
+	  * Bio::FlatFile is improved to accept recent MEDLINE format
+	  * Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
+	  * Bio::KEGG::API is fixed to skip filter when the value is Fixnum
+	  * A number of minor bug fixes
+
+2007-12-12  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/newick.rb:
+
+	  Changed to be compliant with the Gary Olsen's Interpretation of
+	  the "Newick's 8:45" Tree Format Standard.
+
+	* test/unit/bio/db/test_newick.rb
+
+	  More tests are added.
+
+	* lib/bio/io/flatfile/indexer.rb
+
+	  Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
+
+2007-11-28  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/pubmed.rb:
+
+	  Fixed search, query methods (but use of esearch and efetch is
+	  strongly recommended).
+
+	  efetch method is enhanced to accept any PubMed search options
+	  as a hash (to retrieve in XML format etc.)
+
+	  Changed to wait 3 seconds among each access by default to be
+	  compliant with the NCBI terms (Make no more than one request
+	  every 3 seconds).
+
+	  All Bio::PubMed.* class methods are changed to instance methods
+	  (interface as the class methods are remained for the backward
+	  compatibility).
+
+2007-07-19  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 1.1.0 released
+
+2007-07-17  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/das.rb
+
+	  Fixed that mapmaster method to return correct value (mapmaseter's
+	  URL). This bug is reported and fixed by Dave Thorne.
+
+2007-07-16  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/mafft/report.rb
+
+	  For generic multi-fasta formatted sequence alignment,
+	  Bio::Alignment::MultiFastaFormat is newly added based on
+	  Bio::MAFFT::Report class, and Bio::MAFFT::Report is
+	  changed to inherit the new class.
+	  Tests are added in test/unit/bio/appl/mafft/test_report.rb.
+
+	* lib/bio/alignment.rb
+
+	  New modules and classes Bio::Alignment::FactoryTemplate::* are added.
+	  They are used by following three new classes.
+	
+	* lib/bio/appl/muscle.rb
+	* lib/bio/appl/probcons.rb
+	* lib/bio/appl/tcoffee.rb
+
+	  New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
+	  for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
+	  Contributed by Jeffrey Blakeslee and colleagues.
+
+	* lib/bio/appl/clustalw.rb
+	* lib/bio/appl/mafft.rb
+
+	  Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
+	  to follow Bio::Alignment::FactoryTemplate (but not yet changed to
+	  use it).
+
+2007-07-09  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby shell on Rails has new CSS theme
+
+	  Completely new design for BioRuby shell on Rails translated from
+	  the 'DibdoltRed' theme on www.openwebdesign.org which is created by
+	  Darjan Panic and Brian Green as a public domain work!
+
+2007-07-09  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db/kegg/taxonomy.rb
+
+	  Newly added KEGG taxonomy file parser which treats taxonomic tree
+	  structure of the KEGG organisms. The file is available at
+	    ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
+	  and is a replacement of the previously used keggtab file (obsoleted).
+
+	* lib/bio/db/kegg/keggtab.rb
+
+	  Bio::KEGG::Keggtab is obsoleted as the file is no longer provided.
+	  Use Bio::KEGG::Taxonomy (lib/bio/db/kegg/taxonomy.rb) instead.
+
+	* lib/bio/shell/plugin/soap.rb
+
+	  Newly added web service plugins for BioRuby shell which supports
+	  NCBI SOAP, EBI SOAP and DDBJ XML in addition to the KEGG API.
+
+2007-07-09  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/pdb/pdb.rb
+
+	  Pdb_LString.new is changed not to raise error for nil.
+
+	  Fixed a bug when below records does not exist in a PDB entry:
+	  REMARK (remark), JRNL (jrnl), HELIX (helix),
+	  TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
+	  DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
+	  HEADER (entry_id, accession, classification),
+	  TITLE (definition), and REVDAT (version) records (methods).
+
+	  Incompatible change: Bio::PDB#record is changed to return
+	  an empty array for nonexistent record.
+
+	  (reported by Mikael Borg)
+
+2007-07-09  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/io/flatfile.rb
+
+	  Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
+
+2007-06-28  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/setup.rb, core.rb
+
+	  Changed not to use Dir.chdir by caching full path of the save
+	  directory at a start up time, so that user can freely change
+	  the work directory without affecting object/history saving
+	  functionality.
+
+	  Bio::Shell.cache[:savedir] stores the session saving directory
+	  (session means shell/session/{config,history,object} files),
+	  Bio::Shell.cache[:workdir] stores the working directory at a start
+	  up time (can be same directory with the :savedir) and both are
+	  converted and stored as full path allowing user to use Dir.chdir
+	  in the shell session).
+
+	  If --rails (-r) option is applied, 'bioruby' command will run in
+	  the Rails server mode, and the server will start in the :savedir.
+
+	  (A) IRB mode
+
+	  1. run in the current directory and the session will be saved
+	     in the ~/.bioruby directory
+
+	       % bioruby
+
+	  2. run in the current directory and the session will be saved
+	     in the foo/bar directory
+
+	       % bioruby foo/bar
+
+	  3. run in the current directory and the session will be saved
+	     in the /tmp/foo/bar directory
+
+	       % bioruby /tmp/foo/bar
+
+	  (B) Rails mode
+
+	  4. run in the ~/.bioruby directory and the session will also be saved
+	     in the ~/.bioruby directory
+
+	       % bioruby -r
+
+	  5. run in the foo/bar directory and the session will also be saved
+	     in the foo/bar directory
+
+	       % bioruby -r foo/bar
+
+	  6. run in the /tmp/foo/bar directory and the session will also be
+	     saved in the /tmp/foo/bar directory
+
+	       % bioruby -r /tmp/foo/bar
+
+	  (C) Script mode
+
+	  7. run in the current directory using the session saved
+	     in the ~/.bioruby directory
+
+	       % bioruby ~/.bioruby/shell/script.rb
+
+	  8. run in the current directory using the session saved
+	     in the foo/bar directory
+
+	       % bioruby foo/bar/shell/script.rb
+
+	  9. run in the current directory using the session saved
+	     in the /tmp/foo/bar directory
+
+	       % bioruby /tmp/foo/bar/shell/script.rb
+
+2007-06-21  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/setup.rb
+
+	  If no directory is specified to the bioruby command,
+	  use ~/.bioruby directory as the default save directory
+	  instead of the current directory, as suggested by Jun Sese.
+
+	  User can use 'bioruby' command without botherd by directories
+	  and files previously created by the 'bioruby' command
+	  in the current directory even when not needed.
+
+2007-05-19  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/appl/fasta.rb
+
+	  Bug fixed that exec_local fails to exec when @ktup is nil.
+	  This problem is reported and fixed by Fredrik Johansson.
+
+	* lib/bio/db/gff.rb
+
+	  parser_attributes method in GFF3 class is modified to use
+	  '=' char as a separator instead of ' ' (which is used in
+	  GFF2 spec).
+
+2007-04-06  Toshiaki Katayama <k@bioruby.org>
+
+	* COPYING, COPYING.LIB are removed
+
+	  BioRuby is now distributed under the same terms as Ruby.
+
+	  On behalf of the BioRuby developer, I have asked all authors of
+	  the BioRuby code to change BioRuby's license from LGPL to Ruby's.
+	  And we have finished to change license of all modules in the BioRuby
+	  library. This means that Ruby user can freely use BioRuby library
+	  without being annoyed by licensing issues.
+
+	* lib/bio/db/kegg/ko.rb is renamed to lib/bio/db/kegg/ortholog.rb
+
+	  KEGG KO database is renamed to KEGG ORTHOLOG database, thus we
+	  follow the change. Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG.
+	  
+	  Bio::KEGG::ORTHOLOG#genes, dblinks methods are rewrited to use
+	  lines_fetch method.
+
+	* lib/bio/data/aa.rb
+
+	  to_re method is changed that the generated regexp to include
+	  ambiguous amino acid itself - replacement of amino acid X should
+	  include X itself.
+
+2007-04-05  Trevor Wennblom <trevor@corevx.com>
+
+	* License headers are completely rewrited to Ruby's.
+
+2007-04-02  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/mafft.rb
+
+	  Incompatible change: Bio::MAFFT#output is changed to return
+	  a string of multi-fasta formmatted text. To get an array of
+	  Bio::FastaFormat objects (as of 1.0 or before), please use
+	  report.data instead.
+
+2007-03-29  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db/kegg/cell.rb
+
+	  Obsoleted as the KEGG CELL database is not publically available
+	  any more.
+
+2007-03-28  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/rails/.../bioruby_controller.rb
+
+	  BioRuby shell on Rails access is changed to be limited only from
+	  the localhost for security reason (if local_request?).
+
+	* lib/bio/command.rb
+
+	  The post_form method is modified to accept URL as a string and
+	  extended to accept params as
+	    array of string
+	    array of hash
+	    array of array
+	     or
+	    string
+	  in addition to hash (also can be ommited if not needed - defaults
+	  to nil).
+
+	  Keys and parameters of params are forced to use to_s for sure.
+
+	* lib/bio/io/ensembl.rb
+
+	  Re-designed to allows user to use Bio::Ensembl.new without
+	  creating inherited sub class.
+
+	  Changed to use Bio::Command.post_form
+
+	* lib/bio/das.rb
+
+	  Changed to use Bio::Command
+
+	* lib/bio/shell/plugin/das.rb
+
+	  Newly added BioDAS client plugin for BioRuby shell.
+
+	    das.list_sequences
+	    das.dna
+	    das.features
+
+2007-03-15  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/irb.rb
+
+	  Changed to load Rails environment when bioruby shell is invoked
+	  in the Rails project directory. This means that user can use
+	  'bioruby' command as a better './script/console' which has
+	  persistent objects and shared history.
+
+2007-03-08  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db/kegg/drug.rb
+
+	  Newly added KEGG DRUG database parser.
+
+	* lib/bio/db/kegg/glycan.rb
+
+	  Bio::KEGG::GLYCAN#bindings method is removed.
+	  Bio::KEGG::GLYCAN#comment, remarks methods are added.
+	  Bio::KEGG::GLYCAN#orthologs and dblinks methods are changed to use
+	  lines_fetch method.
+
+	* lib/bio/kegg/compound.rb
+
+	  Bio::KEGG::COMPOUND#glycans method is added
+	  Bio::KEGG::COMPOUND#names method is changed to return an array
+	  of stripped strings.
+
+	* lib/bio/db/kegg/genes.rb
+
+	  Bio::KEGG::GENES#orthologs method is added.
+
+2007-03-27  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/command.rb
+
+	  Bio::Command.call_command_fork and query_command_fork methods
+	  are changed to handle all Ruby exceptions in the child process.
+
+	* lib/bio/io/flatfile.rb
+
+	  UniProt format autodetection was changed to follow the change of
+	  UniProtKB release 9.0 of 31-Oct-2006.
+
+2007-02-12  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/io/flatfile.rb
+
+	  Exception class UnknownDataFormatError is added.
+	  It will be raised before reading data from IO when data format
+	  hasn't been specified due to failure of file format autodetection.
+
+2007-02-12  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/flatfile.rb
+
+	  Added support for KEGG EGENES.
+
+2007-02-02  Trevor Wennblom <trevor@corevx.com>
+
+	* lib/bio/util/restriction_enzyme*
+
+	  Bio::RestrictionEnzyme stabilized.
+	
+2007-02-02  Trevor Wennblom <trevor@corevx.com>
+
+	* lib/bio/db/lasergene.rb
+
+	  Bio::Lasergene Interface for DNAStar Lasergene sequence file format
+
+2007-02-02  Trevor Wennblom <trevor@corevx.com>
+
+	* lib/bio/db/soft.rb
+
+	  Bio::SOFT for reading SOFT formatted NCBI GEO files.
+
+2007-01-16  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby shell on Rails new features and fixes
+
+	  New features:
+	  * Input [#] is linked to action for filling textarea from history
+	  * [methods] is separated into columns for readability
+
+	  Fixes and improvements:
+	  * HIDE_VARIABLES is moved from helper to controller to avoid warning
+	    "already initialized constant - HIDE_VARIABLES" repeated on reload.
+	  * <div id="evaluate"> is renamed to "log_#" with number for future
+	    extention.
+	  * <div id="log_#"> are inserted in the <div id="logs">
+
+2007-01-15  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db.rb
+
+	  lines_fetch method (internally used various bio/db/*.rb modules)
+	  is rewrited to concatenate indented sub field.
+
+	* lib/bio/db/kegg/compound.rb
+
+	  Bio::KEGG::COMPOUND#comment method which returns contents of
+	  the COMMENT line is added
+
+	* lib/bio/db/kegg/enzyme.rb
+
+	  Bio::KEGG::ENZYME#entry_id is changed to return EC number only.
+	  Previous version of entry_id method is renamed to entry method
+	  which returns a "EC x.x.x.x   Enzyme" style string.
+
+	  Bio::KEGG::ENZYME#obsolete? method is added which returns boolean
+	  value (true or false) according to the ENTRY line contains
+	  a string 'Obsolete' or not.
+
+	  Bio::KEGG::ENZYME#all_reac, iubmb_reactions, kegg_reactions methods
+	  are added to support newly added ALL_REAC field.
+	
+	  Bio::KEGG::ENZYME#inhibitors and orthologs methods are added.
+
+	  Bio::KEGG::ENZYME#substrates, products, inhibitors, cofactors,
+	  pathways, orthologs, diseases, motifs methods are rewrited to
+	  utilizes new lines_fetch method in db.rb to process continuous
+	  sub field.
+
+	* lib/bio/db/kegg/genome.rb
+
+	  Bio::KEGG::GENOME#scaffolds, gc, genomemap methods are obsoleted.
+	  Bio::KEGG::GENOME#distance, data_source, original_db methods are
+	  added.
+
+2006-12-24  Toshiaki Katayama <k@bioruby.org>
+
+	* bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
+	  (lib/bio/shell/rails/vendor/plugins/generators/)
+
+	  Web functionallity of the BioRuby shell is completely rewrited
+	  to utilize generator of the Ruby on Rails. This means we don't
+	  need to have a copy of the rails installation in our code base
+	  any more. The shell now run in threads so user does not need
+	  to run 2 processes as before (drb and webrick). Most importantly,
+	  the shell is extended to have textarea to input any code and
+	  the evaluated result is returned with AJAX having various neat
+	  visual effects.
+
+	* lib/bio.rb
+
+	  Extended to have Bio.command where command can be any BioRuby
+	  shell methods.
+	    ex. puts Bio.getseq("atgc" * 10).randomize.translate
+
+	* lib/bio/shell/plugin/entry.rb, seq.rb
+
+	  seq, ent, obj commands are renamed to getseq, getent, getobj
+	  respectively. This getseq is also changed to return Bio::Sequence
+	  with @moltype = Bio::Sequence::NA object instead of Bio::Sequence::NA
+	  object.
+
+	* lib/bio/db/kegg/kgml.rb
+
+	  Some method names are changed to avoid confusion:
+	  * entry_type is renamed to category (<entry type="">)
+	  * map is renamed to pathway (<entry map="">)
+
+2006-12-19  Christian Zmasek <czmasek@burnham.org>
+
+	* lib/bio/db/nexus.rb
+
+	  Bio::Nexus is newly developed during the Phyloinformatics hackathon.
+
+2006-12-16  Toshiaki Katayama <k@birouby.org>
+
+	* lib/bio/io/sql.rb
+
+	  Updated to follow recent BioSQL schema contributed by
+	  Raoul Jean Pierre Bonnal.
+
+2006-12-15  Mitsuteru Nakao <n@bioruby.org>
+
+	* lib/bio/appl/iprscan/report.rb
+	
+	  Bio::Iprscan::Report for InterProScan output is newly added.		
+2006-12-15  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/mafft/report.rb
+
+	  Bio::MAFFT::Report#initialize is changed to get a string of
+	  multi-fasta formmatted text instead of Array.
+
+2006-12-14  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/phylip/alignment.rb
+
+	  Phylip format multiple sequence alignment parser class
+	  Bio::Phylip::PhylipFormat is newly added.
+
+	* lib/bio/appl/phylip/distance_matrix.rb
+
+	  Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
+	  (generated by dnadist/protdist/restdist programs) is newly added.
+
+	* lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
+
+	  Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG MSF multiple
+	  sequence alignment format parser, and Bio::GCG::Seq in
+	  lib/bio/appl/gcg/seq.rb for GCG sequence format parser are
+	  newly added.
+
+	* lib/bio/alignment.rb
+
+	  Output of Phylip interleaved/non-interleaved format (.phy),
+	  Molphy alignment format (.mol), and GCG MSF format (.msf)
+	  are supported. Bio::Alignment::ClustalWFormatter is removed
+	  and methods in the module are renamed and moved to
+	  Bio::Alignment::Output.
+
+	* lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
+
+	  Changed to use Bio::Command instead of Open3.popen3.
+	
+2006-12-13  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/tree.rb, lib/bio/db/newick.rb
+
+	  Bio::PhylogeneticTree is renamed to Bio::Tree, and
+	  lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
+	  NHX (New Hampshire eXtended) parser/writer support are added.
+
+2006-12-13  Toshiaki Katayama <k@bioruby.org>
+
+	* doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
+
+2006-10-05  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/newick.rb
+
+	  Bio::Newick for Newick standard phylogenetic tree parser is
+	  newly added (contributed by Daniel Amelang).
+
+        * lib/bio/phylogenetictree.rb
+
+	  Bio::PhylogeneticTree for phylogenetic tree data structure
+	  is newly added.
+
+2006-09-19  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/soapwsdl.rb
+	* lib/bio/io/ebisoap.rb
+	* lib/bio/io/ncbisoap.rb
+
+	  Newly added web service modules.
+
+	* lib/bio/db/kegg/kgml.rb
+
+	  Accessor for the <component> attribute is added.
+
+	* lib/bio/shell/plugin/codon.rb
+
+	  Support for Pyrrolysine and Selenocysteine are added in the
+	  BioRuby shell.
+
+	* lib/bio/sshell/plugin/seq.rb
+
+	  sixtrans, skip, step methods are added in the BioRuby shell.
+	    bioruby> seqtrans(seq)
+
+	    bioruby> seq.step(window_size) {|subseq|
+	      # do something on subseq
+	    }
+
+	    bioruby> seq.skip(window_sizep, step_size) {|subseq|
+	      # do something on subseq
+	    }
+
+2006-07-26  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/data/aa.rb
+
+	  Amino acids J (Xle: I/L), O (Pyl: pyrrolysine) and X (unknown)
+	  are added (now we have consumed 26 alphabets!).
+
+	* lib/bio/io/fastacmd.rb
+
+	  Fixed that new version of fastacmd (in BLAST package) changed
+	  the option from '-D T' to '-D 1', contributed by the author
+	  of this module Shuji Shigenobu.
+
+	* lib/bio/shell/plugin/psort.rb
+
+	  Newly added BioRuby shell plugin for PSORT
+
+	* lib/bio/shell/plugin/blast.rb
+
+	  Newly added BioRuby shell plugin for BLAST search against KEGG GENES
+
+	* lib/bio/db/prosite.rb
+
+	  PROSITE#re instance method is added to translate PATTERN of
+	  the entry to Regexp using PROSITE.pa2re class method.
+
+	* lib/bio/db/kegg/genes.rb
+
+	  Bio::KEGG::GENES#keggclass method is renamed to pathway
+	  Bio::KEGG::GENES#splinks method is removed
+	  Bio::KEGG::GENES#motifs method is added
+	  these reflect changes made in the original KEGG GENES database.
+
+	  Bio::KEGG::GENES#locations method is added to return Bio::Locations
+	  Bio::KEGG::GENES#codon_usage is renamed cu_list (returns as Array)
+	  Bio::KEGG::GENES#cu is renamed to codon_usage (returns as Hash)
+	  Bio::KEGG::GENES#aalen, nalen methods are changed to return
+	  the number written in the entry (use seq.length to obtain calculated
+	  number as before).
+
+	* lib/bio/db/kegg/kgml.rb
+
+	  Names of some accessors have been changed (including bug fixes)
+	  and instance variable @dom is obsoleted. Here's a list of
+	  incompatible attribute names with KGML tags by this change:
+	    <entry>
+	      :id -> :entry_id
+	      :type -> :entry_type 
+	      names()
+	    <graphics>
+	      :name -> :label
+	      :type -> :shape
+	    <relation>
+	      :entry1 -> :node1
+	      :entry2 -> :node2
+	      :type -> :rel
+	    <subtype>
+	      edge()
+	    <reaction>
+	      :name -> :entry_id
+	      :type -> :direction
+
+	* lib/bio/io/das.rb
+
+	  Bug fixed that the value of segment.stop was overwritten by
+	  segment.orientation.
+
+2006-07-14  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/command.rb
+
+          Bio::Command::Tools and Bio::Command::NetTools are combined
+	  and re-constructed into a new Bio::Command module.
+
+	  lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
+	  lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
+	  lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb, 
+	  lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
+	  lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
+	  lib/bio/io/registry.rb are changed to use the new Bio::Command
+	  instead of old Bio::Command or Net::HTTP.
+
+2006-06-29  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/appl/blat/report.rb
+
+	  Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
+	  #score, and #psl_version methods/attributes are newly added,
+	  and psl files without headers are supported (discussed in
+	  bioruby-ja ML).
+
+2006-06-27  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/sequence/na.rb
+
+          Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
+	  are newly added. Bio::Sequence::NA#gc_percent are changed
+	  not to raise ZeroDivisionError and returns 0 when given sequence
+	  is empty.
+
+	* lib/bio/db/pdb/pdb.rb
+
+	  Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
+	  #element are changed to strip whitespaces when initializing.
+	  Bio::PDB::HETATM is also subject to the above changes.
+	  (suggested by Mikael Borg)
+
+2006-06-12  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/io/flatfile.rb
+
+	  Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
+
+2006-05-30  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/io/soapwsdl.rb
+
+	  Generic list_methods method which extracts web service methods
+	  defined in the WSDL file is added.
+
+2006-05-02  Mitsuteru Nakao <n@bioruby.org>
+
+        * lib/bio/appl/pts1.rb
+
+          Bio::PTS1 first commit.
+
+2006-04-30  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/appl/blast/format0.rb
+
+	  Bug fix: parse error for hits whose database sequence names
+	  contain 'Score', and subsequent hits after them would lost
+	  (reported by Tomoaki NISHIYAMA).
+
+2006-04-14  Mitsuteru Nakao <n@bioruby.org>
+
+        * lib/bio/io/ensembl.rb
+
+          Bio::Ensembl first commit. It is a client class for Ensembl Genome
+          Browser.
+
+2006-03-22  Naohisa Goto <ng@bioruby.org>
+
+        * lib/bio/io/flatfile.rb
+
+	  Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
+	  The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
+	  bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
+
+	  Bio::FlatFile#entry_start_pos and #entry_ended_pos are
+	  changed to be enabled only when Bio::FlatFile#entry_pos_flag
+	  is true.
+
+2006-02-27  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 1.0.0 released
+
+2006-02-10  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby shell is changed to use session/ directory under the current
+	  or specified directory to store the session information instead of
+	  ./.bioruby directory.
+
+2006-02-05  Toshiaki Katayama <k@bioruby.org>
+
+	* License to be changed to Ruby's (not yet completed).
+
+2006-02-01  Trevor Wennblom <trevor@corevx.com>
+
+	* Bio::RestrictionEnzyme first commit for comments.
+	  * See lib/bio/util/restriction_enzyme.rb and
+	    test/unit/bio/util/restriction_enzyme
+
+2006-01-28  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/appl/emboss.rb
+
+          EMBOSS USA format is now accepted via seqret/entret commands
+	  and also utilized in the BioRuby shell (lib/bio/shell.rb,
+	  plugin/entry.rb, plugin/emboss.rb).
+
+	* lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)
+
+2006-01-23  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/sequence.rb
+
+	  Bio::Sequence is refactored to be a container class for
+	  any sequence annotations.  Functionality is separared into
+	  several files under the lib/bio/sequence/ direcotry as
+	  common.rb, compat.rb, aa.rb, na.rb, format.rb
+
+2006-01-20  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 0.7.1 is released.
+
+2006-01-12  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
+	  (reported by Alex Gutteridge)
+
+2006-01-04  Naohisa Goto <ng@bioruby.org>
+
+	* Bio::PDB is refactored.  See doc/Changes-0.7 for more details.
+
+2005-12-19  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 0.7.0 is released.
+
+	  See doc/Changes-0.7.rd file for major and incompatible changes.
+
+2005-12-19  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
+	  * Many changes have been made.
+	  * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
+            changed. Now, Record is changed from hash to Struct, and
+            method_missing is no longer used.
+          * In the "MODEL" record, model_serial is changed to serial.
+	  * In any records, record_type is changed to record_name.
+	  * In most records contains real numbers, changed to return
+	    float values instead of strings.
+	  * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
+	    Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
+	    Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
+	    Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
+	    Bio::PDB::DataType.
+	  * There are more and more changes to be written...
+
+	* lib/bio/db/pdb/atom.rb
+	  * Bio::PDB::Atom is removed.
+	    Instead, please use Bio::PDB::Record::ATOM and
+            Bio::PDB::Record::HETATM.
+
+2005-12-02  Naohisa Goto <ng:bioruby.org>
+
+	* lib/bio/alignment.rb
+	  * Old Bio::Alignment class is renamed to
+	    Bio::Alignment::OriginalAlignment.
+	    Now, new Bio::Alignment is a module. However,
+	    you don't mind so much because most of the class methods
+	    previously existed are defined to delegate to the new
+	    Bio::Alignment::OriginalAlignment class,
+            for keeping backward compatibility.
+	  * New classes and modules are introduced. Please refer RDoc.
+	  * each_site and some methods changed to return Bio::Alignment::Site,
+	    which inherits Array (previously returned Array).
+	  * consensus_iupac now returns only standard bases
+	    'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
+	    'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
+	    '?' (or missing_char, in EnumerableExtension#consensus_iupac).
+	    Note that consensus_iupac now does not return u and invalid
+	    letters not defined in IUPAC standard even if all bases
+	    are equal.
+	  * There are more and more changes to be written...
+
+2005-11-05  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/sequence.rb
+
+	  Bio::Sequence.auto(str) method is added which auto detect the
+	  molecular type of the string and then returns the
+	  Bio::Sequence::NA or Bio::Sequence::AA object.
+	  
+	  Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.
+
+	* lib/bio/shell/plugin/codon.rb
+
+	  Newly added plugin to treat codon table.
+	  ColoredCodonTable is ported from the codontable.rb
+
+2005-11-01  Toshiaki Katayama <k@bioruby.org>
+
+	* bin/bioruby, lib/bio/shell/
+
+	  All methods are changed to private methods to avoid adding them
+	  in top level binding, which caused many unexpected behaviors,
+	  as adviced by Koichi Sasada.
+
+	  The MIDI plugin is now able to select musical scales.
+	
+2005-10-23  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/util/color_scheme
+
+	  Newly contributed Bio::ColorScheme
+
+	* lib/bio/db/kegg/kgml.rb
+
+	  Newly added KEGG KGML parser.
+
+2005-10-05  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/shell/plugin/midi.rb
+
+	  Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose
+
+2005-09-25  Toshiaki Katayama <k@bioruby.org>
+
+	* README.DEV
+
+	  Newly added guideline document for the contributors.
+
+	* README
+
+	  Updated and added instructions on RubyGems.
+
+2005-09-23  Toshiaki Katayama <k@bioruby.org>
+
+	* bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
+	  lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
+	  lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb
+
+	  Newly added BioRuby shell, the command line user interface.
+	  Try 'bioruby' command in your terminal.
+
+	* doc/Changes-0.7.rd
+
+	  Newly added document describing incompatible and important
+	  changes between the BioRuby 0.6 and 0.7 versions.
+
+	* lib/bio/sequence.rb
+
+	  Bio::Sequence.guess, Bio::Sequence#guess methods are added
+	  which guess the sequence type by following fomula (default
+	  value for the threshold is 0.9).
+
+	              number of ATGC
+	  --------------------------------------- > threshold
+	    number of other chars - number of N
+
+2005-09-10  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
+	  lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
+	  lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
+	  lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
+	  lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
+	  lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
+	  lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
+	  lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb
+
+	  fixed autoload problem
+
+	* lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb
+
+	  Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
+	  to lib/bio/appl/blast.rb for autoload.
+
+2005-08-31  Toshiaki Katayama <k@bioryby.org>
+
+	* BioRuby 0.6.4 is released.
+
+	* doc/KEGG_API.rd
+
+	  Newly added English version of the KEGG API manual.
+
+	* lib/bio/aa.rb
+
+	  the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
+	  and 'three' methods as aliases for 'to_1' and 'to_3' methods.
+
+2005-08-31  Naohisa Goto <ng@bioruby.org>
+
+	* removed unused file lib/bio/appl/factory.rb
+	  (the functionality had been integrated into lib/bio/command.rb)
+
+	* doc/Tutorial.rd
+
+	  Newly added an English translation of the Japanese tutorial.
+
+2005-08-16  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/command.rb
+
+	  Newly added Bio::Command::Tools module.
+	  Bio::Command::Tools is a collection of useful methods
+	  for execution of external commands.
+
+	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
+	  lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb
+
+	  For security reason, shell special characters are escaped.
+
+	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb
+
+	  Options are stored with an array (@options).
+	  #options and #opions= methods are added.
+
+	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb
+
+	  Bio::Blast.remote and Bio::Fasta.remote is fixed to work
+	  with the recent change of the GenomeNet.
+
+2005-08-11  Toshiaki Katayama <k@bioruby.org>
+
+	* Sequence#to_re method to have compatibility with 0.6.2 for RNA
+
+	* Fixed Bio::Fastacmd#fetch to work
+
+	* Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
+	  renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.
+
+2005-08-09  Toshiaki Katayama <k@bioruby.org>
+
+	* BioRuby 0.6.3 is released.
+
+	  This version would be the final release to support Ruby 1.6 series
+	  (as long as no serious bug is found:).
+
+	* lib/bio/util/sirna.rb:
+
+	  Newly added method for desing of siRNA, contributed by
+	  Itoshi Nikaido.  The lib/bio/util/ directory if reserved
+	  for bioinfomatics algorithms implemented by pure Ruby.
+
+	* lib/bio/io/fastacmd.rb:
+
+	  Newly added wrapper for NCBI fastacmd program, contributed by
+	  Shinji Shigenobu.
+
+	* lib/bio/appl/hmmer/report.rb:
+
+	  Bug fixed by Masashi Fujita when the position of sequence
+	  rarely becomes '-' instead of digits.
+
+2005-08-08  Mitsuteru Nakao <n@bioruby.org>
+
+        * lib/bio/db/embl/sptr.rb:
+
+          Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods. 
+          contributed by Luca Pireddu.
+
+          Changed Bio::SPTR#gn, Bio::SPTR#gene_name and 
+          Bio::SPTR#gene_names methods. contributed by Luca Pireddu.
+
+2005-08-08  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/bl2seq/report.rb:
+
+	  Newly added bl2seq (BLAST 2 sequences) output parser.
+
+	* lib/bio/appl/blast/format0.rb:
+
+	  Added `self.class::` before F0dbstat.new for bl2seq/report.rb
+
+2005-08-07  Toshiaki Katayama <k@bioruby.org>
+
+	* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
+
+	  Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
+	  Data module, and this module is included and extended to make
+	  all methods as both of instance methods and class methods.
+
+	  Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
+	  to_re methods) to use Bio::NucleicAcid.
+
+	  Bio::Sequence::NA#molecular_weight method is fixed to subtract
+	  two hydrogens per each base.
+
+	* lib/bio/db/medline.rb: publication_type (pt) method is added.
+
+2005-08-07  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/db/genbank/common.rb:
+
+	  Avoid NoMethodError (private method `chomp` called for nil:NilClass)
+	  when parsing features of
+
+	    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
+            Salmonella_typhimurium_LT2/AE006468.gbk
+
+2005-07-11  Toshiaki Katayama <k@bioruby.org>
+
+	* bin/br_pmfetch.rb:
+
+	  Added sort by page option (--sort page)
+
+	* lib/io/higet.rb:
+
+	  Newly added Bio::HGC::HiGet class for HiGet SOAP service.
+
+2005-06-28  Toshiaki Katayama <k@bioruby.org>
+
+	* gemspec.rb: newly added RubyGems spec file.
+
+2005-06-21  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/report.rb:
+
+	  Newly added support for reading BLAST -m 7 result files
+	  through Bio::FlatFile by adding
+	  DELIMITER = "</BlastOutput>\n" to Bio::Blast::Report class.
+	  (Note that tab-delimited format (-m 8 and -m 9) are not yet
+	  supported by Bio::FlatFile)
+
+	* lib/bio/io/flatfile.rb:
+
+	  Added file format autodetection of BLAST XML format.
+
+2005-06-20  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/appl/blast/format0.rb: added 'to_s' to store original entry
+
+2005-04-04  Mitsuteru Nakao <n@bioruby.org>
+
+        * lib/bio/db/go.rb:
+
+          Newly added Bio::GO::External2go class for parsing external2go file.
+
+2005-03-10  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/io/flatfile.rb:
+
+	  Added file format autodetection of Spidey (Bio::Spidey::Report).
+
+2005-03-10  Naohisa Goto <ng@bioruby.org>
+
+	* lib/bio/io/flatfile.rb:
+
+	  Added file format autodetection for Bio::KEGG::KO,
+	  Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
+	  and Bio::Sim4::Report.
+
+	  In order to distinguish Bio::KEGG::REACTION and 
+	  Bio::KEGG::COMPOUND, autodetection regexp. of
+	  Bio::KEGG::COMPOUND were modified.
+
+2005-02-09  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* lib/bio/db/kegg/genes.rb:
+
+	  Added cu method which returns codon usage in Hash for the
+	  convenience (codon_usage method returns in Array or Fixnum).
+
+2004-12-13  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* BioRuby 0.6.2 released.
+
+	* test/all_tests.rb:
+
+	  Unit tests for some classes are newly incorporated by
+	  Moses Hohman.  You can try it by 'ruby install.rb test'
+
+	* lib/bio/appl/spidey/report.rb:
+
+	  Newly added Spidey result parser class.
+
+	* lib/bio/appl/blat/report.rb:
+
+	  Newly added BLAT result parser class.
+
+	* fixes and improvements:
+	  * lib/bio/appl/blast/blast/format0.rb
+	    * minor fix for the Blast default format parser
+	  * lib/bio/alignment.rb
+	    * Alignment class
+	  * lib/bio/db/prosite.rb
+	    * bug reported by Rolv Seehuus is fixed
+	    * some methods are added
+
+2004-10-25  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* lib/bio/db/{compound.rb,reaction.rb,glycan.rb}:
+
+	  Newly added parser for KEGG REACTION and KEGG GLYCAN database
+	  entries, fix for KEGG COMPOUND parser to support the new format.
+
+2004-10-09  GOTO Naohisa <ng@bioruby.org>
+
+	* lib/bio/appl/sim4.rb
+
+	  Newly added sim4 wrapper class.
+	  This is test version, specs would be changed frequently.
+
+	* lib/bio/appl/sim4/report.rb
+
+	  Newly added sim4 result parser class.
+
+2004-08-25  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* BioRuby 0.6.1 released.
+	  * fix for the packaging miss of 0.6.0
+	  * bin/*.rb are renamed to bin/br_*.rb (similar to the BioPerl's
+	    convention: bp_*.pl)
+
+2004-08-24  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* BioRuby 0.6.0 released.
+	  * many fixes for Ruby 1.8
+	  * updated for genome.ad.jp -> genome.jp transition
+
+	* lib/bio/db/pdb.rb
+
+	  Newly added parser for PDB contributed by Alex Gutteridge (EBI).
+
+	* lib/bio/data/codontable.rb
+
+	  Bio::CodonTable is rewrited to be a class instead of static variable.
+	  Now it can hold table definition, start codons, stop codons and
+	  added methods to detect start/stop codons and reverse translation.
+
+	  Also includes sample code to show codon table in ANSI colored
+	  ascii art, have fun.
+
+	* lib/bio/sequence.rb
+
+	  Bio::Sequence::NA#translate is rewrited to accept an user defined
+	  codon table as a Bio::CodonTable object and any character can be
+	  specified for the unknown codon.  This method runs about 30% faster
+	  than ever before.
+
+	  Bio::Sequence::AA#to_re method is added for the symmetry.
+
+	  Bio::Seq will be changed to hold generic rich sequence features.
+	  This means Bio::Seq is no longer an alias of Bio::Sequence but
+	  is a sequence object model, something like contents of a GenBank
+	  entry, common in BioPerl, BioJava etc.
+
+	* lib/bio/io/soapwsdl.rb
+
+	  Newly added common interface for SOAP/WSDL in BioRuby
+	  used by keggapi.rb, ddbjxml.rb.
+
+	* lib/bio/io/keggapi.rb
+
+	  Completely rewrited to support KEGG API v3.0
+
+	* lib/bio/io/esoap.rb
+
+	  Newly added client library for Entrez Utilities SOAP interface.
+
+	* lib/bio/db/genbank, lib/bio/db/embl
+
+	  Refactored to use common.rb as a common module.
+
+	* bin/pmfetch.rb
+
+	  Newly added command to search PubMed.
+
+	* bin/biofetch.rb, flatfile.rb, biogetseq.rb
+
+	  Renamed to have .rb suffix.
+
+	* sample/biofetch.rb
+
+	  Rewrited to use KEGG API instead of DBGET
+
+
+2003-10-13  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* BioRuby 0.5.3 released.
+
+	  Fixed bugs in Blast XML parsers: xmlparser.rb is fixed not to
+	  omit the string after ' and " in sequence definitions,
+	  rexml.rb is fixed not to raise NoMethodError as "undefined
+	  method `each_element_with_text' for nil:NilClass".
+
+2003-10-07  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+
+	* lib/bio/db/nbrf.rb
+
+	  Newly added NBRF/PIR flatfile sequence format class.
+
+2003-09-30  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+
+	* lib/bio/db/pdb.rb
+
+	  Newly added PDB database flatfile format class.
+	  This is pre-alpha version, specs shall be changed frequently.
+
+2003-08-22  KATAYAMA Toshiaki <k@bioruby.org>
+
+	* BioRuby 0.5.2 released.
+
+	  Fixed to be loaded in Ruby 1.8.0 without warnings.
+
+	* doc/KEGG_API.rd.ja
+
+	  Newly added a Japanese document on the KEGG API.
+
+2003-08-12  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+
+	* lib/bio/appl/blast/format0.rb
+
+	  Newly added NCBI BLAST default (-m 0) output parser,
+	  which may be 5-10x faster than BioPerl's parser.
+	  This is alpha version, specs may be frequently changed.
+	  PHI-BLAST support is still incomplete.
+	  Ruby 1.8 recommended. In ruby 1.6, you need strscan.
+
+	* lib/bio/appl/blast/wublast.rb
+
+	  Newly added WU-BLAST default output parser.
+	  This is alpha version, specs may be frequently changed.
+	  Support for parameters and statistics are still incomplete.
+	  Ruby 1.8 recommended. In ruby 1.6, you need strscan.
+
+2003-07-25  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+
+	* lib/bio/alignment.rb:
+
+	  Newly added multiple sequence alignment class.
+
+	* lib/bio/appl/alignfactory.rb:
+
+	  Newly added template class for multiple alignment software.
+
+	* lib/bio/appl/clustalw.rb:
+
+	  Newly added CLUSTAL W wrapper.
+	  <http://www.ebk.ac.uk/clustalw/>
+	  <ftp://ftp.ebk.ac.uk/pub/software/unix/clustalw/>
+
+	* lib/bio/appl/clustalw/report.rb:
+
+	  Newly added CLUSTAL W result data (*.aln file) parser.
+
+	* lib/bio/appl/mafft.rb, lib/bio/appl/mafft/report.rb:
+
+	  Newly added MAFFT wrapper and report parser.
+	  (MAFFT is a multiple sequence alignment program based on FFT.)
+	  <http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/>
+
+2003-07-16  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.5.1 released.
+
+	* lib/bio/sequence.rb: some methods (using 'rna?' internally) were
+	  temporally unusable by the changes in 0.5.0 is fixed.
+
+	* lib/bio/io/flatfile.rb: autodetection failure of the fasta entry
+	  without sequence is fixed.  FlatFile.auto method is added.
+
+	* lib/bio/db.rb: sugtag2array fixed.  DB.open now accepts IO/ARGF.
+
+	* lib/bio/db/embl.rb: references method is added.
+
+
+2003-06-25  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.5.0 released.
+
+	* lib/bio/appl/blast/report.rb:
+
+	    Refactored from xmlparser.rb, rexml.rb, and format8.rb files.
+	    Formats are auto detected and parsers are automatically
+	    selected by checking whether XMLParser or REXML are installed.
+	    You can call simply as
+	      Bio::Blast::Report.new(blastoutput)
+	    or you can choose parsers/format explicitly by
+	      Bio::Blast::Report.xmlparser(format7blastoutput)
+	      Bio::Blast::Report.rexml(fomat7blastoutput)
+	      Bio::Blast::Report.tab(format8blastoutput)
+	    You can also use newly added class method reports for multiple
+	    xml blast output.
+	      Bio::Blast.reports(output) # output can be IO or String
+
+	* lib/bio/appl/fasta/report.rb:
+
+	    Refactored from format10.rb, format6.rb and sample/* files.
+
+	* lib/bio/appl/hmmer/report.rb:
+
+	    Bug fix and clean up.
+
+	* bin/biogetseq:
+
+	    Newly added OBDA (BioRegistry) entry retrieval command.
+
+	* etc/bioinformatics/seqdatabase.ini, lib/bio/io/registry.rb:
+	    Updated for new OBDA spec (Singapore version).
+	    Including config file versioning and changes in tag names,
+	    support for OBDA_SEARCH_PATH environmental variable.
+
+	* lib/bio/io/keggapi.rb:
+
+	    Newly added KEGG API client library.
+	    <http://www.genome.ad.jp/kegg/soap/>
+
+	* lib/bio/io/ddbjxml.rb:
+
+	    Newly added DDBJ XML client library (test needed).
+	    <http://xml.nig.ac.jp/>
+
+	* lib/bio/io/das.rb:
+
+	    Newly added BioDAS client library.
+
+	* lib/bio/db/gff.rb:
+
+	    Newly added GFF format parser/store library.
+
+	* lib/bio/appl/tmhmm/report.rb:
+
+	    Newly added TMHMM report parser.
+	    <http://www.cbs.dtu.dk/services/TMHMM/>
+
+	* lib/bio/appl/targetp/report.rb:
+
+	    Newly added TargetP report parser.
+	    <http://www.cbs.dtu.dk/services/TargetP/>
+
+	* lib/bio/appl/sosui/report.rb:
+
+	    Newly added SOSUI report parser.
+	    <http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi>
+
+	* lib/bio/appl/psort/report.rb:
+
+	    Newly added PSORT report parser.
+	    <http://www.psort.org/>, <http://psort.ims.u-tokyo.ac.jp/>
+
+	* lib/bio/appl/genscan/report.rb:
+
+	    Newly added GENSCAN report parser.
+	    <http://genes.mit.edu/GENSCAN.html>
+
+	* lib/bio/db/prosite.rb: bug fix in ps2re method.
+
+	* lib/bio/db/fantom.rb:
+
+	    Newly added FANTOM database parser (XML).
+	    <http://fantom2.gsc.riken.go.jp/>
+
+	* lib/bio/db/go.rb:
+
+	    Newly added GO parser.
+	    <http://www.geneontology.org/>
+
+	* lib/bio/feature.rb:
+	
+	    'each' method now accepts an argument to select specific feature.
+
+	* lib/bio/db/fasta.rb: definition=, data= to change comment line.
+
+	* lib/bio/db/genbank.rb:
+	
+	    References and features now accept a block. 'acc_version' method
+	    is added to return the Accsession.Version string.
+	    'accession' method now returns Accession part of the acc_version.
+	    'version' method now returns Version part of the acc_version as
+	    an integer.
+
+	* lib/bio/db/keggtab.rb:
+
+	    Rewrited for bug fix and clean up (note: some methods renamed!)
+	    * gsub('abrev', 'abbrev') in method names
+	    * db_path_by_keggorg is changed to db_path_by_abbrev
+	    * @bio_root is changed to @bioroot (ENV['BIOROOT'] overrides)
+	    * Bio::KEGG::DBname is changed to Bio::KEGG::Keggtab::DB
+	      * @database is added (a hash with its key db_abbreb)
+	      * database, name, path methods added with its argument db_abbreb
+
+	* lib/bio/io/flatfile.rb:
+
+	   Enumerable mix-in is included.
+
+	* lib/bio/io/flatfile/indexer.rb:
+
+	    Indexing of the FASTA format file is now supported with various
+	    type of definition line.
+
+	* bin/dbget:
+
+	    Removed (moved under sample directory because the port of the
+	    dbget server is now closed).
+
+	* install.rb:
+
+	    Changed to use setup 3.1.4 to avoid installing CVS/ directory.
+
+	* sample/goslim.rb:
+
+	    Added a sample to generate histogram from GO slim.
+
+	* sample/tdiary.rb:
+
+	    Added for tDiary <http://www.tdiary.org/> users. have fun. :)
+
+2003-01-28  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.4.0 released.
+	* bin/bioflat:
+	  * newly added for the BioFlat indexing
+	* lib/bio/io/flatfile.rb, flatfile/{indexer.rb,index.rb,bdb.rb}:
+	  * flatfile indexing is supported by N. Goto
+	* lib/bio/db/genbank.rb: changed to contain common methods only
+	  * lib/bio/db/genbank/genbank.rb
+	  * lib/bio/db/genbank/genpept.rb
+	  * lib/bio/db/genbank/refseq.rb
+	  * lib/bio/db/genbank/ddbj.rb
+	* lib/bio/db/embl.rb: changed to contain common methods only
+	  * lib/bio/db/embl/embl.rb
+	  * lib/bio/db/embl/sptr.rb
+	  * lib/bio/db/embl/swissprot.rb
+	  * lib/bio/db/embl/trembl.rb
+	* lib/bio/appl/emboss.rb:
+	  * added - just a generic wrapper, no specific parsers yet.
+	* lib/bio/appl/hmmer.rb:
+	  * added - execution wrapper
+	* lib/bio/appl/hmmer/report.rb:
+	  * added - parsers for hmmsearch, hmmpfam contributed by H. Suga
+	* lib/bio/db.rb: open method added for easy use of flatfile.
+	* lib/bio/db/kegg/genes.rb:
+	  * fixed bug in codon_usage method in the case of long sequence >999
+	  * eclinks, splinks, pathways, gbposition, chromosome methods added
+	* lib/bio/db/aaindex.rb:
+	  * adapted for the new AAindex2 format (release >= 6.0).
+	* lib/bio/db/fasta.rb: entry_id is changed to return first word	only
+	* lib/bio/data/na.rb, aa.rb, keggorg.rb:
+	  * moved under class NucleicAcid, AminoAcid, KEGG (!)
+	* in the test codes, DBGET is replaced by BioFetch
+
+2002-08-30  Yoshinori K. Okuji  <okuji@enbug.org>
+
+	* lib/bio/matrix.rb: Removed.
+	* lib/bio/db/aaindex.rb: Require matrix instead of bio/matrix.
+	* lib/bio/db/transfac.rb: Likewise.
+	* lib/bio/pathway.rb: Likewise.
+	  (Pathway#dump_matrix): Don't use Matrix#dump.
+
+2002-07-30  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.3.9 released.
+	* lib/bio/location.rb:
+	  * Locations#length (size) methods added (contributed by N. Goto)
+	  * Locations#relative method added  (contributed by N. Goto)
+	  * Locations#absolute method is renamed from offset
+	  * Locations#offset, offset_aa methods removed
+	    * use absolute/relative(n, :aa) for _aa
+          * Locations#[], range methods added
+	  * Location#range method added
+	* lib/bio/db/embl.rb:
+	  * fix accession method.
+	* lib/bio/db/genpept.rb:
+	  * temporally added - in the next release, we will make refactoring.
+	* lib/bio/reference.rb:
+	  * in bibtex and bibitem format, "PMIDnum" is changed to "PMID:num".
+	* lib/bio/io/pubmed.rb:
+	  * esearch, efetch methods are added.
+	* lib/bio/db/aaindex.rb:
+	  * fix serious bug in the index method to support negative values.
+	* lib/bio/db.rb:
+	  * fix fetch method to cut tag without fail.
+	* lib/bio/extend.rb:
+	  * added first_line_only option for the prefix in fill method.
+	* doc/Tutorial.rd.ja:
+	  * added docs on BibTeX etc.
+
+2002-06-26  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.3.8 released.
+	* lib/bio/sequence.rb:
+	  * normalize! method added for clean up the object itself.
+	  * 'to_seq' method was renamed to 'seq' (!)
+	    * to_xxxx should be used when the class of the object changes.
+	* lib/bio/appl/blast/xmparser.rb:
+	  * each_iteration, each_hit, each, hits, statistics, message methods
+	    are added in Report class.
+	  * statistics, message methods are added in Iteration class.
+	  * methods compatible with Fasta::Report::Hit are added in Hit class.
+	* lib/bio/appl/blast/rexml.rb:
+	  * many APIs were changed to follow the xmlparser.rb's. (!)
+	* lib/bio/appl/{blast.rb,fasta.rb]:
+	  * class method parser() is added for loading specified Report class.
+	* etc/bioinformatics/seqdatabase.ini: added for OBDA (!)
+	  * sample setup for BioRegistry - Open Bio Sequence Database Access.
+	* lib/bio/extend.rb: added (!)
+	  * This module adds some functionarity to the existing classes and
+	    not loaded by default. User should require specifically if needed.
+	* lib/bio/util/*: removed and merged into lib/bio/extend.rb (!)
+	* lib/bio/id.rb: removed (!)
+	* lib/bio/db/{embl.rb,sptr.rb,transfac.rb}: added entry_id
+	* lib/bio/data/keggorg.rb: updated
+	* sample/genes2* sample/genome2*: updated
+	* doc/Tutrial.rd.ja: updated
+
+2002-06-19  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* BioRuby version 0.3.7 released.
+	* lib/bio/sequence.rb: Sequence inherits String again (!)
+	* lib/bio/db.rb, db/embl.rb, db/sptr.rb: moved EMBL specific methods
+
+2002-06-18  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* lib/bio/feature.rb: Bio::Feature#[] method added
+	* doc/Tutrial.rd.ja: changed to use Feature class
+
+2002-05-28  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* lib/bio/appl/fasta.rb: parser separated, API renewal (!)
+	  * lib/bio/appl/fasta/format10.rb: moved from fasta.rb
+
+	* lib/bio/appl/blast.rb: parser separated, API renewal (!)
+	  * lib/bio/appl/blast/format8.rb: newly added
+	  * lib/bio/appl/blast/rexml.rb: newly added
+	  * lib/bio/appl/blast/xmlparser.rb: moved from blast.rb
+
+2002-05-16  KATAYAMA Toshiaki  <k@bioruby.org>
+
+	* lib/bio/sequence.rb: added alias 'Seq' for class Sequence
+	* lib/bio/db/fasta.rb: entry method added
+
+2002-05-15  KATAYAMA Toshiaki  <k@bioruby.org>
+	
+	* lib/bio/io/dbget.rb: bug fixed for pfam (was wrongly skip # lines)
+	* lib/bio/location.rb: offset method added, eased range check
+
+2002-04-26  KATAYAMA Toshiaki  <k@bioruby.org>
+	
+	* sample/biofetch.rb: new 'info=' option added
+
+2002-04-22  KATAYAMA Toshiaki  <k@bioruby.org>
+	
+	* lib/bio/appl/fasta.rb: follow changes made at fasta.genome.ad.jp
+	* sample/gb2tab.rb: fixed to use authors.inspect for reference
+
+2002-04-15  KATAYAMA Toshiaki  <k@bioruby.org>
+	
+	* sample/gb2fasta.rb: changed to follow new genbank.rb spec.
+	* sample/gt2fasta.rb: changed to follow new genbank.rb spec.
+	* sample/gbtab2mysql.rb: added for loading tab delimited data.
+
+2002/04/08
+	* version 0.3.6 released -k
+	  * fixed inconsistency among db.rb, genbank.rb, genome.rb -k
+	  * lib/bio/db/genbank.rb : serious bug fixed in locus method -k
+	  * lib/bio/feature.rb : method name 'type' has changed -k
+
+2002/03/27
+	* sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k
+
+2002/03/26
+	* sample/gb2tab.rb use ruby instead of perl in the example -o
+	* sample/gb2fasta.rb updated -o
+
+2002/03/11
+	* version 0.3.5 released -k
+
+2002/03/04
+	* lib/bio/sequence.rb to_a, to_ary methods renamed to names, codes -k
+	* sample/biofetch.rb added for BioFetch server -k
+	* bin/biofetch added for BioFetch client -k
+	* lib/bio/io/fetch.rb added for BioFetch library -k
+	* lib/bio/io/sql.rb added for BioSQL -k
+	* lib/bio/io/registry.rb added for BioDirectory/Registry -k
+	* lib/bio/feature.rb added for BioSQL, GenBank, EMBL etc. -k
+	* lib/bio/db/genbank.rb rewrited to use Features, References -k
+	* lib/bio/db/{genes,genome}.rb clean up -k
+	* lib/bio/reference.rb added class References -k
+
+2002/02/05
+	* changed to use 'cgi' instead of 'cgi-lib' -n,k
+
+2002/01/31
+	* version 0.3.4 released -k
+	  * lib/bio/db/genbank.rb -k
+	    * fix for multiple 'allele' in the feature key. (thanx Lixin)
+
+2002/01/07
+	* lib/bio/appl/blast.rb -n
+	  * remote blast support etc.
+
+2001/12/18
+	* lib/bio/id.rb -k
+	  * newly created
+	* lib/bio/io/brdb.rb -k
+	  * newly created
+	* lib/bio/db.rb -k
+	  * template methods are deleted
+	  * detailed docuement added
+	* lib/bio/sequence.rb -k
+	  * to_fasta, complement, translate fixed (due to the changes made
+	    in 0.3.3)
+	  * Sequence::NA#initialize doesn't replace 'u' with 't' any longer
+	    * gc_percent, complement, translate, to_re, molecular_weight
+	      methods are adapted to this change
+	  * molecular_weight changed to calculate more precisely
+	  * test code added 
+	* lib/bio.rb -k
+	  * rescue for require 'bio/appl/blast' is deleted
+
+2001/12/15
+	* lib/bio/sequence.rb -o
+	  * Sequence#to_str added
+
+2001/12/15
+	* version 0.3.3 released -k
+