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  • Last update: 6 years ago
  • Total downloads: 124
  • Operating system: Mac OS X
  • Publisher: BioRuby Team
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mac default iconBioRuby For Mac Publisher's description

Open source bioinformatics library for Ruby...

Open source bioinformatics library for Ruby

* We had the first BioRuby world wide IRC conference on Dec 19th 2010 and agreed to continue weekly IRC meeting on every Thursday (details). The log is available here.

* We will discontinue our bug tracking system on RubyForge. Instead, use GitHub for bug reports.
Project overview

BioRuby project provides an integrated environment in bioinformatics for the Ruby language. This project is supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

BioRuby: Bioinformatics software for the Ruby programming language

What's New in This Release:

New features:
В· PAML Codeml support is significantly improved
В· PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins.
В· KEGG PATHWAY and KEGG MODULE parser:Parsers for KEGG PATHWAY and KEGG MODULE data are added. The code is developed by Kozo Nishida and Toshiaki Katayama.
Bio::KEGG improvements:
Following new methods are added:
В· Bio::KEGG::GENES#keggclass, keggclasses, names_as_array, names, motifs_as_strings, motifs_as_hash, motifs
В· Bio::KEGG::GENOME#original_databases
В· Test codes are added and improved:They are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto.
Other new methods:
В· Bio::Fastq#mask
В· Bio::Sequence#output_fasta
В· Bio::ClustalW::Report#get_sequence
В· Bio::Reference#==
В· Bio::Location#==
В· Bio::Locations#==
В· Bio::FastaNumericFormat#to_biosequence
Bug fixes:
Following methods did not work correctly:
В· Bio::Tree#collect_edge!
В· Bio::Tree#remove_edge_if
В· Bio::KEGG::GENES and Bio::KEGG::

System Requirements:

В· MacRuby
Program Release Status: New Release
Program Install Support: Install and Uninstall

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