title: BioRuby: bioinformatics software for the Ruby programming language.
abstract: CONCLUSIONS
  The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.
  
  
  BACKGROUND
  BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/.
  
  
  BACKGROUND
  katayama@bioruby.org
authors.affiliation: Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan.
authors.forename: Naohisa
authors.initials: N
authors.lastname: Goto
authors.forename: Pjotr
authors.initials: P
authors.lastname: Prins
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Raoul
authors.initials: R
authors.lastname: Bonnal
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Katayama
mesh_terms: D019295:Computational Biology; D016208:Databases, Factual; D016239:MEDLINE; D010802:Phylogeny; D011381:Programming Languages; D020539:Sequence Analysis, Protein; D012984:Software