BioRuby: bioinformatics software for the Ruby programming language

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 suppor...

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Bibliographic Details
Published in:Bioinformatics 2010-10, Vol.26 (20), p.2617-2619
Main Authors: Goto, Naohisa, Prins, Pjotr, Nakao, Mitsuteru, Bonnal, Raoul, Aerts, Jan, Katayama, Toshiaki
Format: Article
Language:English
Subjects:
Applications Note
Biological and medical sciences
biology
Computational Biology
Databases, Factual
environment
Fundamental and applied biological sciences. Psychology
General aspects
life
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
MEDLINE
Phylogeny
Programming Languages
Sequence Analysis, Protein
Software
toolkit
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Description
Summary: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. Availability: 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/. Contact: katayama@bioruby.org
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btq475