BioRuby

BioRuby is a free and open-source software toolkit for bioinformatics and molecular biology, written in the Ruby programming language. It offers components for sequence analysis, pathway analysis, protein modeling, and phylogenetic analysis, and supports widely used data formats and access to databases, external programs, and public web services, such as BLAST, KEGG, GenBank, MEDLINE, and GO. BioRuby is available on all platforms that support Ruby, including Linux, Mac OS X, and Windows, and with JRuby, it can run on the Java Virtual Machine. It comes with a tutorial, documentation, and an interactive environment for use in the shell and web browser.

Topic

Computational biology;Data management;Bioinformatics;Software engineering

Detail

  • Operation: Deposition;Service invocation;Aggregation

  • Software interface: Library

  • Language: Ruby;Mature

  • License: -

  • Cost: Free

  • Version name: 2.0.4

  • Credit: Information-technology Promotion Agency Japan (IPA), Database Center for Life Science (DBCLS) Japan, Human Genome Center, Institute of Medical Science, University of Tokyo, Open Bioinformatics Foundation (OBF), the National Evolutionary Synthesis Center (NESCent), Google Summer of Code.

  • Input: -

  • Output: -

  • Contact: Toshiaki Katayama katayama@bioruby.org

  • Collection: -

  • Maturity: Stable

Publications

  • BioRuby: bioinformatics software for the Ruby programming language.
  • Goto N, et al. BioRuby: bioinformatics software for the Ruby programming language. BioRuby: bioinformatics software for the Ruby programming language. 2010; 26:2617-9. doi: 10.1093/bioinformatics/btq475
  • https://doi.org/10.1093/bioinformatics/btq475
  • PMID: 20739307
  • PMC: PMC2951089

Download and documentation

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