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BioRuby: bioinformatics software for the Ruby programming language.

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BioRuby is a free, open-source toolkit for bioinformatics and molecular biology research. It offers tools for sequence, pathway, protein, and phylogenetic analysis, supporting various data formats and web services.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • BioRuby is a free and open-source software toolkit.
  • It is available under the Ruby license and runs on multiple platforms (Linux, Mac OS X, Windows).
  • JRuby enables BioRuby to run on the Java Virtual Machine.

Purpose of the Study:

  • To provide a comprehensive set of development tools and libraries for bioinformatics and molecular biology.
  • To support various analytical tasks including sequence, pathway, protein, and phylogenetic analysis.
  • To facilitate easy access to biological databases, external programs, and public web services.

Main Methods:

  • Developed using the Ruby programming language.
  • Incorporates components for diverse bioinformatics analyses.
  • Supports numerous widely used data formats.

Main Results:

  • Offers integrated tools for sequence analysis, pathway analysis, protein modelling, and phylogenetic analysis.
  • Provides seamless connectivity to essential biological databases and web services like BLAST, KEGG, GenBank, MEDLINE, and Gene Ontology (GO).
  • Includes a tutorial, documentation, and an interactive environment for shell and web browser use.

Conclusions:

  • BioRuby serves as a versatile and accessible toolkit for researchers in bioinformatics and molecular biology.
  • Its comprehensive features and broad compatibility enhance research capabilities.
  • The toolkit promotes efficient data analysis and integration with external biological resources.