BioRuby: bioinformatics software for the Ruby programming language

Abstract

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

Fig. 1.

BioRuby shell example of fetching a KEGG graph using BioRuby's KEGG API (Kanehisa et al., 2008). After installing BioRuby, the ‘bioruby’ command starts the interactive shell. With the bfind command, the KEGG MODULE database is queried for entries involved in the metabolic ‘cytrate cycle’ or tricarboxylic acid cycle. The purple and blue colours, in input and output, reflect two modules in the carbon oxidation pathway. The user loads and confirms entries by using flatparse and pathways commands. Next, KEGG ORTHOLOGY database IDs are fetched and the colours are assigned to enzymes in each module. Finally, KEGG generates the coloured image of the ‘cytrate cycle’ pathway and the image is saved locally.

Fig. 2.

BioRuby example of masking sequences from next generation sequencing data in FASTQ format using a defined quality_threshold, and writing the results in FASTA format.