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

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

“…The Newbler output, 454 HCDiff.txt, is a file of sequence alignments surrounding all the high confidence polymorphic loci. A Ruby (Goto et al, 2010) script was written to test the linkage of two adjacent loci by enumerating the occurrence of the four sequence combinations: consensus-consensus, consensus-variant, variant-consensus and variant-variant. If w80 % of the sequences occurred only as two sequence combinations, the two loci were considered linked.…”

Pipengine: an ultra light YAML-based pipeline execution engine

“…Pipengine is written in Ruby and is available for download as a BioRuby Gem (Goto N 2010;Bonnal RJP 2012).…”

EMBnet.journal 19 Suppl. B

“…BioPerl (Stajich et al, 2002), BioJava (Prlić et al, 2012), Biopython (Cock et al, 2009), and BioRuby and BioGems (Goto et al, 2010;Bonnal et al, 2012) groups worked together to develop Abstract Sprints, Hackathons and Codefests are all names used for informal software developer meetings, especially popular in open source communities. These meetings, along side more traditional conferences, are a vital part of the international network of interactions between software developers working in bioinformatics and computational biology, and complement purely online interactions such as project mailing lists, online chat, web forums and more recently voice and video calls.…”