{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T08:35:58Z","timestamp":1773131758728,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2230,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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\/.<\/jats:p>\n               <jats:p>Contact: \u00a0katayama@bioruby.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq475","type":"journal-article","created":{"date-parts":[[2010,8,26]],"date-time":"2010-08-26T00:33:02Z","timestamp":1282782782000},"page":"2617-2619","source":"Crossref","is-referenced-by-count":126,"title":["BioRuby: bioinformatics software for the Ruby programming language"],"prefix":"10.1093","volume":"26","author":[{"given":"Naohisa","family":"Goto","sequence":"first","affiliation":[{"name":"1 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan, 2Department of Nematology, Wageningen University and Groningen Bioinformatics Centre, The Netherlands, 3Database Center for Life Science, Research Organization of Information and Systems, Tokyo, Japan, 4Integrative Biology Program, Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy, 5Genome Dynamics and Evolution, Wellcome Trust Sanger Institute, Cambridge, UK and 6Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pjotr","family":"Prins","sequence":"additional","affiliation":[{"name":"1 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan, 2Department of Nematology, Wageningen University and Groningen Bioinformatics Centre, The Netherlands, 3Database Center for Life Science, Research Organization of Information and Systems, Tokyo, Japan, 4Integrative Biology Program, Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy, 5Genome Dynamics and Evolution, Wellcome Trust Sanger Institute, Cambridge, UK and 6Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mitsuteru","family":"Nakao","sequence":"additional","affiliation":[{"name":"1 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan, 2Department of Nematology, Wageningen University and Groningen Bioinformatics Centre, The Netherlands, 3Database Center for Life Science, Research Organization of Information and Systems, Tokyo, Japan, 4Integrative Biology Program, Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy, 5Genome Dynamics and Evolution, Wellcome Trust Sanger Institute, Cambridge, UK and 6Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raoul","family":"Bonnal","sequence":"additional","affiliation":[{"name":"1 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan, 2Department of Nematology, Wageningen University and Groningen Bioinformatics Centre, The Netherlands, 3Database Center for Life Science, Research Organization of Information and Systems, Tokyo, Japan, 4Integrative Biology Program, Fondazione Istituto Nazionale di Genetica Molecolare, Milan, Italy, 5Genome Dynamics and Evolution, Wellcome Trust Sanger Institute, Cambridge, UK and 6Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Aerts","sequence":"additional","affiliation":[{"name":"1 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan, 2Department of Nematology, Wageningen University and Groningen Bioinformatics Centre, The Netherlands, 3Database Center for Life Science, Research Organization of 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