70
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      BioRuby: bioinformatics software for the Ruby programming language

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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@ 123456bioruby.org

          Related collections

          Most cited references10

          • Record: found
          • Abstract: found
          • Article: not found

          The Bioperl toolkit: Perl modules for the life sciences.

          The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            The MPI Bioinformatics Toolkit for protein sequence analysis

            The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at .
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              BioJava: an open-source framework for bioinformatics

              Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher. Contact: andreas.prlic@gmail.com. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.
                Bookmark

                Author and article information

                Journal
                Bioinformatics
                bioinformatics
                bioinfo
                Bioinformatics
                Oxford University Press
                1367-4803
                1367-4811
                15 October 2010
                25 August 2010
                25 August 2010
                : 26
                : 20
                : 2617-2619
                Affiliations
                1Department 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
                Author notes
                * To whom correspondence should be addressed.

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Associate Editor: Dmitrij Frishman

                Article
                btq475
                10.1093/bioinformatics/btq475
                2951089
                20739307
                904a5c19-b6dc-403a-a191-b769018a0b21
                © The Author(s) 2010. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 June 2010
                : 11 August 2010
                : 12 August 2010
                Categories
                Applications Note
                Sequence Analysis

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

                Comments

                Comment on this article