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      BioJava: an open-source framework for bioinformatics

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          Abstract

          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@ 123456gmail.com . All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

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          The Bioperl toolkit: Perl modules for the life sciences.

          Jason E Stajich, David Block, Kris Boulez … (2002)
          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.
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            The Bio* toolkits--a brief overview.

            Harry J Mangalam (2002)
            Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.
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              The Bio* toolkits -- a brief overview

              H. Mangalam (2002)
              Article 0 comments Cited 6 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1460-2059
                Publication date (Print): 15 September 2008
                Publication date (Electronic): 8 August 2008
                Publication date PMC-release: 8 August 2008
                Volume: 24
                Issue: 18
                Pages: 2096-2097
                Affiliations
                1European Bioinformatics Institute (EMBL-EBI), Genome Campus, Hinxton, Cambridgeshire CB10 1SD, 2Gurdon Institute and Department of Genetics, Cambridge CB2 1QN, 3University Newcaste Upon Tyne, Newcastle Upon Tyne, NE1 7RU, 4Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, 5Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, 6Laboratory in Genetics and Genomic Medicine of Inflammation, Montreal Heart Institute, Montreal, Canada H1T 1C8, 7Eberhard Karls University Tübingen, Center for Bioinformatics (ZBIT), Tübingen, Germany, 8Harbinger Partners, Inc. St. Paul, MN, USA and 9Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos #05-01, Singapore 138670
                Author notes
                *To whom correspondence should be addressed.

                Associate Editor: Anna Tromontano

                Article
                Publisher ID: btn397
                DOI: 10.1093/bioinformatics/btn397
                PMC ID: 2530884
                PubMed ID: 18689808
                SO-VID: 492505f1-8928-46ea-a867-832514bbc744
                Copyright © © 2008 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 23 May 2008
                Date revision received : 30 June 2008
                Date accepted : 25 July 2008
                Categories
                Subject: Applications Note
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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