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      BioJava: an open-source framework for bioinformatics in 2012

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          Abstract

          Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.

          Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

          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 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists

          Contact: andreas. prlic@ 123456gmail.com

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          Identification of common molecular subsequences.

          T.F. Smith, M.S. Waterman (1981)
          Article 0 comments Cited 1696 times – based on 0 reviews     Review now
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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 generic genome browser: a building block for a model organism system database.

              Lincoln D. Stein, Christopher John Mungall, ShengQiang Shu … (2002)
              The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
              Article 0 comments Cited 533 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 15 October 2012
                Publication date (Electronic): 9 August 2012
                Publication date PMC-release: 9 August 2012
                Volume: 28
                Issue: 20
                Pages: 2693-2695
                Affiliations
                1San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 3Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA, 4College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK, 5Department of Computer Science, University of Wisconsin-Madison, WI 53706, USA, 6Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 7NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597, Singapore, 8Genetics and Genomics Medicine of Inflammation, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8, 9Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK, 10Faculty of Mathematics and Informatics, Vilnius University, LT-03225 Vilnius, Lithuania, 11Harbinger Partners, Inc., St Paul, MN 55127, USA, 12University of Applied Sciences Upper Austria, 4232 Hagenberg, Austria, 13Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA and 14Genomics Core, Scripps Florida, Jupiter, FL 33458, USA
                Author notes
                *To whom correspondence should be addressed.

                Associate Editor: Alex Bateman

                Article
                Publisher ID: bts494
                DOI: 10.1093/bioinformatics/bts494
                PMC ID: 3467744
                PubMed ID: 22877863
                SO-VID: 6432e09b-9d34-4d6d-99a2-5bb24f811de4
                Copyright © © The Author 2012. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 28 May 2012
                Date revision received : 30 July 2012
                Date accepted : 2 August 2012
                Page count
                Pages: 3
                Categories
                Subject: Applications Note
                Subject: Structural Bioinformatics

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

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