Amr ALHOSSARY, Andreas Prlic, Dmytro Guzenko, Hannes Brandstätter-Müller, Jose Manuel Duarte, Thomas Down, Michael L Heuer, Peter Troshin, JianJiong Gao, Aleix Lafita, Peter Rose, Spencer Bliven
Initial release
2002; 22 years ago (2002)
Stable release
6.0.3
/ December 19, 2021; 2 years ago (2021-12-19)
Repository
github.com/biojava
Written in
Java
Platform
Web browser with Java SE
Available in
English
Type
Bioinformatics
License
Lesser GPL 2.1
Website
biojava.org
BioJava is an open-source software project dedicated to provide Java tools to process biological data.[1][2][3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more.[4] This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
Additional projects from BioJava include rcsb-sequenceviewer, biojava-http, biojava-spark, and rcsb-viewers.
^Prlić A, Yates A, Bliven SE, et al. (October 2012). "BioJava: an open-source framework for bioinformatics in 2012". Bioinformatics. 28 (20): 2693–5. doi:10.1093/bioinformatics/bts494. PMC 3467744. PMID 22877863.
^Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, et al. (2008). "BioJava: an open-source framework for bioinformatics". Bioinformatics. 24 (18): 2096–7. doi:10.1093/bioinformatics/btn397. PMC 2530884. PMID 18689808.
^VS Matha and P Kangueane, 2009, Bioinformatics: a concept-based introduction, 2009. p26
^Cite error: The named reference Jmol was invoked but never defined (see the help page).
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part of the Open Bioinformatics Foundation, including: Biopython BioJavaBioRuby BioPHP BioJS Bioconductor Stajich, J. E.; Block, D.; Boulez, K.; Brenner...
capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew...
Blosum matrices. Examples are the blosum module for Python, or the BioJava library for Java. Sequence alignment Point accepted mutation Henikoff, S.; Henikoff...
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SciLab, Octave, BioPAX and RDF/XML. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which...
chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and...
adopting GMOD components for model organism databases. Bioperl, BioJava, Biopython, BioRuby, etc. Ensembl Gene Ontology DAS Genomics Unified Schema Manatee:...
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Perl and Java) at that time. Nevertheless, the BioMOBY system exhibits what can only be described as Semantic Web-like behaviours. The BioMOBY Object...
methods installed server-side for BioUML clients (workbench and web edition) over the Internet. BioUML Workbench is a Java application that can work standalone...
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