BioJava

BioJava
Original author(s)Andreas Prlić
Developer(s)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 release2002; 22 years ago (2002)
Stable release
6.0.3 / December 19, 2021; 2 years ago (2021-12-19)
Repositorygithub.com/biojava
Written inJava
PlatformWeb browser with Java SE
Available inEnglish
TypeBioinformatics
LicenseLesser GPL 2.1
Websitebiojava.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.

  1. ^ 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.
  2. ^ 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.
  3. ^ VS Matha and P Kangueane, 2009, Bioinformatics: a concept-based introduction, 2009. p26
  4. ^ Cite error: The named reference Jmol was invoked but never defined (see the help page).