BioJava  BioJava is an open-source software project dedicated to provide Java tools to process biological data. 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 huge 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. 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. BioJava provides software modules for many of the typical tasks of bioinformatics programming. These include:   The BioJava project grew out of work by Thomas Down and Matthew Pocock to create an API to simplify development of Java-based Bioinformatics tools. BioJava is an active open source project that has been developed over more than 12 years and by more than 60 developers. BioJava is one of a number of Bio* projects designed to reduce code duplication. Examples of such projects that fall under Bio* apart from BioJava are BioPython, BioPerl, BioRuby, EMBOSS etc. In October 2012, the first paper on BioJava was published. This paper detailed BioJava's modules, functionalities, and purpose. As of November 2018 Google Scholar counts more than 130 citations. The most recent paper on BioJava was written in February 2017. This paper detailed a new tool named BioJava-ModFinder. This tool can be used for identification and subsequent mapping of protein modifications to 3D in the Protein Data Bank (PBD). The package was also integrated with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. More than 30,000 structures with protein modifications were identified by using BioJava-ModFinder and can be found on the RCSB PDB website. In the year 2008, BioJava's first Application note was published. It was migrated from its original CVS repository to Git hub in April 2013.