Everything about BioJava
BioJava is an open-source software project dedicated to providing Java tools for processing 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 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. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: BioJavaA 5-minute orientation
- Read the landmark paper: BioJava: an open-source framework for bioinformaticsCited 179 times
- Go sideways: European Bioinformatics InstituteA closely related topic
- Go sideways: Protein Data BankA closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
BioJava: an open-source framework for bioinformatics
BioJava: an open-source framework for bioinformatics in 2012
BioJava 5: A community driven open-source bioinformatics library
BioJava
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank
Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for Primitive Bioinformatics Tasks and Choosing a Suitable Language
Comparative Analysis of Software Repository Metrics in BioPerl, BioJava and BioRuby
📚 Books worth reading
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🔗 Related topics
- European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory…
- Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which…
- Biological data visualization Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information…
- List of biological databases Biological databases are stores of biological information. The journal Nucleic Acids Research regularly publishes special issues on biological databases…
- Structural alignment Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This…
- BioPerl BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role…
- Helen M. Berman Helen Miriam Berman is an American chemist who is a Distinguished Professor of Quantitative and Computational Biology at the USC Dornsife College of Letters…
- PDBsum PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank (PDB). The original…