BioJava
Encyclopedia
The BioJava Project is an open source
project dedicated to providing Java tools for processing biological
data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA
interoperability, DAS
, access to AceDB
, dynamic programming, and simple statistical routines. The BioJava library is useful for automating many daily and mundane bioinformatics
tasks. The BioJava libraries have been used in many scientific studies.
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 10 years and by more than 50 developers. BioJava is one of a number of Bio* projects designed to reduce code duplication.
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
project dedicated to providing Java tools for processing biological
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA
Çorba
Chorba , ciorbă , shurpa , shorpo , or sorpa is one of various kinds of soup or stew found in national cuisines across Middle East...
interoperability, DAS
Distributed Annotation System
The Distributed Annotation System is used in bioinformatics to share and collate genomic annotation information. It is an open source project.From the web site:...
, access to AceDB
AceDB
AceDB is a biological database for handling genomic data. It was developed by Richard M. Durbin and Jean Thierry-Mieg....
, dynamic programming, and simple statistical routines. The BioJava library is useful for automating many daily and mundane bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
tasks. The BioJava libraries have been used in many scientific studies.
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 10 years and by more than 50 developers. BioJava is one of a number of Bio* projects designed to reduce code duplication.
Features
BioJava provides software modules for many of the typical tasks of bioinformatics programming. These include:- Accessing nucleotide and peptidePeptide sequencePeptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain in peptides and proteins. The sequence is generally reported from the N-terminal end containing free amino group to the C-terminal end containing free carboxyl group...
sequence data from local and remote databasesBiological databaseBiological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray... - Transforming formats of database/ file records
- Protein structure parsing and manipulation
- Manipulating individual sequences
- Searching for similar sequences
- Creating and manipulating sequence alignmentSequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
s
See also
- Open Bioinformatics FoundationOpen Bioinformatics FoundationThe Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....
- BioPerlBioPerlBioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project....
, BioPythonBioPythonThe Biopython Project is an international association of developers of freely available Python tools for computational molecular biology, as well as bioinformatics.-References:*refer to the Biopython website for other , and a list of over one hundred ....
, BioRubyBioRubyBioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools. Recently, tools for structural biology have been added.-External links:* ,*... - BioclipseBioclipseThe Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform...