BioJava 4.0.0 Released

02/10

BioJava is an open source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and support manipulation of sequences and 3D structures.

Through BioJava, RCSB PDB releases algorithms and file parsers used at rcsb.org, including algorithms used in the protein Comparison Tool, some of the tracks of the Protein Feature View, and the algorithm for detecting symmetry in biological assemblies.

BioJava also contains a reference implementation for parsing and processing PDBx/mmCIF format data files.

A BioJava tutorial is available to help  facilitate rapid application development for bioinformatics.

BioJava: an open-source framework for bioinformatics in 2012.
Bioinformatics (2012) 28: 2693-2695.

News Index

• 12/29 Happy Holidays

• 12/22 Poster Prize Awarded at AsCA

• 12/15 Smart Searching

• 12/08 Tour of Ligand Deposition

• 12/01 Validate Before Depositing to Save Time

• 11/24 Advanced Search: Multiple ID Search

• 11/17 Comparison Tool for Exploring Sequence and Structure Alignments

• 11/10 Visualize Structure Quality and Mutations with Protein Feature View

• 11/03 Structure Summary Pages Redesigned

• 10/27 Upcoming Meeting: SACNAS

• 10/20 Molecular Origami: Insulin

• 10/13 Fall Newsletter Published

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• 09/29 Poster Prize Awarded at ISMB/ECCB

• 09/22 Poster Prize Awarded at ECM29

• 09/15 RCSB PDB Software Shared on GitHub

• 09/08 Head Back to School with PDB-101

• 09/01 Poster Prize Awarded at ACA

• 08/25 Annual Report Published

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• 08/04 Explore PDB Structures by Browsing Annotations

• 07/28 Web Services for Accessing PDB Data

• 07/21 Summer Newsletter Published

• 07/14 Membrane Query and Annotation

• 07/07 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 07/07 Poster Prize Awarded at ICSG

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• 06/23 Map Genomic Position to Protein Sequence and Structure

• 06/16 HIV Video Challenge Awards

• 06/09 Science Olympiad National Protein Modeling Results

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• 05/26 Visualize in 3D with PV

• 05/19 Download Batches of Data

• 05/12 Molecule of the Month Paper Published

• 05/05 HS Video Challenge Deadline: May 31

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• 04/28 Join our Development Team in San Diego

• 04/28 Access New Website Features

• 04/21 DNA Day 2015: April 25

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• 04/14 Education Corner: The Science of HIV

• 04/07 Spring Newsletter Published

• 03/31 Take an Interactive Tour of the Protein Data Bank

• 03/24 Join the RCSB PDB Team

• 03/24 Build 3D Paper Models of Biomolecules

• 03/17 Visit the San Diego Festival of Science and Engineering on March 22

• 03/10 2015 High School Video Challenge

• 03/03 New Publications

• 03/03 San Diego Science Olympiad Protein Modeling Results

• 02/24 Exploring Structure Quality

• 02/17 2015 High School Video Challenge Materials

• 02/10 BioJava 4.0.0 Released

• 02/03 NJ Science Olympiad Protein Modeling Results

• 01/27 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 01/20 RCSB PDB Mobile for iOS and Android Update

• 01/13 Winter Newsletter Published

• 01/06 Video Challenge for High School Students

• 01/06 New Calendar Celebrates 15th Anniversary of Molecule of the Month