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PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. eCollection 2019 Feb.

BioJava 5: A community driven open-source bioinformatics library.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
2
Zurich University of Applied Sciences (ZHAW), Zurich CH-8021, Switzerland.
3
San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA.
4
Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
5
Structural Bioinformatics Laboratory, San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA.
6
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.
7
Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
8
Diamond Light Source Ltd., Didcot OX11 0DE, UK.
9
Genomnia srl, Bresso, Milan, Italy.
10
Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA.
11
RISELab, University of California Berkeley, Berkeley, CA, USA.
12
DNASTAR, Madison, WI, USA.
13
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
14
Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA.

Abstract

BioJava is an open-source project that provides a Java library for processing biological data. The project aims to simplify bioinformatic analyses by implementing parsers, data structures, and algorithms for common tasks in genomics, structural biology, ontologies, phylogenetics, and more. Since 2012, we have released two major versions of the library (4 and 5) that include many new features to tackle challenges with increasingly complex macromolecular structure data. BioJava requires Java 8 or higher and is freely available under the LGPL 2.1 license. The project is hosted on GitHub at https://github.com/biojava/biojava. More information and documentation can be found online on the BioJava website (http://www.biojava.org) and tutorial (https://github.com/biojava/biojava-tutorial). All inquiries should be directed to the GitHub page or the BioJava mailing list (http://lists.open-bio.org/mailman/listinfo/biojava-l).

PMID:
30735498
PMCID:
PMC6383946
DOI:
10.1371/journal.pcbi.1006791
[Indexed for MEDLINE]
Free PMC Article

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