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

BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita  1 , Spencer Bliven  2 , Andreas Prlić  3 , Dmytro Guzenko  4 , Peter W Rose  5 , Anthony Bradley  6   7   8 , Paolo Pavan  9 , Douglas Myers-Turnbull  10 , Yana Valasatava  4 , Michael Heuer  11 , Matt Larson  12 , Stephen K Burley  4   13   14 , Jose M Duarte  4
Affiliations

BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita et al. PLoS Comput Biol. .

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).

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Multiple structure alignment of circularly permuted lectins generated and visualized with BioJava.
Implementations of CE-CP and CE-MC were used for the structural alignment, visualized using the Jmol based structure panel (left), the multiple alignment panel (top right), and a Forester based dendrogram of structural similarities (bottom right).
Fig 2
Fig 2. Yearly count of the number of articles that mention the BioJava project (“Biojava”), the Biojava website, or cite the BioJava publications (Pocock 2000 [1], Holland 2008 [2] and Prlić 2012 [3]).
Data collected in December 2018 from Google Scholar (https://scholar.google.com).
See this image and copyright information in PMC

References

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    1. Holland RCG, Down TA, Pocock M, Prlic A, Huen D, James K, et al. BioJava: An open-source framework for bioinformatics. Bioinformatics. 2008;24(18):2096–2097. 10.1093/bioinformatics/btn397 - DOI - PMC - PubMed
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