BioJava 5: A community driven open-source bioinformatics library

Lafita, Aleix; Bliven, Spencer; Prlić, Andreas; Guzenko, Dmytro; Rose, Peter W.; Bradley, Anthony; Pavan, Paolo; Myers-Turnbull, Douglas; Valasatava, Yana; Heuer, Michael; Larson, Matt; Burley, Stephen K.; Duarte, Jose M.

doi:10.1371/journal.pcbi.1006791

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

Journal Article · 08 February 2019 · PLoS Computational Biology (Online)

DOI: https://doi.org/10.1371/journal.pcbi.1006791 · OSTI ID:1601670

^[1];

^[2]; Prlić, Andreas ^[3]; Guzenko, Dmytro ^[3];

^[3];

^[4]; Pavan, Paolo ^[5];

^[6];

^[3];

^[7];

^[8]; Burley, Stephen K. ^[9];

^[3]

European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom); RCSB Protein Data Bank
Zurich Univ. of Applied Sciences (ZHAW) (Switzerland)
Univ. of California, San Diego, CA (United States)
Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Diamond Light Source, Ltd.; Univ. of Oxford (United Kingdom)
Genomnia srl, Milan (Italy)
Univ. of California, San Francisco, CA (United States)
Univ. of California, Berkeley, CA (United States)
DNASTAR, Madison, WI (United States)
Univ. of California, San Diego, CA (United States); Rutgers Univ., Piscataway, NJ (United States); Rutgers Univ., New Brunswick, NJ (United States)

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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Research Organization:: Rutgers Univ., New Brunswick, NJ (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0019749

OSTI ID:: 1601670

Journal Information:: PLoS Computational Biology (Online), Journal Name: PLoS Computational Biology (Online) Journal Issue: 2 Vol. 15; ISSN 1553-7358

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Assessment of protein assembly prediction in CASP13 Guzenko, Dmytro; Lafita, Aleix; Monastyrskyy, Bohdan Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12 https://doi.org/10.1002/prot.25795	journal	August 2019
StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map Bittrich, Sebastian; Schroeder, Michael; Labudde, Dirk Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55047-4	journal	December 2019
Convergent functional genomics of cocaine misuse in humans and animal models Forero, Diego A.; González-Giraldo, Yeimy The American Journal of Drug and Alcohol Abuse, Vol. 46, Issue 1 https://doi.org/10.1080/00952990.2019.1636384	journal	August 2019

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