BioJava 5: A community driven open-source bioinformatics library

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

doi:10.1371/journal.pcbi.1006791

BioJava 5: A community driven open-source bioinformatics library

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

Authors

Aleix Lafita¹, Spencer Bliven², Andreas Prlić³, Dmytro Guzenko⁴, Peter W Rose⁵, Anthony Bradley^{6

7

8}, Paolo Pavan⁹, Douglas Myers-Turnbull¹⁰, Yana Valasatava⁴, Michael Heuer¹¹, Matt Larson¹², Stephen K Burley^{4

13

14}, Jose M Duarte⁴

Affiliations

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).

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Access to Information
Algorithms
Computational Biology / methods*
Gene Library
Genome / genetics
Genomics
Information Storage and Retrieval
Internet
Software

Abstract

Publication types

MeSH terms

Grants and funding