BioJava: an open-source framework for bioinformatics in 2012
By Andreas Prlic, Andrew D. Yates, Spencer E. Bliven, Peter W. Rose, Julius O. B. Jacobsen, Peter V. Troshin, M. Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy and 6 more. 2012
302 citations recorded by the source corpus.
Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model. Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists Contact: andreas.prlic@gmail.com
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Jose M. Duarte
- Yana Valasatava
- Marta Szachniuk
- Tomasz Zok
- Mariusz Popenda
- Antonín Pavelka
- Peter W. Rose
- Anthony R. Bradley
Citations in the corpus
- MCQ4Structures to compute similarity of molecule structures (2013, methodology): “Both, BioJava and Jmol have been incorporated into our software and there is no requirement for their separate installation.”
- MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures (2017, methodology): “We benchmarked three commonly used software libraries: BioPython [19] (http://biopython. org/), NGL Viewer [20] (https://github.com/arose/ngl), and BioJava [21] (http://biojava.org/) written in Python, JavaScript, and Java, respectively.”