BioJava: an open-source framework for bioinformatics

By Richard C. G. Holland, Thomas A. Down, M. Pocock, Andreas Prlic, David S. Huen, K. James, Sylvain Foisy, A. Dräger, Andy Yates, Michael L. Heuer and 1 more. 2008

221 citations recorded by the source corpus.

Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. 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 1.5 or higher. Contact: andreas.prlic@gmail.com. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

Subfields: Molecular Biology

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In Molecular Biology

1. Robbie P. Joosten
2. G. Vriend
3. Stephen K. Burley
4. Elmar Krieger
5. Alisdair R. Fernie
6. John D. Westbrook
7. Tim A. H. te Beek
8. Mark Stitt

Citations in the corpus

• RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics (2012, methodology): “net/) is used for import of SAM/BAM files, and libraries developed by the biojava project (27) are used for working with GFF3 annotation files.”
• Interactive microbial genome visualization with GView (2010, unknown): “…packages: easeof-use; customizability; interactivity; ability to generate circular and linear maps; ability to read standard sequence file formats; ready incorporation in pipelines and third-party applications; and the ability to generate aesthetically pleasing, publication quality image output.”
• PRISM 3: expanded prediction of natural product chemical structures from microbial genomes (2017, methodology): “An improved sequence file parser, implemented in BioJava (19), automates sequence file type detection and facilitates GBFF file input.”
• HDX Workbench: Software for the Analysis of H/D Exchange MS Data (2012, methodology): “The open source projects BioJava [25] and JFreechart [26] were integrated to provide plots, spectral views, and sequence coverage heat maps.”
• The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, background): “Alternatively, the annotation has been inferred indirectly, as for Pfam domains (46), or calculated, as for hydropathy scores (47) and propensity for protein disorder score based on JRONN (P.”
• A series of PDB-related databanks for everyday needs (2014, background): “Projects like BioJava (19), BioPerl (20) and Biopython (21) provide parsers for these Stockholm-formatted files.”
• The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, methodology): “PM definitions and the software to identify them are available from the BioJava project (21) (https://github.”
• The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants (2009, background): “We discuss the history of the FASTQ format, describing key variants, and conventions adopted by the Open Bioinformatics Foundation (OBF, http://www.open-bio .org) projects Biopython (5), BioPerl (6), BioRuby (http://www.bioruby.org), BioJava (7), and EMBOSS (8) (each represented here by an author) f”
• Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions (2015, unknown): “…such as TOPS-MODE, Cinfony, Dragon, CODESSA, PROFEAT, BioJava, BioPython, PseAAC, ProPy, etc (Cao et al., 2013a, c; Cock et al., 2009; Du et al., 2012; Holland et al., 2008; Katritzky et al., 1994; Li et al., 2006; O'Boyle et al., 2008; P erez-Gonz alez et al., 2003; Todeschini et al., 2010).”
• BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (2016, methodology): “Several bioinformatics packages for computing structural and physicochemical features of proteins or DNAs/ RNAs have been previously developed, including PRO-FEAT [41], BioJava [42], PseAAC, propy [43], repDNA [44], repRNA [45], protr [46] etc.”