BioJava:BioJavaInside

From BioJava

If you use BioJava in an application or publication please cite:

BioJava: an Open-Source Framework for Bioinformatics
R.C.G. Holland; T. Down; M. Pocock; A. Prlić; D. Huen; K. James; S. Foisy; A. Dräger; A. Yates; M. Heuer; M.J. Schreiber
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn397

Projects

The following projects make use of BioJava. If you know of other projects please add them to the list.

• Metabolic Pathway Builder: Software suite dedicated to the exploration of connections among genes, proteins, reactions and metabolic pathways

• DengueInfo: a Dengue genome information portal that uses BioJava in the middleware and talks to a biosql database.

• Dazzle: A BioJava based DAS server.

• Biosense: A commercial informatics offering from Inforsense that uses BioJava under the hood.

• Bioclipse: A free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc.

• PROMPT: A free, open source framework and application for the comparison and mapping of protein sets. Uses BioJava for handling most input data formats.

• Cytoscape: An open source bioinformatics software platform for visualizing molecular interaction networks.

• BioWeka: An open source biological data mining application.

• Geneious: A molecular biology toolkit.

• MassSieve: An open source application to analyze mass spec proteomics data.

• Strap: A tool for multiple sequence alignment and sequence based structure alignment.

• Jstacs: A Java framework for statistical analysis and classification of biological sequences

• jLSTM "Long Short-Term Memory" for protein classification

• LaJolla Structural alignment of RNA and proteins using an index structure for fast alignment of thousands of structures. Including an easy to use command line interface. Open source at Sourceforge.

• GenBeans: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.

Publications

BioJava has been used in the following publications. If you know of other publications please add them.

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Bauer, R.; Rother, K.; Moor, P.; Reinert, K.; Steinke, T.; Bujnicki, J. M.; Preissner, R. Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2009, 2, 692-709. open access full text

More biojava publications can be found in Google Scholar.