If you use BioJava in an application or publication please cite:
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 plugin
for the InforSense Suite, an analytics software platform by
IDBS that unitizes BioJava.
- 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.
- 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.
- eQuant: A model
quality assessment server to state the reliability of protein
structures.
Publications
In 2008 we published our first Application note. As of Nov. 2014 Google
Scholar counts more than 170
citations.
18689808
Below a list of publications in which BioJava has been used. If you know
of other publications please add them.
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2003
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2004
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2005
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2006
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2007
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2008
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See above for a link to all recent citations on Google Scholar.
2009
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 at Google
Scholar.