---
title: BioJava:BioJavaInside
---
**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](http://www.genostar.com/): Software
suite dedicated to the exploration of connections among genes,
proteins, reactions and metabolic pathways
- [DengueInfo](http://www.dengueinfo.org/): a Dengue genome
information portal that uses BioJava in the middleware and talks to
a biosql database.
- [Dazzle](http://www.derkholm.net/thomas/dazzle): A BioJava based DAS
server.
- [BioSense](http://www.idbs.com/InforSenseSuite/BioSense): A plugin
for the InforSense Suite, an analytics software platform by
[IDBS](http://www.idbs.com/) that unitizes BioJava.
- [Bioclipse](http://www.bioclipse.net): A free, open source,
workbench for chemo- and bioinformatics with powerful editing and
visualization capabilities for molecules, sequences, proteins,
spectra etc.
- [PROMPT](http://webclu.bio.wzw.tum.de/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](http://www.cytoscape.org): An open source bioinformatics
software platform for visualizing molecular interaction networks.
- [BioWeka](http://www.bioweka.org): An open source biological data
mining application.
- [Geneious](http://www.biomatters.com): A molecular biology toolkit.
- [MassSieve](http://www.ncbi.nlm.nih.gov/staff/slottad/MassSieve/):
An open source application to analyze mass spec proteomics data.
- [Strap](http://www.charite.de/bioinf/strap/): A tool for multiple
sequence alignment and sequence based structure alignment.
- [Jstacs](http://www.jstacs.de): A Java framework for statistical
analysis and classification of biological sequences
- [jLSTM](http://www.bioinf.jku.at/software/LSTM_protein/) "Long
Short-Term Memory" for protein classification
- [LaJolla](http://lajolla.sourceforge.net) 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](http://www.geneinfinity.org/genbeans/index.html): A rich
client platform for bioinformatics primarily focused on molecular
biology and sequence analysis.
- [eQuant](http://bioservices.hs-mittweida.de/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](http://scholar.google.com/scholar?cites=3048631375755320177&as_sdt=2005&sciodt=0,5&hl=en).