Bioclipse depends on several other open source projects, see list below. If you find anything missing from the list, please send an email to the bioclipse-devel mailing list.
| Name | License | Link |
| The Chemistry Development Kit | LGPLv2 | http://sourceforge.net/projects/cdk/ |
| Libsvm | BSD license | http://www.csie.ntu.edu.tw/~cjlin/libsvm/ |
| Jmol | LGPLv2 | http://jmol.sourceforge.net/ |
| OPSIN | Artistic License 2.0 | http://www-ucc.ch.cam.ac.uk/products/software/opsin-0 |
| JNATI | LGPL | http://sourceforge.net/projects/jnati/ |
| InChI | LGPLv2.1 | http://www.iupac.org/home/publications/e-resources/inchi.html |
| XOM | LGPL | http://www.xom.nu/ |
| Logback | LGPLv2.1 | http://logback.qos.ch/ |
| Jasper Reports | LGPL | http://jasperforge.org/projects/jasperreports |
| Apache commons | APL 2.0 | http://commons.apache.org/ |
| Rhino | MPL | http://www.mozilla.org/rhino/ |
| Groovy | APL 2.0 | http://groovy.codehaus.org/ |
| MetaPrint2D | LGPL | http://sourceforge.net/projects/metaprint2d/ |
| Statet | EPL, LGPL | http://www.walware.de/ |
| Balloon | Balloon EULA | http://users.abo.fi/mivainio/balloon |
| XWS4J | ELP | http://xws4j.sourceforge.net/ |
