http://en.wikipedia.org/wiki/Biopython
| ioRuby | Ruby language toolkit | Website | Platform | License | Open Bioinformatics Foundation |
| caCORE | ontologic representation environment | Website - Articles | Platform | License | National Cancer Institute |
| caArray | ontologic representation environment | [1] - [2] | Platform | License | National Cancer Institute |
| Integrated Genome Browser | Java-based desktop genome browser | Website | Linux, Mac OS X, Windows | CPL 1.0 | GenoViz |
| IntAct | molecular interaction database | Website - Articles | Platform | License | European Bioinformatics Institute |
| Java Treeview | microarray data viewer | Website - Articles | Cross-platform | License | Developer |
| LabKey Server | platform for integrating, analyzing and sharing data | Website | Linux, Mac OS X, Windows | Apache License | LabKey Software Foundation |
| UGENE | integrated bioinformatics tools | Website - Podcast | Linux, Mac OS X, Windows | GPL2 License | Unipro |