Name: Stuttgart Neural Network Simulator (SNNS) - a powerful yet flexible simulator for artificial neural networks. Runs on Unix Workstations and Unix-PCs.
System: Windows, Linux, various Unix variants
License: SNNS license
 

Name: Java Neural Network Simulator (JavaNNS) - successor of SNNS with SNNS kernel and Java user interface.
System: Windows, Linux, Mac, Solaris
License: JavaNNS license

Name: JOELib - Cheminformatics library: Assignment of atom types, substructure search, descriptor calculation, Java3D molecule visualization, conversion of different chemical file formats (e.g. SDF, SMILES, MOL2).
System: platform independent (JDK1.4)
License: GNU GPL

Name: JCell - A Java based framework to reconstruct genetic interactions from microarray data.
System: platform independent (JDK1.4)
License: JCell License

Name: OAK - A Java implementation of the optimal assignment kernel for molecules
System: platform independent (JDK1.4)

Name: BlueDesc - A ready-to-use executable jar that calculates the molecular descriptors available in JOELib and CDK
System: platform independent (JDK1.6)
License: GNU GPL

Name: SBMLsqueezer - A Java-based CellDesigner plugin to generate kinetic rate equations for biochemical networks.
System: platform independent (JDK1.5)
License: SBMLsqueezer License

Name: SBML2LaTeX - Conversion of SBML files into human-readable reports.
System: platform independent (webservice and JDK1.6)
License: GPL version 3

Name: ProDGe - A Sequence and Protein Interaction Viewer.
System: platform independent (JDK1.6)

Name: ModuleMaster - a new tool to decipher transcriptional regulatory networks
System: platform independent (webstart and JDK1.6)

Name: SABINE - Prediction of the binding specificity of transcription factors using support vector regression.
System: Linux (webservice and JDK1.6)
License: GPL version 3

Name: EDISA - Extracting biclusters from multiple time-series of gene expression profiles.
System: Windows and Linux (webservice and Matlab™)
License: Creative Commons License Attribution 2.0 Generic

Name: EvA2 - Evolutionary Algorithms workbench: Monte-Carlo search, Hill-Climber, Simulated Annealing, Genetic Algorithms, Evolution Strategies, Genetic Programming, Differential Evolution, Particle Swarm Optimization, TRIBES, Cluster-based Niching, Population Based Incremental Learning, Model-Assisted Evolution Strategies, Grammatical Evolution.
System: platform independent (JDK1.5)
License: GNU LGPL