Name: Bioinformatics Webservices of the ZBIT - An online toolkit providing open access to various tools developed at the Center for Bioinformatics Tübingen (ZBIT)
System: Windows, Linux, Mac OS (only web browser is required)
 

Name: TFpredict - Identification and structural characterization of transcription factors based on supervised machine learning.
System: platform independent (webservice and JDK1.6)
License: GPL version 3
Last Release: 2012-04-20

Name: SABINE - Prediction of the binding specificity of transcription factors using support vector regression.
System: Linux (webservice and JDK1.6)
License: GPL version 3
Last Release: 2012-04-19

Name: BioPAX2SBML - Translation of BioPAX into SBML including the Qualitative Models extension
System: platform independent (webtool)
License: LGPL version 3
Last Release: 2012-04-02

Name: InCroMAP - Integrated analysis of Cross-platform MicroArray and Pathway data.
InCroMAP is a powerful tool for pathway-based analysis or visualization of heterogeneous cross-platform microarray datasets (mRNA, miRNA, DNA methylation and protein).
System: platform independent (webstart and JDK1.6)
License: LGPL version 3
Last Release: 2012-03-15

Name: SBMLsimulator - An efficient Java™ solver implementation for SBML
Simulation and calibration of quantitative biological models.
System: platform independent (webstart and JDK1.6)
License: LGPL version 3
Last Release: 2012-03-01

Name: KEGGtranslator - Visualizing and translating the KEGG PATHWAY database.
Conversion of KGML files into SBML, GraphML, GML and various other output formats.
System: platform independent (webstart and JDK1.6)
License: LGPL version 3
Last Release: 2011-07-04

Name: JSBML - A flexible Java library for working with SBML.
System: platform independent (JDK 1.5)
License: LGPL version 2.1
Last Release: 2011-12-12

Name: SBML2LaTeX - Conversion of SBML files into human-readable reports.
System: platform independent (webservice and JDK1.6)
License: GPL version 3
Last Release: 2011-12-15

Name: SBMLsqueezer - A verstatile Java-based generator for kinetic equations in biochemical networks that can be used via its API, as a stand-alone tool, or as a plug-in for CellDesigner.
System: platform independent (JDK1.5)
License: SBMLsqueezer License
Last Release: 2010-04-02

Name: ProDGe - A protein interaction viewer at the domain level.
System: platform independent (JDK1.6)
License: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License
Last Release: 2011-05-09

Name: ModuleMaster - A tool to identify transcription factor binding sites and decipher transcriptional regulatory networks
System: platform independent (webstart and JDK1.6)
License: Creative Commons Attribution-NonCommercial 3.0 License.
Last Release: 2011-05-09

Older bioinformatics software projects:

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
Last Release: 2009-10-13

Name: JCell - A Java based framework to reconstruct genetic interactions from microarray data.
System: platform independent (JDK1.4)
License: JCell License
Last Release: 2006-04-10

Name: 4D FAP - 4D Flexible Atom-Pair kernel on conformational ensembles for QSAR/QSPR
System: platform independent (JDK1.6)
License: GNU LGPL
Last Release: 2011-04-28

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
Last Release: 2005-01-20

Name: OAK - A Java implementation of the optimal assignment kernel for molecules
System: platform independent (JDK1.4)
License: GNU GPL
Last Release: 2007-10-05

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
Last Release: 2008-10-03

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
Last Release: 2011-05-05

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
Last Release: 2008-07-06

Name: Java Neural Network Simulator (JavaNNS) - successor of SNNS with SNNS kernel and Java user interface.
System: Windows, Linux, Mac, Solaris
License: JavaNNS license
Last Release: 2007-01-08

Name: SCPSolver - Simple Java Linear Programming Framework
System: Linux, Mac Os X, Windows
License: Framework: Creative Commons License Attribution 2.0 Generic. License of the Solver Packs depends on the solvers licensing terms.
Last Release: 2010-12-14