Software

Bioinformatics Webservices
Systems Biology and Bioinformatics
Cheminformatics
Artificial Neural Networks and Evolutionary Algorithms
Robotics and Computer Vision
Other Applications

Bioinformatics Webservices

Bioinformatics Webservices of the ZBIT

Name: ZBIT Bioinformatics Toolbox - 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)
 

 

Systems Biology and Bioinformatics

ToxDBScan

Name: ToxDBScan - Large Scale Similarity Screening of Toxicological Databases for Drug Candidates.
System: platform independent (web application)
License: LGPL version 3
Last Release: 2014-08-29


SBMLsqueezer

Name: SBMLsqueezer - A verstatile generator for kinetic equations in biochemical networks that can be used via its API, as stand-alone tool, as a Garuda gadget, on-line program, or as plug-in for CellDesigner.
System: platform independent (JDK1.6)
License: GPL version 3
Last Release: 2014-06-30


SBMLsimulator

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: 2014-04-24


MARCARDataTools

Name: MARCAR DataTools - A collection of tools for visualization and analysis of microarray data.
MARCAR DataTools offer various tools to facilitate the analysis of microarray data obtained from short-term drug exposure assays in rodents that was generated in the course of the IMI MARCAR project. Currently, MARCAR DataTools are only available for members of the MARCAR Consortium. General access will be granted when the datasets enter the public domain at the end of the MARCAR project.
System: platform independent (webservice)
License: LGPL version 3
Last Release: 2014-04-07


Name: Systems Biology Simulation Core Library - Java library with algorithms for the interpretation and numerical simulation of models given in SBML.
System: platform independent (JDK1.6)
License: LGPL version 3
Last Release: 2014-03-17


RPPApipe

Name: RPPApipe - A pipeline for the analysis of reverse-phase protein array data.
RPPApipe offers predefined and custom-built workflows for the preprocessing, annotation, statistical analysis, clustering, pathway analysis and visualization of Reverse-Phase Protein Array (RPPA) data.
System: platform independent (webservice)
License: GPL version 3
Last Release: 2013-11-15


InCroMAP

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: 2012-09-28


GWASPathwayIdentifier

Name: GWAS Pathway Identifier - Pathway- and Protein-Interaction-Based Identification of Disease Specific SNP sets in Genome-Wide Accociation Studies.
System: platform independent (JDK1.6)
License: LGPL version 3
Last Release: 2012-06-25


TFpredict

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


SABINE

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


BioPAX2SBML

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


KEGGtranslator

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: 2012-07-24


JSBML

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



SBML2LaTeX

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


ProDGe

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


ModuleMaster

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:

EDISA

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


BowTieBuilder

Name: BowTieBuilder - Modeling signal transduction pathways.
System: platform independent (webservice)
Last Release: 2015-03-06


JCell

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

 

Cheminformatics

jCompoundMapper

Name: jCompoundMapper - An Open Source Java Library and Command-Line Tool for Chemical Fingerprints.
System: platform independent (JDK 1.6)
License: LGPL version 2
Last Release: 2012-12-03


4D FAP

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


JOELib

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



OAK

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


BlueDesc

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


 

Artificial Neural Networks and Evolutionary Algorithms

EvA2

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: 2015-12-19


SNNS

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


JavaNNS

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


 

Robotics and Computer Vision

Robust Occupancy Mapping

Name: CS::APEX - The Algorithm Prototyper and EXperimentor is a tool for visual programming and data flow driven design, written in C++. The framework provides a platform for rapid prototyping of cognitive algorithms, like computer vision and point cloud processing. To achieve reusability, functionality is implemented using computation nodes.
System: Linux
License: BSD
Last Release: 2015-03-04


Robust Occupancy Mapping

Name: Robust and Efficient Volumetric Occupancy Mapping - A method for creating volumetric occupancy maps that is robust against noisy measurements, as they result from stereo matching.
System: platform independent (source code only)
License: New BSD
Last Release: 2013-02-04


exFAST / HPSSM

Name: exFAST / HPSSM - Feature detector and High-Performance Sparse Stereo Matcher.
System: platform independent (source code only)
License: GNU GPL v3
Last Release: 2012-10-05


 

 

Other Applications

SCP Solver

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


STOWS Name: Simple Tool for Organizing Web Sites (STOWS) - a simple to use tool for keeping hundreds of Web pages under control. Provides for uniform layout and navigation between the pages.
System: platform independent (PERL)
License: GNU GPL
Last Release: 2001-05-14