FERN - A Java Framework for Stochastic Simulation and Evaluation of Reaction Networks

FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java. It includes state of the art algorithms for stochastic simulation and a powerful visualization system based on gnuplot and Cytoscape.

GGEA - Gene Graph Enrichment Analysis

GGEA is an intuitive method to detect consistently and coherently enriched gene sets in gene expression data. GGEA comes embedded in the EnrichmentBrowser, a multi-functional platform for enrichment analysis that includes a variety of enrichment methods and accompanying visualization capabilites.

HALO - Precise transcript half-life determination in Java

HALO is a software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied as well as a graphical user interface, command line tools and a well-documented Java API.

ProCope - Protein Complex Prediction and Evaluation

ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments.

Vorolign

Fast and flexible structural alignment using Voronoi contacts (Server Version).

Apriori on Patterns

Quasar

RelEx - Extraktion von Objekt-Objekt Wechselwirkungen aus biomedizinischen Texten

RelEx verwendet den Stanford Dependency Parser, um Abhängigkeitsbäume für Sätze zu berechnen. Durch einige wenige Baumtransformationsregeln werden Relationen und zwischen den ?named entities? extrahiert und zu verschiedenen Relationstypen zugeordnet.

Syngrep - Suche nach benannten Objekten in biomedizinischen Texten

syngrep findet benannte biologische Objekte in Freitext. In weniger als 10 Minuten kann die gesamte PubMed Datenbank gleichzeitig auf Hits gegen mehrere Synonymlisten durchsucht werden.

ConceptMaker - Analyse von Geneexpressionsdaten mit Literaturwissen

ConceptMaker analysiert Hochdurchsatzdaten um Anfragen gegen einen indizierten Datenbestand zu erzeugen. Damit wird Literaturwissen automatisch in einen funktionellen Zusammenhang mit den Messdaten gebracht.

CheckShift - A Tool for Rereferencing Chemical Shifts

CheckShift is a tool for preprocessing chemical shift data to detect and correct referencing errors.

SimShiftDB - A Tool for Analyzing Chemical Shifts

SimShiftDB is tool that searches for similarities between a target protein with assigned chemical shifts and a database of template proteins for which both chemical shift data and 3D coordinates are available in order to support NMR-spectrocopists.

MIRTFnet- Analysis of miRNA regulated TFs

ProSAS Database

Database for analyzing alternative splicing events in several mamalian genomes with respect to protein structure (implemented in Java using the Zkoss framework).

AutoPSI Database

Database combining AutoSCOP and Vorolign predictions for protein sequences and structures (implemented in Java using the Zkoss framework).