Software and Services

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.

Hybroscale - Computation of hybridization networks

Hybroscale is developed specifically for the research of hybridization networks including its computation and visualization. More specifically, the program aims at calculating all phylogenetic networks displaying a set of non-binary input trees with minimum hybridization number.

ISAR - Isoform Structure Alignment Representation

We present an efficient alignment algorithm to construct Isoform Structure Alignment Representations (ISARs) from sets of isoforms, paralogs and orthologs by exploiting information on the gene structure and the phylogeny

MIRTFnet- Analysis of miRNA regulated TFs

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.

Quasar

REA - RIP-chip enrichment analysis

This is a collection of methods for (R)IP-chip (E)nrichment (A)nalysis. A table of normalized expression values from a RIP-chip experiment is read (e.g. as produced by the Affymetrix PowerTools) and two main steps are performed: Subtraction of the background of non target genes and secondary normalization for differing IP efficiencies.

RelEx - Extraktion von Objekt-Objekt Wechselwirkungen aus biomedizinischen Texten

RelEx uses semantic dependency trees to extract relations and relation types between named entities from the entire PubMed. Due to the dependency trees only few tree rules are required to harvest a wide range of complex relationship phrases.

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.

Syngrep - Suche nach benannten Objekten in biomedizinischen Texten

syngrep is a fast named entity recognition tool that scans the entire PubMed for matches against multiple synonym lists in less than ten minutes.

Vorolign

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

AutoPSI Database

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

COIN-DB

CroCo

ConReg

DiauxicGRN

ProSAS Database

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