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Medical Systems Biology

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COVID-19 Software


Pareto-optimal balancing conflicting objectives in genome subgroup analysis


A Microsoft Excel add-in that visualizes gene expression ratios. The software is freely available upon request.

HCMV drug resistance mutations

A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes: HCMV drug resistance mutations


An open-source Java program for visualizing genomic abnormalities: IdeogramBrowser Software


JANet (Javascript AgeFactDB Network-viewer) is a specialized 3D Network Exploration and Visualization for Lifespan Data Exploration from AgeFactDB.

MCGH Analyzer

Software to analyze array CGH data with direct GPR import (Microsoft Excel add-in, Windows): MCGH Analyzer Software.


McKmeans: A highly efficient multi-core k-means algorithm for clustering extremely large datasets.


Structural RNA alignment by multi-objective optimization: RNA-Pareto

RNASeq Count Analyzer

Differential expression analysis for sequence count data: RNASeq Count Analyzer


Perl program to create receiver operator charateristic (ROC) curves:


Clojure Framework for parallelization: Sputnik


Visualization of Ant Colony Optimization (contributed by Michael Grönert): Swarm


Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/ RNA sequences and protein sequences.


TraqBio is a intuitively useable and a readily implementable open-source web application for progress tracking in core units. Its main intention is the communication of projects status between a core unit and its users: Source and Documentation


An open-source Java program for drawing area proportional Venn/Euler diagrams:VennMaster Software


ViSiBooL-visualization and simulation of Boolean networks with temporal constraints


A document-centered environment for simulation and visualization of algorithms: Vital


R Packages


An R package for the generation, reconstruction, simulation and analysis of Boolean networks: BoolNet R package


An R package toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets: GiANT R package


An R package that analyzes cluster alternatives based on multi-objective optimization of cluster validation indices: MOCCA R package


An R package that provides fast screening procedures for reflections of ordinal phenotype relations in highdimensional feature representations. It allows the detection of evidence for hypothesised orderings and explorative screenings for unknown relationships.


An R package for multi-objective parameter selection for classifiers: TunePareto R package

Latest News


Our paper "Unraveling the Molecular Tumor-Promoting Regulation of Cofilin-1 in Pancreatic Cancer" has been published in MDPI Cancers.


Our paper "Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases" has been published online first in Briefings in Bioinformatics.