An R package for multi-objective parameter selection for classifiers: TunePareto R package
McKmeans: A highly efficient multi-core k-means algorithm for clustering extremely large datasets.
An R package that analyzes cluster alternatives based on multi-objective optimization of cluster validation indices: MOCCA R package
An R package for the generation, reconstruction, simulation and analysis of Boolean networks: BoolNet R package
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
An open-source Java program for drawing area proportional Venn/Euler diagrams: VennMaster Software
A Microsoft Excel add-in that visualizes gene expression ratios. The software is freely available upon request.
Software to analyze array CGH data with direct GPR import (Microsoft Excel add-in, Windows): MCGH Analyzer Software.
Perl program to create receiver operator charateristic (ROC) curves: http://www.CPAN.org.
A document-centered environment for simulation and visualization of algorithms: Vital
ViSiBooL-visualization and simulation of Boolean networks with temporal constraints
Structural RNA alignment by multi-objective optimization: RNA-Pareto
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.
Differential expression analysis for sequence count data: RNASeq Count Analyzer
Clojure Framework for parallelization: Sputnik
Our paper "Assessing phenotype order in molecular data" has been published in Scientific Reports.
Our paper "Representing dynamic biological networks with multi-scale probabilistic models"has been published in Communications Biology.