Institute of Medical Systems Biology

Tools

The Core Unit Bioinformatics uses different tools to enhance their services:

 

TunePareto

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

McKmeans

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

MOCCA

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

BoolNet

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

HCMV drug resistance mutations

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

IdeogramBrowser

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

VennMaster

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

GExVis

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

MCGH Analyzer

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

ROC

Perl program to create receiver operator charateristic (ROC) curves: http://www.CPAN.org.

Vital

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

RNA-Pareto

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

Swarm

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

Swat

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

RNASeq Count Analyzer

Differential expression analysis for sequence count data: RNASeq Count Analyzer

Sputnik

Clojure Framework for parallelization: Sputnik