Medical Systems Biology

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Software

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

ViSiBooL

ViSiBooL-visualization and simulation of Boolean networks with temporal constraints

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

TraqBio

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

JANet

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


Latest News

 

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.