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Medical Systems Biology

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Software

COVID-19 Software



AVAtar

Pareto-optimal balancing conflicting objectives in genome subgroup analysis

GExVis

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

IdeogramBrowser

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

JANet

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

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

RNA-Pareto

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

RNASeq Count Analyzer

Differential expression analysis for sequence count data: RNASeq Count Analyzer

ROC

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

Sputnik

Clojure Framework for parallelization: Sputnik

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.

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

VennMaster

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

ViSiBooL

ViSiBooL-visualization and simulation of Boolean networks with temporal constraints

Vital

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

 


R Packages

BoolNet

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

GiANT

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

MOCCA

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

ORION

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.

TunePareto

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

Latest News

Our paper "Awakening the HSC: Dynamic Modeling of HSC Maintenance Unravels Regulation of the TP53 Pathway and Quiescence" has been published in Frontiers in Physiology.

 

Our review article "Concepts in Boolean Network Modeling - What Do They All Mean?" has been published in Computational and Structural Biotechnology Journal.