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

Job Openings

Wissenschaftlicher Mitarbeiter (m/w/d) 

 

Latest News

 

  1. Our paper "Prediction of resistance to bevacizumab plus FOLFOX in metastatic colorectal cancer-Results of the prospective multicenter PERMAD trial" has been published in PLoS One.

     

  2. "Introducing a machine learning algorithm for delirium prediction—the Supporting SURgery with GEriatric Co-Management and AI project (SURGE-Ahead)has been published in Age and Ageing.

Our paper "Segmentation-based cardiomegaly detection based on semi-supervised estimation of cardiothoracic ratio" has been published in Scientific Reports.

 

"Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study" has been published in Neurological Research and Practice.

 

Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.

 

Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.

 

"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.

 

Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.

 

"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.

 

Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.

 

"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.

 

"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.


Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.