Algorithmen der Bioinformatik

Team Project (AB)

Title Team Projekt (aka Programmierprojekt) "Algorithmen der Bioinformatik"
Lecturers Caner Bağcı and Prof. Daniel Huson
Time and place Please contact Caner Bağcı for details.
Module BSc Bioinformatik: Pflichtmodul Programmierprojekt
Language English
Links Campus:

Project description

JavaFX implementation of an interactive tool for visualizing and analyzing correlation networks for the use with ecological profiling data, with applications in microbiome analysis. 

In a typical microbiome study, one has hundreds of microbiome samples corresponding to different individuals, locations or time points.

Each sample possesses a taxonomic profile that summarizes which microbiomes have been identified in the sample, and how abundant each of them is.

A correlation network is a graph in which each node represents a taxon (type of microbiome) and two such nodes are connected by a positive edge, if the two corresponding types of microbiomes tend to occur in samples, and a negative edge, if their occurrence is anti-correlated. There is no edge between two nodes, if there is no positive or negative cooccurrence pattern.

A nice layout and visualization of the graph allows one to detect patterns in the cooccurrence of microbiomes.

The goal of this project is to build a correlation graph viewer using JavaFX. The program will be able to import data in a number of formats. It will construct, layout and display a correlation graph. It will allow the user to interactively work with the graph in a useful way. It will allow the user to project different types of data onto the graph.