Karsten Klein

 


   
Karsten Klein  

Address

Life Science Informatics Group
Dep. of Computer Science
Konstanz University

78457 Konstanz, Germany

Contact Information

Email:

karsten.klein  <at> uni-konstanz.de

PGP:

PGP key

Phone:

+49 7531 88-4086

Fax:

+49 7531 88-4365

Room:

Z718

 



I am a member of the Life Science Informatics group at the University of Konstanz, an adjunct fellow with Monash University, and an associate fellow with The University of Sydney. Konstanz University icon Monash University icon Sydney University icon


Research Topics | Teaching | Research | Projects | Publications


Research Topics


RINalyzer protein analysis tool InterDom Breast Cancer Protein Domain Network Layout UML Class Diagram Layout Large Graph Multilevel Layout Scaffold Hunter Visual Analysis of Chemical Compound Databases

Research

I am a Postdoctoral Research Fellow at the CS department at the University of Konstanz, where I work on the design and implementation of visual analytics approaches for complex data from application areas, in particular from the life sciences, and on network analysis and graph drawing algorithms as well as their underlying graph theoretical principles. A further focus of my research is on Immersive Analytics, a research direction that studies how technologies can facilitate a deep cognitive, perceptual and/or emotional involvement of humans when understanding and reasoning with data.
I am involved in a variety of research collaborations with researchers from the life sciences, and participate in a number of software projects that realize the developed concepts in free open source software for use in the corresponding communities, see below. Due to the nature of my research, my interests overlap with a variety of research fields, including visual/immersive analytics, information visualization, HCI, network visualization, graph drawing, and algorithm engineering.


Projects

Immersive Analytics

At Konstanz university, I am co-managing the IA lab, where we investigate the use of IA approaches for a variety of application areas, in particular from the life sciences (biology, chemistry, health, medicine). We are part of the Immersive Analytics (IA) initiative, and I am one of the editors of the first book on IA (to be published soon).

Open Graph Drawing Framework (OGDF)

The Open Graph Drawing Framework (OGDF) is an open source software project that provides a library of datastructures and graph layout algorithms. OGDF is the successor of AGD, the library of algorithms for graph drawing.

Scaffold Hunter Screenshot

Scaffold Hunter Scaffold Hunter icon

Scaffold Hunter is a tool for the interactive exploration of chemical space. It facilitates navigation by graphical visualization of structural relationships and provides methods for the analysis of large data sets, e.g., to correlate chemical structure and biochemical activity. Scaffold Hunter is implemented in Java and freely available under the GPL.

VANTED logo

VANTED VANTED logo

VANTED is a free Java based extendable network visualisation and analysis tool with focus on applications in the life sciences. It allows users to create and edit networks, as well as to map experimental data onto networks. The functionality of VANTED can be extended by installing one or more of the provided Addons using the built-in Addon Manager, e.g. to add an SBGN editor.

RINalyzer logo

RINalyzer RINalyzer logo

RINalyzer allows to analyze and visualize protein residue interaction networks (RINs). A RIN is constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, together with the corresponding molecular 3D structure visualized in UCSF Chimera. RINalyzer is available as a Java plugin for Cytoscape, a free software platform for the analysis and visualization of molecular interaction networks.


Teaching

I am teaching both introductory and advanced courses, mainly on algorithms and computational systems biology, and I supervise software projects in life science informatics. I also supervise bachelor, master, and PhD students, and I am always looking for talented students!
Current PhD students:


Older teaching information can be found here.

Selected Publications

(More here)