Pathway Exploration
Visualizing
pathways, i. e. models of cellular functional networks, is a challenging
task in computer assisted biomedicine. Pathways are represented as large
collections of interwoven graphs, with complex structures present in
both the individual graphs and their interconnections. This situation
requires the development of novel visualization techniques to allow
efficient visual exploration. The Caleydo framework incorporates
a number of approaches to handle such pathways. Navigation in the
network of pathways is facilitated by a hierarchical approach which
dynamically selects a working set of individual pathways for closer
inspection. These pathways are interactively rendered together with
visual interconnections in a 2.5D view using graphics hardware
acceleration. The layout of individual graphs is not computed
automatically, but taken from the KEGG and BioCarta databases, which use
layouts that life scientists are familiar with. Therefore they encode
essential meta-information. While the KEGG and BioCarta pathways use a
pre-defined layout, interactions such as linking+brushing, neighborhood
search or detail on demand are still fully interactive in Caleydo.
We have evaluated the Caleydo Pathway Explorer with pathologists working on the determination of unknown gene functions. Informal reports confirm that Caleydo is useful in both generating and validating such hypotheses.
Publications
- Marc Streit, Michael Kalkusch, Karl Kashofer, Dieter
Schmalstieg:
Navigation and Exploration of Interconnected Pathways
Proceedings of EuroVis 2008, Eindhoven, Netherlands, May 2008.
- Marc Streit, Michael Kalkusch, Dieter Schmalstieg:
Interactive Visualization of Metabolic Pathways
In Proceedings of IEEE Visualization 2007, Sacramento, USA, November 2007.
- Marc Streit:
Master Thesis: Metabolic pathways influencing gene-expression analysis
Supervision: Prof. Dieter Schmalstieg and Michael Kalkusch, June 2007.
website maintained by Marc
Streit and Alexander
Lex
last updated on 2010-02-17