The metabolism constitutes the universe of biochemical reactions taking place in
a cell of an organism. These processes include the synthesis, transformation, and
degradation of molecules for an organism to grow, to reproduce and to interact
with its environment. A good way to capture the complexity of these processes
is the representation as metabolic network, in which sets of molecules are transformed
into products by a chemical reaction, and the products are being processed
further. The underlying graph model allows a structural analysis of this network
using established graphtheoretical algorithms on the one hand, and a visual representation
by applying layout algorithms combined with information visualization
techniques on the other.
In this thesis we will take a look at three different aspects of graph visualization
within the context of biochemical systems: the representation and interactive
exploration of static networks, the visual analysis of dynamic networks, and the
comparison of two network graphs. We will demonstrate, how established infovis
techniques can be combined with new algorithms and applied to specific problems
in the area of metabolic network visualization.
We reconstruct the metabolic network covering the complete set of chemical reactions
present in a generalized eucaryotic cell from real world data available from
a popular metabolic pathway data base and present a suitable data structure. As
the constructed network is very large, it is not feasible for the display as a whole.
Instead, we introduce a technique to analyse this static network in a top-down
approach starting with an overview and displaying detailed reaction networks on
demand. This exploration method is also applied to compare metabolic networks
in different species and from different resources. As for the analysis of dynamic
networks, we present a framework to capture changes in the connectivity as well
as changes in the attributes associated with the network’s elements.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa.de:bsz:15-qucosa-160528 |
| Date | 09 February 2015 |
| Creators | Rohrschneider, Markus |
| Contributors | Universität Leipzig, Fakultät für Mathematik und Informatik / Bild- und Signalverarbeitung und Visalisierung, Prof. Dr. Gerik Scheuermann, Prof. Dr. Falk Schreiber, Prof. Dr. Gerik Scheuermann |
| Publisher | Universitätsbibliothek Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | doc-type:doctoralThesis |
| Format | application/pdf |
Page generated in 0.0025 seconds