Visual network analysis of dynamic metabolic pathways

Authors:
Markus Rohrschneider;Alexander Ullrich;Andreas Kerren;Peter F. Stadler;Gerik Scheuermann
Affiliations:
Leipzig University, Department of Computer Science, Germany;Leipzig University, Department of Computer Science, Germany;Linnaeus University, School of Computer Science, Physics and Mathematics, Sweden;Leipzig University, Department of Computer Science, Germany;Leipzig University, Department of Computer Science, Germany
Venue:
ISVC'10 Proceedings of the 6th international conference on Advances in visual computing - Volume Part I
Year:
2010

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Abstract

We extend our previous work on the exploration of static metabolic networks to evolving, and therefore dynamic, pathways. We apply our visualization software to data from a simulation of early metabolism. Thereby, we show that our technique allows us to test and argue for or against different scenarios for the evolution of metabolic pathways. This supports a profound and efficient analysis of the structure and properties of the generated metabolic networks and its underlying components, while giving the user a vivid impression of the dynamics of the system. The analysis process is inspired by Ben Shneiderman's mantra of information visualization. For the overview, user-defined diagrams give insight into topological changes of the graph as well as changes in the attribute set associated with the participating enzymes, substances and reactions. This way, "interesting features" in time as well as in space can be recognized. A linked view implementation enables the navigation into more detailed layers of perspective for in-depth analysis of individual network configurations.