Semi-automatic drawing of metabolic networks

Abstract

In the living cell, biochemical reactions catalyzed by enzymes are the drivers for metabolic processes like growth, energy production, and replication. Metabolic networks are the representation of these processes describing the complex interactions of biochemical compounds. The large amount of manifold data concerning metabolic networks continually arising from current research activities in biotechnology leads to the great challenge of information visualization. Visualizing information in networks first of all requires appropriate network diagrams. In the context of metabolic networks, historical conventions regarding the network layout have been established. These layouts are not realizable by prevailing algorithms for automatic graph drawing. Hence, manual graph drawing is the predominating way to set up metabolic network diagrams. This is very time-consuming without software support, especially considering large networks with more than 500 nodes. We present a semi-automatic approach to drawing networks which relies on manual editing supported by two concepts of the interactive and automatic arrangement of nodes and edges. The first concept, called the layout pattern, uses an arbitrarily shaped skeleton as a backbone for the arrangement of nodes and edges. The second concept allows us to wrap a set of repeating drawing steps onto a so-called motif stamp, which can be appended to other parts of a diagram during the drawing process. Finally, a case study demonstrates that both semi-automatic drawing techniques diminish the time to be devoted for the manual network drawing process.