Graph drawing by force-directed placement
Software—Practice & Experience
Which Aesthetic has the Greatest Effect on Human Understanding?
GD '97 Proceedings of the 5th International Symposium on Graph Drawing
Visualizing biological pathways: requirements analysis, systems evaluation and research agenda
Information Visualization - Special issue: Bioinformatics visualization
Metabolic network visualization using constraint planar graph drawing algorithm
IV '06 Proceedings of the conference on Information Visualization
Tools for visually exploring biological networks
Bioinformatics
Customizable Visualization of Multi-omics Data in the Context of Biochemical Networks
VIZ '09 Proceedings of the 2009 Second International Conference in Visualisation
Bioinformatics
CompIMAGE'10 Proceedings of the Second international conference on Computational Modeling of Objects Represented in Images
A novel grid-based visualization approach for metabolic networks with advanced focus&context view
GD'09 Proceedings of the 17th international conference on Graph Drawing
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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.