A Novel Grid-Based Visualization Approach for Metabolic Networks with Advanced Focus&amp;Context View

Rohrschneider, Markus; Heine, Christian; Reichenbach, A.; Kerren, Andreas; Scheuermann, Gerik

doi:10.1007/978-3-642-11805-0_26

Cited by 16 publications

(22 citation statements)

References 20 publications

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“…Rohrschneider et al tried to overcome that problem for biological networks by first computing a stress-based node-placement on a grid, followed by an edge routing heuristic [44]. This approach does not allow group information to be taken into account, and the graph structure is hard to conceive from the layouts.…”

Section: Related Workmentioning

confidence: 99%

High-Quality Ultra-Compact Grid Layout of Grouped Networks

Yoghourdjian

Dwyer

Gange

et al. 2016

IEEE Trans. Visual. Comput. Graphics

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Fig. 1: Grid systems in typographic layout, UI design and an example of our proposed grid layout for a power-graph. With graphic designers playing an increasing role in the design of user interfaces for phone, tablet and desktop operating systems, this traditional grid-based design aesthetic is becoming more popular in these media. A case in point is Microsoft's "Modern" interface which seeks to unify app-design across devices. This resurgence of the grid-design aesthetic in new media leads us to re-examine some of the aesthetic assumptions that have been made in designing layout methods for network diagrams.Abstract-Prior research into network layout has focused on fast heuristic techniques for layout of large networks, or complex multi-stage pipelines for higher quality layout of small graphs. Improvements to these pipeline techniques, especially for orthogonal-style layout, are difficult and practical results have been slight in recent years. Yet, as discussed in this paper, there remain significant issues in the quality of the layouts produced by these techniques, even for quite small networks. This is especially true when layout with additional grouping constraints is required. The first contribution of this paper is to investigate an ultra-compact, grid-like network layout aesthetic that is motivated by the grid arrangements that are used almost universally by designers in typographical layout. Since the time when these heuristic and pipeline-based graph-layout methods were conceived, generic technologies (MIP, CP and SAT) for solving combinatorial and mixed-integer optimization problems have improved massively. The second contribution of this paper is to reassess whether these techniques can be used for high-quality layout of small graphs. While they are fast enough for graphs of up to 50 nodes we found these methods do not scale up. Our third contribution is a large-neighborhood search meta-heuristic approach that is scalable to larger networks.

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Section: Related Workmentioning

confidence: 99%

High-Quality Ultra-Compact Grid Layout of Grouped Networks

Yoghourdjian

Dwyer

Gange

et al. 2016

IEEE Trans. Visual. Comput. Graphics

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“…Recently, Rohrschneider et al [22] presented a grid-based visualization approach for metabolic networks supported by a focus&context view. This view is based on a Table Lens method [19], which provides multiple foci and together with the grid-layout the preservation of the user's mental map [17].…”

Section: Background and Related Workmentioning

confidence: 99%

Guiding the interactive exploration of metabolic pathway interconnections

Jusufi

Klukas

Kerren

et al. 2011

Information Visualization

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Abstract-Approaches to investigate biological processes have been of strong interest in the last years and are in the focus of several research areas, especially Systems Biology. Biochemical networks are very important for such a comprehensive understanding of living beings. Drawings of these networks are often visually overloaded and do not scale. A common solution to deal with this complexity is to divide the complete network, e.g., the metabolism, into a large set of single pathways that are hierarchically structured. If those pathways are visualized, this strategy generates additional navigation and exploration problems as the user looses the context within the complete network. In this paper, we present a general solution of this problem of visualizing interconnected pathways and discuss it in context of biochemical networks. Our new visualization approach supports the analyst to get an overview to related pathways if he/she is working within a particular pathway of interest. By using glyphs, brushing, and topological information of the related pathways, our interactive visualization tool is able to intuitively guide the exploration and navigation process, and thus the analysis processes too. To deal with real data and current networks, our tool has been implemented as plugin for the VANTED system.

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“…The number of potential fluxes through a graph element is represented by the node size, or edge width, respectively. We used here the orthogonal grid based layout [74]. Nodes lie on even integer grid positions.…”

Section: Visualizationmentioning

confidence: 99%

Evolution of metabolic networks: a computational frame-work

et al. 2010

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Background: The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis of extant genomes. Alternatively, the principles of metabolic evolution can be studied by direct computer simulation. This requires, however, an explicit implementation of all pertinent components: a universe of chemical reaction upon which the metabolism is built, an explicit representation of the enzymes that implement the metabolism, of a genetic system that encodes these enzymes, and of a fitness function that can be selected for. Results: We describe here a simulation environment that implements all these components in a simplified ways so that large-scale evolutionary studies are feasible. We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toy-version of quantum chemistry to derive thermodynamic parameters. Minimalist organisms with simple string-encoded genomes produce model ribozymes whose catalytic activity is determined by an ad hoc mapping between their secondary structure and the transition state graphs that they stabilize. Fitness is computed utilizing the ideas of metabolic flux analysis. We present an implementation of the complete system and first simulation results. Conclusions: The simulation system presented here allows coherent investigations into the evolutionary mechanisms of the first steps of metabolic evolution using a self-consistent toy universe.

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A Novel Grid-Based Visualization Approach for Metabolic Networks with Advanced Focus&Context View

Cited by 16 publications

References 20 publications

High-Quality Ultra-Compact Grid Layout of Grouped Networks

High-Quality Ultra-Compact Grid Layout of Grouped Networks

Guiding the interactive exploration of metabolic pathway interconnections

Evolution of metabolic networks: a computational frame-work

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