Metabolic network visualization eliminating node redundance and preserving metabolic pathways

<p>Abstract</p> <p>Background</p> <p>The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.</p> <p>Results</p> <p>We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.</p> <p>Conclusion</p> <p>The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.</p

A layout algorithm for signaling pathways

Cataloged from PDF version of article.Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named PATIKA, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. PATIKA version 1.0 beta is available upon request at http://www.patika.org. (C) 2004 Elsevier Inc. All rights reserved

Planarization With Fixed Subgraph Embedding

The visualization of metabolic networks using techniques of graph drawing has recently become an important research area. In order to ease the analysis of these networks, readable layouts are required in which certain known network components are easily recognizable. In general, the topology of the drawings produced by traditional graph drawing algorithms does not reflect the biologists' expert knowledge on particular substructures of the underlying network. To deal with this problem we present a constrained planarization method---an algorithm which computes a graph layout in the plane preserving the predefined shape for the specified substructures while minimizing the overall number of edge-crossings

Incremental Grid-like Layout Using Soft and Hard Constraints

We explore various techniques to incorporate grid-like layout conventions into a force-directed, constraint-based graph layout framework. In doing so we are able to provide high-quality layout---with predominantly axis-aligned edges---that is more flexible than previous grid-like layout methods and which can capture layout conventions in notations such as SBGN (Systems Biology Graphical Notation). Furthermore, the layout is easily able to respect user-defined constraints and adapt to interaction in online systems and diagram editors such as Dunnart.Comment: Accepted to Graph Drawing 201

Planarization With Fixed Subgraph Embedding

The visualization of metabolic networks using techniques of graph drawing has recently become an important research area. In order to ease the analysis of these networks, readable layouts are required in which certain known network components are easily recognizable. In general, the topology of the drawings produced by traditional graph drawing algorithms does not reflect the biologists' expert knowledge on particular substructures of the underlying network. To deal with this problem we present a constrained planarization method---an algorithm which computes a graph layout in the plane preserving the predefined shape for the specified substructures while minimizing the overall number of edge-crossings

Algorithms for visualization of graph-based structures

Buildings today are built to maintain a healthy indoor environment and an efficient energy usage which is probably why damages caused by dampness has increased since the 1960’s. A study between year 2008 and 2010 showed that 26 percent of the 110 000 examined houses had damages and flaws caused by dampness that could prove to be harmful later on. This means that one out of four bathrooms risk the chance to develop damages by dampness. Approximately 2 percent of the houses had already developed water damages. It is here where the problems appear. A house or a building that is damaged by water of dampness need time to dry out before any renovation can take place. This means that damaged parts must be removed and allowed to dry out, this takes a long time to do and the costs are high and at the same time it can cause inconvenience to the residents. Here is where the Air Gap Method enters the picture. The meaning with the method is to drain and dry out the moisture without the need to perform a larger renovation. The Air Gap Method is a so called "forgiving"-system that is if water damages occur the consequences will be small. The Air Gap method means that an air gap is created in the walls, ceiling and the floor where a heating cable in the gap heats up the air and creates an air movement. The point is to create a stack effect in the gap that with the help of the air movement transports the damp air through an opening by the ceiling. The aim of this thesis is to examine if it’s necessary with the heating cable in the air gap and if there is a specific drying out pattern of the water damaged bathroom floor. The possibility of mould growth will also be examined. The study showed that the damped floor did dry out even without a heating cable, but as one of the studies showed signs of mould growth it is shown that the risk for mould growth is higher without a heating cable. There was a seven days difference in the drying out time between the studies with and without the heating cable; this difference can be decisive for mould growth which is why the heating cable is recommended. The Air Gap method is quite easy to apply in houses with light frame constructions simply by using a smaller dimension on the studs to create the air gap in the floor and walls. The method can also be applied in apartment buildings with a concrete frame by using the room-in- room principal. When renovating existing bathrooms it’s easier to use prefabricated elements to create the air gap in the floor and walls. ~

Pathway Preserving Representation of Metabolic Networks

International audienceImprovements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while respecting biological drawing conventions. These constraints complicate the automatic generation of such visualization as it raises graph drawing issues. In this paper we propose a method to lay out the entire metabolic network while preserving the pathway informa- tion as much as possible. That method is flexible as it enables the user to define whether or not node duplication should be performed, to preserve or not the network topology. Our technique combines partitioning, node place- ment and edge bundling to provide a pseudo-orthogonal visualization of the metabolic network. To ease pathway information retrieval, we also provide complementary interaction tools that emphasize relevant pathways in the entire metabolic context