Object-oriented modelling of municipal waste management systems

The paper presents the adaptive, reactive computer assistance system design methodology, making modelling, analysis, and testing possible of the integrated waste management systems. The presented model is defined in a multilayer open architecture, i.e.-, it consists of the logical spaces of the constituent models (submodels) of the object classes and real processes of the waste management system. Topics covered by the paper include elements of a literature review on the modelling of systems and waste management processes, review of the programming environments employed, as well as a description of the object- -oriented waste management systems design methodology

Visualization of Barrier Tree Sequences

Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods that help to analyze the validity of these models. We focus on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; thus they are huge and high dimensional. Their most salient features, however, are encapsulated by their so-called barrier tree that reflects the local minima and their connecting saddle points. For each length of the growing RNA chain there exists a folding landscape. We visualize the sequence of folding landscapes by an animation of the corresponding barrier trees. To generate the animation, we adapt the foresight layout with tolerance algorithm for general dynamic graph layout problems. Since it is very general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a modified DOT algorithm, and presentation techniques for the final animatio

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

Graph layout using subgraph isomorphisms

Today, graphs are used for many things. In engineering, graphs are used to design circuits in very large scale integration. In computer science, graphs are used in the representation of the structure of software. They show information such as the flow of data through the program (known as the data flow graph [1]) or the information about the calling sequence of programs (known as the call graph [145]). These graphs consist of many classes of graphs and may occupy a large area and involve a large number of vertices and edges. The manual layout of graphs is a tedious and error prone task. Algorithms for graph layout exist but tend to only produce a 'good' layout when they are applied to specific classes of small graphs. In this thesis, research is presented into a new automatic graph layout technique. Within many graphs, common structures exist. These are structures that produce 'good' layouts that are instantly recognisable and, when combined, can be used to improve the layout of the graphs. In this thesis common structures are given that are present in call graphs. A method of using subgraph isomorphism to detect these common structures is also presented. The method is known as the ANHOF method. This method is implemented in the ANHOF system, and is used to improve the layout of call graphs. The resulting layouts are an improvement over layouts from other algorithms because these common structures are evident and the number of edge crossings, clusters and aspect ratio are improved

Visualisierung biochemischer Reaktionsnetze

In dieser Arbeit werden Anforderungen an die Darstellung biochemischer Reaktionsnetze untersucht und die Netze unter dem Gesichtspunkt der Visualisierung modelliert. Anschliessend wird ein Algorithmus zum Zeichnen biochemischer Reaktionsnetze entwickelt und analysiert.In this dissertation we investigate the requirements for the visualisation of biochemical reaction networks. We compose a model for these networks that lends itself to visualisation and develop and analyse an algorithm to create drawings of the networks

Theory and Practice of Graph Drawing

A workshop on Theory and Practice of Graph Drawing was held in conjunction with the $20^{\text{\tiny th}}$ International Symposium on Graph Drawing to celebrate Peter Eades's $60^{\text{\tiny th}}$ birthday. The workshop was hosted by Microsoft Research in Redmond, Washington, USA, on September 18, 2012. This report reviews the contents of the workshop

Advances in the theory and practice of graph drawing

AbstractThe visualization of conceptual structures is a key component of support tools for complex applications in science and engineering. Foremost among the visual representations used are drawings of graphs and ordered sets. In this talk, we survey recent advances in the theory and practice of graph drawing. Specific topics include bounds and tradeoffs for drawing properties, three-dimensional representations, methods for constraint satisfaction, and experimental studies