Konzeption und prototypische Implementierung eines Generators zur Softwarevisualisierung in 3D

Softwareentwicklungsprojekte bringen viele verschiedene Artefakte hervor. Artefakte stellen unterschiedliche Aspekte wie Struktur (statische Informationen), Verhalten (dynamische Informationen) oder Evolution (historisierte Informationen) von Softwaresystemen dar. Die Softwarevisualisierung ist darauf ausgelegt, solche Artefakte in eine visuelle Form zu überführen. Externe Umfragen und eine intensive Literaturrecherche zeigen jedoch Defizite dieses Gebietes auf. So sind viele Werkzeuge zur Visualisierung vom Entwicklungsprozess entkoppelt, bieten unzureichenden Im- und Export von Visualisierungen und besitzen teilweise einen geringen Automatisierungsgrad des Visualisierungsprozesses, insbesondere bei Werkzeugen zur dreidimensionalen Visualisierung. In dieser Arbeit wurde durch Adaption und Kombination bestehender Theorien und Werkzeuge der generativen und der modellgetriebenen Softwareentwicklung in Verbindung mit Techniken aus der Softwarevisualisierung ein Konzept entwickelt, das beschreibt, wie dreidimensionale Visualisierungen von Softwaresystemen vollautomatisch generiert werden können. Im Mittelpunkt steht ein Generator, der ausgehend von einer Anforderungsspezifikation vollautomatisiert 3D-Modelle erzeugt. Zur Validierung des entwickelten Konzeptes wurde ein Prototyp implementiert, der auf die Visualisierung der Struktur von Softwaresystemen abzielt. Dieser lässt sich als Plugin in die Entwicklungsumgebung Eclipse integrieren und erzeugt aus Ecore-basierten Modellen nach Benutzeranforderungen mittels Modelltransformationen ein 3D-Modell im freien und standardisierten X3D-Format. Die Transformationen sind dabei mit dem Werkzeug openArchitectureWare realisiert. Schließlich wurde der Prototyp selbst einer Evaluation gemäß etablierten Kriterien aus der Softwarevisualisierung unterzogen

Trau, SCHAU, wem? - V-IDS oder eine andere Sicht der Dinge

Die ständig wachsende Flut der in einem Netzwerk anfallenden sicherheitsrelevanten Daten macht in zunehmendem Maße neue Darstellungsformen notwendig. Nur so können diese Daten ausreichend schnell und in angemessenem Umfang erfassbar und beherrschbar bleiben. Wesentlich schneller und intuitiver als reinen Text können wir den Inhalt von Bildern erfassen, grafische Darstellungen machen Geschehnisse in der Regel leichter erfassbar. Informationen können zusätzlich stärker verdichtet dargestellt werden, ohne dass der transportierte Inhalt darunter leidet. Die Darstellung von Sicherheitsdaten in grafischer Form steht derzeit noch sehr am Anfang, es gibt wenig Erfahrung, welche Darstellungen mehr und welche weniger geeignet sind. V-IDS soll Grundlagen legen für eine dynamische, dreidimensionale Darstellung solcher Daten. Es soll ein einfaches Experimentieren mit verschiedenen und neuartigen Darstellungen ermöglichen. Damit können dann vorhandene und zukünftige Ideen einfach und ohne längere Entwicklungszeit prototypisch umgesetzt und bewertet werden

Modularization of biochemical networks based on classification of Petri net t-invariants

<p>Abstract</p> <p>Background</p> <p>Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.</p> <p>With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system.</p> <p>Methods</p> <p>Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied.</p> <p>Results</p> <p>We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in <it>Saccharomyces cerevisiae</it>) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability.</p> <p>Conclusion</p> <p>We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.</p

Visualizing three-dimensional graph drawings

viii, 110 leaves : ill. (some col.) ; 29 cm.The GLuskap system for interactive three-dimensional graph drawing applies techniques of scientific visualization and interactive systems to the construction, display, and analysis of graph drawings. Important features of the system include support for large-screen stereographic 3D display with immersive head-tracking and motion-tracked interactive 3D wand control. A distributed rendering architecture contributes to the portability of the system, with user control performed on a laptop computer without specialized graphics hardware. An interface for implementing graph drawing layout and analysis algorithms in the Python programming language is also provided. This thesis describes comprehensively the work on the system by the author—this work includes the design and implementation of the major features described above. Further directions for continued development and research in cognitive tools for graph drawing research are also suggested

Visualização de informação

O relatório está dividido em duas partes. Na primeira parte, é abordado o problema da visualização exactamente no que diz respeito à subtil correlação existente entre as técnicas (e respectivas metáforas), o utilizador e os dados. Na segunda parte, são analisadas algumas aplicações, projectos, ferramentas e sistemas de Visualização de Informação. Para categorizalos, serão considerados sete tipos de dados básicos subjacentes a eles: unidimensional, bidimensional, tridimensional, multi-dimensional, temporal, hierárquico, rede e workspace.O tema deste relatório é a visualização da informação. Esta é uma área actualmente muito activa e vital no ensino, na pesquisa e no desenvolvimento tecnológico. A ideia básica é utilizar imagens geradas pelo computador como meio para se obter uma maior compreensão e apreensão da informação que está presente nos dados (geometria) e suas relações (topologia). É um conceito simples, porém poderoso que tem criado imenso impacto em diversas áreas da engenharia e ciência.The theme of this report is information visualization. Nowadays, this is a very active and vital area of research, teaching and development. The basic idea of using computer generated pictures to gain information and understanding from data and relationships is the key concept behind it. This is an extremely simple, but very important concept which is having a powerful impact on methodology of engineering and science. This report is consisted of two parts. The first one, is an overview of the subtle correlation between the visual techniques, the user perception and the data. In the second part, several computer applications, tools, projects and information visualization systems are analyzed. In order to categorize them, seven basic types of data are considered: onedimensional, two- dimensional, three-dimensional, multidimensional, temporal, hierarchic, network and workspace

Web-based drawing software for graphs in 3D and two layout algorithms

A new web-based software system for visualization and manipulation of graphs in 3D, named We3Graph is presented with a focus on accessibility, customizability for applications of graph drawing, usability and extendibility. The software system allows multiple users to work on the same graph at the same time and is accessible through web browsers. The software can be extended using plugins written in any programming language and custom render engines written in the Javascript language. Also two new algorithms are proposed to answer the following question, previously raised in [53]: Given a graph G with n vertices, V = fv1;v2; : : : ;vng, and given a set of n distinct points P = fp1; p2; : : : ; png each with integer coordinates in three dimensions, can G be drawn crossing-free on P with vi at pi and with a number of bends polynomial in n and in a volume polynomial in n and the dimension of P

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

Social media analysis for disaster management

People use social networks, with increasing frequency, to communicate and publish status information. Twitter and Facebook are prominent examples. This status information contains useful, disaster related data together with an overwhelming amount of noise. For this reason, there are dedicated tools that filter this information to aid in disaster discovery, management and relief. Their development requires a lot of time and effort, which results in high costs. Generic visual analytics tools are relatively well known, supported and continuously developed by large companies. They may be a valid alternative to specifically developed tools that require specific, non-transferable training. The primary aim of this study is to evaluate generic visual analytics tools with respect to their ability to handle disaster management scenarios. This includes, specifically, their ability to visualise and analyse the geospatial meta information provided by social media

Event-Based Dynamic Graph Visualisation

Dynamic graph drawing algorithms take as input a series of timeslices that standard, force-directed algorithms can exploit to compute a layout. However, often dynamic graphs are expressed as a series of events where the nodes and edges have real coordinates along the time dimension that are not confined to discrete timeslices. Current techniques for dynamic graph drawing impose a set of timeslices on this event-based data in order to draw the dynamic graph, but it is unclear how many timeslices should be selected: too many timeslices slows the computation of the layout, while too few timeslices obscures important temporal features, such as causality. To address these limitations, we introduce a novel model for drawing event-based dynamic graphs and the first dynamic graph drawing algorithm, DynNoSlice, that is capable of drawing dynamic graphs in this model. DynNoSlice is an offline, force-directed algorithm that draws event-based, dynamic graphs in the space-time cube (2D+time). We also present a method to extract representative small multiples from the space-time cube. To demonstrate the advantages of our approach, DynNoSlice is compared with state-of-the-art timeslicing methods using a metrics-based experiment. Finally, we present case studies of event-based dynamic data visualised with the new model and algorithm

Evaluating Extensible 3D (X3D) Graphics For Use in Software Visualisation

3D web software visualisation has always been expensive, special purpose, and hard to program. Most of the technologies used require large amounts of scripting, are not reliable on all platforms, are binary formats, or no longer maintained. We can make end-user web software visualisation of object-oriented programs cheap, portable, and easy by using Extensible (X3D) 3D Graphics, which is a new open standard. In this thesis we outline our experience with X3D and discuss the suitability of X3D as an output format for software visualisation