Development of a Fully Automated Image Analysis Method for High Density cDNA and array CGH Microarray Based Genomic Studies

In this thesis, different techniques for image analysis of high density microarrays have been investigated. Most of the existing image analysis techniques require prior knowledge of image specific parameters and direct user intervention for microarray image quantification. The objective of this research work was to develop of a fully automated image analysis method capable of accurately quantifying the intensity information from high density microarrays images. The method should be robust against noise and contaminations that commonly occur in different stages of microarray development.

Ein XML-basiertes Modell für synchrone Gruppenarbeit auf gemeinsamen Informationsräumen

In dieser Arbeit wird ein generisches Modell fuer synchrone Gruppenarbeit auf gemeinsamen Informationsraeumen entwickelt. Fuer die Entwicklung dieses Modells muessen die Grundfunktionen fuer Anwendungen der synchronen Gruppenarbeit realisiert werden. Neben der Modellierung des Datenraumes (Datenmodell) und der operationellen Schnittstelle (Interaktionsmodell), muessen Mechanismen fuer die Darstellung der Aktivitaeten der Gruppenmitglieder auf dem Informationsraum (Awareness), sowie fuer die Synchronisierung gleichzeitiger Zugriffe verschiedener Benutzer auf dem Datenraum realisiert werden (Nebenlaeufgkeitskontrolle). Das Grundproblem bei der Loesung der Nebenlaeufigkeit liegt bei der Aufgabe der Isolation aus den klassischen ACID-Transaktionen zu gunsten von Awareness. Die rapide Entwicklung von Techniken der mobilen Kommunikation ermoeglicht den Einsatz dieser Geraete fuer den Zugriff auf Daten im Internet. Durch UMTSund WLAN-Technologien koennen Mobilgeraete fuer Anwendungen ueber die reine Kommunikation hinaus eingesetzt werden. Eine natuerliche Folge dieser Entwicklung sind Anwendungen fuer die Zusammenarbeit mehrerer Benutzer. In der Arbeit wird daher auf die Unterstuetzung mobiler Geraete besonderen Wert gelegt. Die Interaktion der Benutzer auf den gemeinsamen Datenraum wird durch einfache Navigationsoperationen mit einem Cursor (Finger) realisiert, wobei der Datenraum durch XML-Dokumente dargestellt wird. Die Visualisierung basiert auf der Transformierung von XML-Dokumenten in andere XML-basierte Sprachen wie HTML oder SVG durch XSLT-Stylesheets. Awareness-Informationen werden, aehnlich dem Fokus/Nimbus-Modell, von der Interaktion der Benutzer und der Ermittlung der sichtbaren Objekte bei dem Benutzer hergeleitet. Fuer eine geeignete Kontrolle der Nebenlaeufigkeit wurde der Begriff der visuellen Transaktion eingefuehrt, wo die Auswirkungen einer Transaktion von anderen Benutzern (Transaktionen) beobachtet werden koennen. Die Synchronisierung basiert auf einem Sperrverfahren und der Einfuehrung der neuen W-Sperre und der Grundoperationen readV und writeV. Das Modell (Groupware-Server) wird in der Arbeit in einem Prototyp implementiert. Weiterhin wird eine Java-Anwendung sowohl auf einem Desktop PC als auch auf einem Pocket PC (iPAQ 3970) implementiert, welche die Einsetzbarkeit dieses Prototyps demonstriert.

Genetic Programming meets Model-Driven Development

Genetic programming is known to provide good solutions for many problems like the evolution of network protocols and distributed algorithms. In such cases it is most likely a hardwired module of a design framework that assists the engineer to optimize specific aspects of the system to be developed. It provides its results in a fixed format through an internal interface. In this paper we show how the utility of genetic programming can be increased remarkably by isolating it as a component and integrating it into the model-driven software development process. Our genetic programming framework produces XMI-encoded UML models that can easily be loaded into widely available modeling tools which in turn posses code generation as well as additional analysis and test capabilities. We use the evolution of a distributed election algorithm as an example to illustrate how genetic programming can be combined with model-driven development. This example clearly illustrates the advantages of our approach – the generation of source code in different programming languages.

User Profile Management and Selection in Context-Aware Service Platforms for Networks Beyond 3G

In recent years, progress in the area of mobile telecommunications has changed our way of life, in the private as well as the business domain. Mobile and wireless networks have ever increasing bit rates, mobile network operators provide more and more services, and at the same time costs for the usage of mobile services and bit rates are decreasing. However, mobile services today still lack functions that seamlessly integrate into users’ everyday life. That is, service attributes such as context-awareness and personalisation are often either proprietary, limited or not available at all. In order to overcome this deficiency, telecommunications companies are heavily engaged in the research and development of service platforms for networks beyond 3G for the provisioning of innovative mobile services. These service platforms are to support such service attributes. Service platforms are to provide basic service-independent functions such as billing, identity management, context management, user profile management, etc. Instead of developing own solutions, developers of end-user services such as innovative messaging services or location-based services can utilise the platform-side functions for their own purposes. In doing so, the platform-side support for such functions takes away complexity, development time and development costs from service developers. Context-awareness and personalisation are two of the most important aspects of service platforms in telecommunications environments. The combination of context-awareness and personalisation features can also be described as situation-dependent personalisation of services. The support for this feature requires several processing steps. The focus of this doctoral thesis is on the processing step, in which the user’s current context is matched against situation-dependent user preferences to find the matching user preferences for the current user’s situation. However, to achieve this, a user profile management system and corresponding functionality is required. These parts are also covered by this thesis. Altogether, this thesis provides the following contributions: The first part of the contribution is mainly architecture-oriented. First and foremost, we provide a user profile management system that addresses the specific requirements of service platforms in telecommunications environments. In particular, the user profile management system has to deal with situation-specific user preferences and with user information for various services. In order to structure the user information, we also propose a user profile structure and the corresponding user profile ontology as part of an ontology infrastructure in a service platform. The second part of the contribution is the selection mechanism for finding matching situation-dependent user preferences for the personalisation of services. This functionality is provided as a sub-module of the user profile management system. Contrary to existing solutions, our selection mechanism is based on ontology reasoning. This mechanism is evaluated in terms of runtime performance and in terms of supported functionality compared to other approaches. The results of the evaluation show the benefits and the drawbacks of ontology modelling and ontology reasoning in practical applications.

The Human in the Loop: User Participation in Self-Adaptive Software

Self-adaptive software provides a profound solution for adapting applications to changing contexts in dynamic and heterogeneous environments. Having emerged from Autonomic Computing, it incorporates fully autonomous decision making based on predefined structural and behavioural models. The most common approach for architectural runtime adaptation is the MAPE-K adaptation loop implementing an external adaptation manager without manual user control. However, it has turned out that adaptation behaviour lacks acceptance if it does not correspond to a user’s expectations – particularly for Ubiquitous Computing scenarios with user interaction. Adaptations can be irritating and distracting if they are not appropriate for a certain situation. In general, uncertainty during development and at run-time causes problems with users being outside the adaptation loop. In a literature study, we analyse publications about self-adaptive software research. The results show a discrepancy between the motivated application domains, the maturity of examples, and the quality of evaluations on the one hand and the provided solutions on the other hand. Only few publications analysed the impact of their work on the user, but many employ user-oriented examples for motivation and demonstration. To incorporate the user within the adaptation loop and to deal with uncertainty, our proposed solutions enable user participation for interactive selfadaptive software while at the same time maintaining the benefits of intelligent autonomous behaviour. We define three dimensions of user participation, namely temporal, behavioural, and structural user participation. This dissertation contributes solutions for user participation in the temporal and behavioural dimension. The temporal dimension addresses the moment of adaptation which is classically determined by the self-adaptive system. We provide mechanisms allowing users to influence or to define the moment of adaptation. With our solution, users can have full control over the moment of adaptation or the self-adaptive software considers the user’s situation more appropriately. The behavioural dimension addresses the actual adaptation logic and the resulting run-time behaviour. Application behaviour is established during development and does not necessarily match the run-time expectations. Our contributions are three distinct solutions which allow users to make changes to the application’s runtime behaviour: dynamic utility functions, fuzzy-based reasoning, and learning-based reasoning. The foundation of our work is a notification and feedback solution that improves intelligibility and controllability of self-adaptive applications by implementing a bi-directional communication between self-adaptive software and the user. The different mechanisms from the temporal and behavioural participation dimension require the notification and feedback solution to inform users on adaptation actions and to provide a mechanism to influence adaptations. Case studies show the feasibility of the developed solutions. Moreover, an extensive user study with 62 participants was conducted to evaluate the impact of notifications before and after adaptations. Although the study revealed that there is no preference for a particular notification design, participants clearly appreciated intelligibility and controllability over autonomous adaptations.

Capaware: plataforma de desarrollo de software libre para aplicacines geográficas 3D multicapa

En este trabajo se presenta Capaware, una plataforma de software libre para el desarrollo de aplicaciones geográficas 3D multicapa, que surge a partir de la iniciativa del Instituto Tecnológico de Canarias en colaboración con la Universidad de Las Palmas de Gran Canaria. Este entorno simplifica la creación de aplicaciones 3D sobre territorios geográficos extensos, disponiendo de una herramienta muy visual que aporta un nuevo punto de vista muy importante para una toma de decisiones eficaz. Capaware proporciona una interfaz fácil de usar y muy flexible que simplifica el desarrollo de nuevas aplicaciones, permitiéndonos crear rápidamente entornos virtuales con múltiples capas de información sobre el terreno. Con las capacidades clásicas de un Sistema de Información Geográfica (SIG), Capaware permite actualmente la carga de capas WMS sobre entornos 3D, añadir objetos 3D sobre el terreno, y visualizar elementos dinámicos, ofreciendo una nueva perspectiva de la información analizada. Así mismo, podemos administrar las capas de recursos y elementos que se pueden representar sobre la zona geográfica en cuestión. (...)

Seminar: Symbol Management systems to support democracy in development of an online Symbol Dictionary

Abstract This seminar will introduce an initial year of research exploring participation in the development of a bilingual symbol dictionary. Symbols can be a communication and literacy ‘lifeline’ for those unable to communicate through speech or writing. We will discuss how an online system has been built to overcome language, cultural and literacy skill issues for a country where 86% are expatriates but the target clients are Arabic born individuals with speech and language impairments. The symbols in use at present are inappropriate and yet there is no democratic way of providing a ‘user voice’ for making choices, let alone easy mechanisms for adapting and sharing newly developed symbols across the nation or extended Arabic world. This project aims to change this situation. Having sourced a series of symbols that could be adapted to suit user’s needs, the team needed to encourage those users, their carers and therapists to vote on whether the symbols would be appropriate and work with those already in use. The first prototype was developed and piloted during the WAISfest in 2013. The second phase needs further voting on the most suitably adapted symbols for use when communicating with others. There is a requirement to have mechanisms for evaluating the outcome of the votes, where symbols fail to represent accurate meanings, have inappropriate colours, representations and actions etc. There also remains the need to collect both quantitative and qualitative data. Not easy in a climate of acceptance of the expert view, a culture where to be critical can be a problem and time is not of the essence.

Involving users in expert system development

The ultimate criterion of success for interactive expert systems is that they will be used, and used to effect, by individuals other than the system developers. A key ingredient of success in most systems is involving users in the specification and development of systems as they are being built. However, until recently, system designers have paid little attention to ascertaining user needs and to developing systems with corresponding functionality and appropriate interfaces to match those requirements. Although the situation is beginning to change, many developers do not know how to go about involving users, or else tackle the problem in an inadequate way. This paper discusses the need for user involvement and considers why many developers are still not involving users in an optimal way. It looks at the different ways in which users can be involved in the development process and describes how to select appropriate techniques and methods for studying users. Finally, it discusses some of the problems inherent in involving users in expert system development, and recommends an approach which incorporates both ethnographic analysis and formal user testing.

Modelling oil absorption during post-frying cooling - I: model development

Several studies have highlighted the importance of the cooling period in oil absorption in deep-fat fried products. Specifically, it has been established that the largest proportion of oil which ends up into the food, is sucked into the porous crust region after the fried product is removed from the oil bath, stressing the importance of this time interval. The main objective of this paper was to develop a predictive mechanistic model that can be used to understand the principles behind post-frying cooling oil absorption kinetics, which can also help identifying the key parameters that affect the final oil intake by the fried product. The model was developed for two different geometries, an infinite slab and an infinite cylinder, and was divided into two main sub-models, one describing the immersion frying period itself and the other describing the post-frying cooling period. The immersion frying period was described by a transient moving-front model that considered the movement of the crust/core interface, whereas post-frying cooling oil absorption was considered to be a pressure driven flow mediated by capillary forces. A key element in the model was the hypothesis that oil suction would only begin once a positive pressure driving force had developed. The mechanistic model was based on measurable physical and thermal properties, and process parameters with no need of empirical data fitting, and can be used to study oil absorption in any deep-fat fried product that satisfies the assumptions made.

Generic control interface for networked haptic virtual environments

As Virtual Reality pushes the boundaries of the human computer interface new ways of interaction are emerging. One such technology is the integration of haptic interfaces (force-feedback devices) into virtual environments. This modality offers an improved sense of immersion to that achieved when relying only on audio and visual modalities. The paper introduces some of the technical obstacles such as latency and network traffic that need to be overcome for maintaining a high degree of immersion during haptic tasks. The paper describes the advantages of integrating haptic feedback into systems, and presents some of the technical issues inherent in a networked haptic virtual environment. A generic control interface has been developed to seamlessly mesh with existing networked VR development libraries.

A novel haptic interface for navigation in large volume environments

Haptic interfaces can provide highly realistic interaction with objects within their workspace, but the task of interacting with objects over large areas or volumes is made difficult by the limits of interface travel. This paper details the development of a custom haptic interface - for navigating a large virtual environment (a simulated supermarket), and investigation into different control methods which allow for haptic interaction over extremely large workspaces.

A decade of research and development in disability, virtual reality and associated technologies: review of ICDVRAT 1996−2006

The International Conference (series) on Disability, Virtual Reality and Associated Technologies (ICDVRAT) this year held its sixth biennial conference, celebrating ten years of research and development in this field. A total of 220 papers have been presented at the first six conferences, addressing potential, development, exploration and examination of how these technologies can be applied in disabilities research and practice. The research community is broad and multi-disciplined, comprising a variety of scientific and medical researchers, rehabilitation therapists, educators and practitioners. Likewise, technologies, their applications and target user populations are also broad, ranging from sensors positioned on real world objects to fully immersive interactive simulated environments. A common factor is the desire to identify what the technologies have to offer and how they can provide added value to existing methods of assessment, rehabilitation and support for individuals with disabilities. This paper presents a brief review of the first decade of research and development in the ICDVRAT community, defining technologies, applications and target user populations served.

New high technology product development: The case of light emitting diodes

New high technology products usher in novel possibilities to transform the design, production and use of buildings. The high technology companies which design, develop and introduce these new products by generating and applying novel scientific and technical knowledge are faced with significant market uncertainty, technological uncertainty and competitive volatility. These characteristics present unique innovation challenges compared to low- and medium technology companies. This paper reports on an ongoing Construction Knowledge Exchange funded project which is tracking, real time, the new product development process of a new family of light emitting diode (LEDs) technologies. LEDs offer significant functional and environmental performance improvements over incumbent tungsten and halogen lamps. Hitherto, the use of energy efficient, low maintenance LEDs has been constrained by technical limitations. Rapid improvements in basic science and technology mean that for the first time LEDs can provide realistic general and accent lighting solutions. Interim results will be presented on the complex, emergent new high technology product development processes which are being revealed by the integrated supply chain of a LED module manufacture, a luminaire (light fitting) manufacture and end user involved in the project.

Decision theory and real estate development: a note on uncertainty

Real estate development appraisal is a quantification of future expectations. The appraisal model relies upon the valuer/developer having an understanding of the future in terms of the future marketability of the completed development and the future cost of development. In some cases the developer has some degree of control over the possible variation in the variables, as with the cost of construction through the choice of specification. However, other variables, such as the sale price of the final product, are totally dependent upon the vagaries of the market at the completion date. To try to address the risk of a different outcome to the one expected (modelled) the developer will often carry out a sensitivity analysis on the development. However, traditional sensitivity analysis has generally only looked at the best and worst scenarios and has focused on the anticipated or expected outcomes. This does not take into account uncertainty and the range of outcomes that can happen. A fuller analysis should include examination of the uncertainties in each of the components of the appraisal and account for the appropriate distributions of the variables. Similarly, as many of the variables in the model are not independent, the variables need to be correlated. This requires a standardised approach and we suggest that the use of a generic forecasting software package, in this case Crystal Ball, allows the analyst to work with an existing development appraisal model set up in Excel (or other spreadsheet) and to work with a predetermined set of probability distributions. Without a full knowledge of risk, developers are unable to determine the anticipated level of return that should be sought to compensate for the risk. This model allows the user a better understanding of the possible outcomes for the development. Ultimately the final decision will be made relative to current expectations and current business constraints, but by assessing the upside and downside risks more appropriately, the decision maker should be better placed to make a more informed and “better”.