Mit mehr als 120 Millionen registrierten Internetadressen (Stand: März 2007) symbolisiert das Internet heutzutage das größte Informationsmedium unserer Zeit. Täglich wächst das Internet um eine unüberschaubare Menge an Informationen. Diese Informationen sind häufig in Dokumenten hinterlegt, welche zur Auszeichnung die Hypertext Markup Language verwenden. Seit Beginn der Neunziger Jahre hat sich dieses System bewährt, da dadurch der einzelne Nutzer in die Lage versetzt wird, auf einfache und effiziente Weise Dokumentinhalte mit Darstellungsanweisungen zu versehen und diese eigenständig im Internet zu veröffentlichen. Diese Layoutinformationen können bei Abruf der entsprechenden Ressource durch ein Computerprogramm leicht ausgewertet und zur Darstellung der Inhalte genutzt werden. Obwohl sowohl die Layoutinformationen als auch die eigentlichen Dokumentinhalte in einem textuellen Format vorliegen, konnten die Nutzertextinhalte durch eine Maschine bisher nur sehr eingeschränkt verarbeitet werden. Während es menschlichen Nutzern keinerlei Probleme bereitet, die Bedeutung einzelner Texte auf einer Webseite zu identifizieren, stellen diese für einen Rechner prinzipiell nur eine Aneinanderreihung von ASCII-Zeichen dar. Sobald es möglich werden würde, die Bedeutung von Informationen durch ein Computerprogramm effizient zu erfassen und weiterzuverarbeiten, wären völlig neue Anwendungen mit qualitativ hochwertigeren Ergebnissen im weltweiten Datennetz möglich. Nutzer könnten Anfragen an spezielle Agenten stellen, welche sich selbstständig auf die Suche nach passenden Resultaten begeben; Informationen verschiedener Informationsquellen könnten nicht nur auf semantischer Ebene verknüpft, sondern daraus sogar neue, nicht explizit enthaltene Informationen abgeleitet werden. Ansätze dazu, wie Dokumente mit semantischen Metadaten versehen werden können, gibt es bereits seit einiger Zeit. Lange umfasste dies jedoch die redundante Bereitstellung der Informationen in einem eigenen Dokumentenformat, weswegen sich keines der Konzepte bis in den Privatbereich durchsetzen konnte und als Endkonsequenz in den vergangenen Monaten besonderes Forschungsinteresse darin aufkam, Möglichkeiten zu finden, wie semantische Informationen ohne großen Zusatzaufwand direkt in bestehende HTML-Dokumente eingebettet werden können. Die vorliegende Diplomarbeit möchte diese neuen Möglichkeiten im Bereich des kollaborativen Arbeitens näher untersuchen. Ziel ist es dazu, eine Webapplikation zur Abwicklung typischer Projektmanagement-Aufgaben zu entwickeln, welche jegliche Informationen unter einem semantischen Gesichtspunkt analysieren, aufbereiten und weiterverarbeiten kann und unabhängig von der konkreten Anwendungsdomain und Plattform systemübergreifend eingesetzt werden kann. Die Konzepte Microformats und RDFa werden dabei besonders herausgestellt und nach Schwächen und zukünftigen Potentialen hin untersucht. / The World Wide Web supposably symbolizes with currently more than 120 million registered internet domains (March 2007) the most comprehensive information reference of all times. The amount of information available increases by a storming bulk of data ever day. Those information is often embedded in documents which utilize the Hypertext Markup Language. This enables the user to mark out certain layout properties of a text in an easy and efficient fashion and to publish the final document containing both layout and data information. A computer application is then able to extract style information from the document resource and to use it in order to render the resulting website. Although layout information and data are both equally represented in a textual manner, a machine was hardly capable of processing user content so far. Whereas human consumers have no problem to identify and understand the sense of several paragraphs on a website, they basically represent only a concatenation of ASCII characters for a machine. If it were possible to efficiently disclose the sense of a word or phrase to a computer program in order to process it, new astounding applications with output results of high quality would be possible. Users could create queries for specialized agents which autonomously start to search the web for adequate result matches. Moreover, the data of multiple information sources could be linked and processed together on a semantic level so that above all new, not explicitly stated information could be inferred. Approaches already exist, how documents could be enhanced with semantic metadata, however, many of these involve the redundant provision of those information in a specialized document format. As a consequence none of these concepts succeeded in becoming a widely used method and research started again to find possibilities how to embed semantic annotations without huge additional efforts in an ordinary HTML document. The present thesis focuses on an analysis of these new concepts and possibilities in the area of collaborative work. The objective is to develop the prototype of a web application with which it is possible to manage typical challenges in the realm of project and workflow management. Any information available should be processable under a semantic viewpoint which includes analysis, conditioning and reuse independently from a specific application domain and a certain system platform. Microformats and RDFa are two of those relatively new concepts which enable an application to extract semantic information from a document resource and are therefore particularly exposed and compared with respect to advantages and disadvantages in the context of a “Semantic Web”.

Die Dissertation beschäftigt sich mit der automatischen Erkennung chirurgischer Aktivitäten im Operationssaal, welche einen wichtigen Bestandteil im automatischen chirurgischen Assistenzprozess darstellt. Die automatische Assistenz ist eine der wichtigen Entwicklungen bei der fortschreitenden Technisierung in der Chirurgie. Es werden Anforderungen an ein Erkennungssystem definiert sowie ein entsprechendes Erkennungsmodell entworfen und untersucht. Die Evaluation bedient sich simulierter chirurgischer Eingriffe mit hoher Realitätsnähe. Die Ergebnisse zeigen eine grundlegende Eignung des Modells für die automatische Aktivitätserkennung multipler Eingriffstypen. Mögliche Weiterentwicklungen könnten die vorgestellte Lösung weiter vorantreiben.

La récente introduction de l'approche à services a relancé la technologie des workflow. Cette technologie utilise le concept de modèle de procédé pour coordonner et automatiser la réalisation d'un ensemble de tâches. Ce patron de construction d'applications par assemblage de briques logicielles en utilisant un modèle de procédé fournit un mécanisme qui simplifie la spécification et l'évolution des applications orientées procédé. Cette thèse s'intéresse à la conception, la spécification et l'exécution d'applications orientées procédé en général, et plus particulièrement à l'orchestration de services. Nous partons de la technologie workflow comme base de notre canevas FOCAS et nous proposons de suivre une approche d'ingénierie dirigée par les modèles (IDM) pour la spécification abstraite d'une orchestration. Dans FOCAS, la description abstraite de l'application est découplée des services (ou applications) supportant son exécution. Cette description permet d'abord, une indépendance vers la technologie utilisée pour l'implémentation de services, ainsi qu'une liaison dynamique à l'exécution aux services disponibles. Nous proposons également des mécanismes permettant d'étendre notre canevas dans différents domaines ainsi que pour supporter des aspects non-fonctionnels. L'outillage supportant notre approche a été implémenté et validé par son utilisation dans les projets européens ITEA : S4ALL et SODA, et pour la réalisation d'une plateforme complète d'orchestration repartie et dynamique.

本研究遵循模型驅動架構的概念，發展一適用於現實商業流程之工作流程模型，採用創新的方式對於工作流程做描述，我們只需要按照固定的步驟，便可以將真實的商業流程發展成可用的模型，以利於後續發展工作流程系統之用。在發展模型時，我們採用了IBM的資訊框架（IFW）做為塑模的方式，以及利用統一塑模語言中的狀態移轉圖和循序圖的概念來做為呈現工作流程模型，解決了傳統流程無法表達流程內部資料變化所帶來的影響，除此之外，我們在模型發展後，採用包含事件-驅動概念的工作流程引擎來產生工作流程系統，我們將商業流程視為一個個的物件，物件收發事件導致狀態的改變而引發另一個事件的發生，如此循環下去，直到整個流程完成。

Technological advancements in mass spectrometry allowing quantification of almost complete proteomes make proteomics a key platform for generating unique functional molecular data. Furthermore, the integrative analysis of genomic and proteomic data, termed proteogenomics, has emerged as a new field revealing insights into gene expression regulation, cell signalling, and disease processes. However, the lack of software tools for high-throughput integration and unbiased modification and variant detection hinder efforts for large-scale proteogenomics studies. The main objectives of this work are to address these issues by developing and applying new software tools and data analysis methods. Firstly, I address mapping of peptide sequences to reference genomes. I introduce a novel tool for high-throughput mapping and highlight its unique features facilitating quantitative and post-translational modification mapping alongside accounting for amino acid substitutions. The performance is benchmarked. Furthermore, I offer an additional tool that permits generation of web accessible hubs of genome wide mappings. To enable unbiased identification of post-translational modifications and amino acid substitutions for high resolution mass spectrometry data, I present algorithmic updates the mass tolerant blind spectrum comparison tool ’MS SMiV’. I demonstrate the applicability of the changes by benchmarking against a published mass tolerant database search of a high resolution tandem mass spectrometry dataset. I then present the application of ‘MS SMiV’ on a panel of 50 colorectal cancer cell lines. I show that the adaption of ‘MS SMiV’ outperforms traditional sequence database based identification of single amino acid variants. Furthermore, I highlight the utility of mass tolerant spectrum matching in combination with isobaric labelled quantitative proteomics in distinguishing between post-translational modifications and amino acid variants of similar mass. In the last part of this work I integrate both tools with a high-throughput proteogenomic identification pipeline and apply it to a pilot study of chondrocytes derived from 12 osteoarthritic individuals. I show the value of this approach in identifying variation between individuals and molecular levels and highlight them with individual examples. I show that multi-plexed proteogenomics can be used to infer genotypes of individuals.

Dans cette thèse, nous traitons des problèmes de la détection des personnes et de l'estimation de leurs poses dans la Salle Opératoire (SO), deux éléments clés pour le développement d'applications d'assistance chirurgicale. Nous percevons la salle grâce à des caméras RGB-D qui fournissent des informations visuelles complémentaires sur la scène. Ces informations permettent de développer des méthodes mieux adaptées aux difficultés propres aux SO, comme l'encombrement, les surfaces sans texture et les occlusions. Nous présentons des nouvelles approches qui tirent profit des informations temporelles, de profondeur et des vues multiples afin de construire des modèles robustes pour la détection des personnes et de leurs poses. Une évaluation est effectuée sur plusieurs jeux de données complexes enregistrés dans des salles opératoires avec une ou plusieurs caméras. Les résultats obtenus sont très prometteurs et montrent que nos approches surpassent les méthodes de l'état de l'art sur ces données cliniques. / In this thesis, we address the two problems of person detection and pose estimation in Operating Rooms (ORs), which are key ingredients in the development of surgical assistance applications. We perceive the OR using compact RGB-D cameras that can be conveniently integrated in the room. These sensors provide complementary information about the scene, which enables us to develop methods that can cope with numerous challenges present in the OR, e.g. clutter, textureless surfaces and occlusions. We present novel part-based approaches that take advantage of depth, multi-view and temporal information to construct robust human detection and pose estimation models. Evaluation is performed on new single- and multi-view datasets recorded in operating rooms. We demonstrate very promising results and show that our approaches outperform state-of-the-art methods on this challenging data acquired during real surgeries.

The Ph.D. project has evolved from focusing on the technical problem of the integration and interoperability of an assemblage of complex systems and SoS within a flight training system to development of a workflow process using frameworks to aid the decision making process for the selection of optimal flight training blending mixes. The focus of the research involved developing a methodology to satisfy research project proposal requirements agreed upon with the industrial sponsor. This thesis investigates the complexity of a modern flight training systems and the need for understanding that it is supported by a complex Family of Systems (FoS) including Virtual Reality Training Environments such as flight simulators, to live training aircraft with various configurations of avionic controls. One of the key technical problems today is how best to develop and assemble a family of flight training system into an integrated Live/Synthetic mix for aircrew training to optimise organisation and training objectives. With the increased use of emulation/synthetic data on aircraft for live training, the synthetic boundary is becoming increasingly blurred. Systematic consideration of the most appropriate blend is needed. The methodology used in the research is model driven and the architecture produced is described at a level of abstraction to enable communication to all stakeholders for the means of understanding the structure involved in the system design process. Relational Oriented Systems Engineering and Technology Trade-Off Analysis (ROSETTA) frameworks are described using Model Based Systems Engineering (MBSE) techniques for supporting capability based trade-off decisions for selection of optimal flight training FoS mixes dependent on capability. The research proposes a methodology and associated methods including a high-level systematic closed loop information management structure for blended device/tool aircrew training and a modelling and analysis approach for the FoS aviation training problem to enhance the existing training programmes to provide a more efficient and agile training environment. The mathematical formalisms used provide a method of quantifying subjective opinions and judgements for trade studies to be accomplished on the suitability of technology for each student pilot in relation to training and organisational objectives. The methodology presented is by no means a final solution, but a path for further research to enable a greater understanding of the suitability of training tools/technology used to train individual pilots at various stages throughout the training pipeline lifecycle(s).

Globaliseringen och omvärldens påverkan av de moderna organisationerna har skapat nya krav och mål för våra svenska arbetsgivare. Flexibilitet och snabba förändringar måste dagens arbetsgivare vara väl anpassad för. Detta i sin tur innebär att även arbetstagaren måste vara redo att klara av liknande krav. Ny teknik och nya sätt att arbeta på har givit den moderna kontorsarbetaren en vardag som kan vara helt papperslös och inte heller knuten till en och samma plats. Det centrala för det nya arbetssättet är självfallet att öka lönsamheten, men fördelar som ökad kreativitet och ökat samarbete medarbetarna emellan lyfts fram som fördelar från arbetsgivarens sida. Denna studie utgår från en kvalitativ ansats. Målet med studien var att fånga medarbetarnas upplevelser av att arbeta aktivitetsbaserat. Studien har inte som avsikt att förklara om detta nya arbetssätt är bra eller dåligt för arbetstagaren utan enbart som för avsikt att fånga deras upplevelse. Studien visar att den generella upplevelsen av att arbeta aktivitetsbaserat är god, men att upplevelserna varierar mellan olika individer. Slutsatsen är att de anställda behöver ha en känsla av att kunna kontrollera sin vardag och möjligheter att välja rätt plats för rätt arbetsuppgift för att detta arbetssätt skall upplevas bra. Studien anser vi har ett värde på grund av att den mäter medarbetarnas upplevelse. Det är något som inte har forskats mycket om tidigare i detta allt mer förekommande sätt att utforma moderna kontor på. Om vi fångar medarbetarnas upplevelse av att arbeta i denna miljö kan vi enklare förstå hur den upplevs och med bättre förutsättningar förbättra arbetsmiljön på sikt i ett samhälle som löpande ställer nya krav på organisationerna och de anställda. / Globalization and the outside world's influence on modern organizations have created new demands and goals for our Swedish employers. Flexibility and rapid changes demand that today's employers must be well-suited for change. This in turn means that the employee must also be ready to meet similar requirements. New technology and new ways of working have given the modern office worker a daily life that can be completely paperless and because of this the employee isn't linked to one specific workstation. The key reason for to the new way of working is to increase profitability, but benefits such as increased creativity and increased cooperation among employees are highlighted as benefits from the employer. This study is based on a qualitative approach. The aim of the study was to capture the employees experiences of working activity-based. The study does not intend to explain whether this new way of working is good or bad for the employee, but only for the purpose of capturing their experience. The study shows that the overall experience of working activity-based is good, but that experiences vary between different individuals. The conclusion is that employees need to have the feeling of being able to control their everyday lives and opportunities to choose the right place for the right task for this work method to be experienced well. The value of this research lies in the fact that because employee experience is something that has not been the center of the research before, and we need to know more about the effects of this increasingly popular way of designing modern offices. If we capture the employee's experience of working in this environment, we can more easily understand how it is perceived and better conditions improve the working environment in the long term in a society that continually places new demands on organizations and employee's.

Cette thèse a pour objectif la conception de méthodes pour la reconnaissance automatique des activités chirurgicales. Cette reconnaissance est un élément clé pour le développement de systèmes réactifs au contexte clinique et pour des applications comme l’assistance automatique lors de chirurgies complexes. Nous abordons ce problème en utilisant des méthodes de Vision puisque l’utilisation de caméras permet de percevoir l’environnement sans perturber la chirurgie. Deux types de vidéos sont utilisées : des vidéos laparoscopiques et des vidéos multi-vues RGBD. Nous avons d’abord étudié les résultats obtenus avec les méthodes de l’état de l’art, puis nous avons proposé des nouvelles approches basées sur le « Deep learning ». Nous avons aussi généré de larges jeux de données constitués d’enregistrements de chirurgies. Les résultats montrent que nos méthodes permettent d’obtenir des meilleures performances pour la reconnaissance automatique d’activités chirurgicales que l’état de l’art. / The main objective of this thesis is to address the problem of activity recognition in the operating room (OR). Activity recognition is an essential component in the development of context-aware systems, which will allow various applications, such as automated assistance during difficult procedures. Here, we focus on vision-based approaches since cameras are a common source of information to observe the OR without disrupting the surgical workflow. Specifically, we propose to use two complementary video types: laparoscopic and OR-scene RGBD videos. We investigate how state-of-the-art computer vision approaches perform on these videos and propose novel approaches, consisting of deep learning approaches, to carry out the tasks. To evaluate our proposed approaches, we generate large datasets of recordings of real surgeries. The results demonstrate that the proposed approaches outperform the state-of-the-art methods in performing surgical activity recognition on these new datasets.

Modern science relies on workflow technology to capture, process, and analyse data obtained from scientific instruments. Scientific workflows are precise descriptions of experiments in which multiple computational tasks are coordinated based on the dataflows between them. Orchestrating scientific workflows presents a significant research challenge: they are typically executed in a manner such that all data pass through a centralised computer server known as the engine, which causes unnecessary network traffic that leads to a performance bottleneck. These workflows are commonly composed of services that perform computation over geographically distributed resources, and involve the management of dataflows between them. Centralised orchestration is clearly not a scalable approach for coordinating services dispersed across distant geographical locations. This thesis presents a scalable decentralised service-oriented orchestration system that relies on a high-level data coordination language for the specification and execution of workflows. This system's architecture consists of distributed engines, each of which is responsible for executing part of the overall workflow. It exploits parallelism in the workflow by decomposing it into smaller sub-workflows, and determines the most appropriate engines to execute them using computation placement analysis. This permits the workflow logic to be distributed closer to the services providing the data for execution, which reduces the overall data transfer in the workflow and improves its execution time. This thesis provides an evaluation of the presented system which concludes that decentralised orchestration provides scalability benefits over centralised orchestration, and improves the overall performance of executing a service-oriented workflow.