Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

Information technologies as instruments of social transformation : the computerization of classical scholarship

Computer-based technologies are often seen as instruments that effect radical transformation within workplaces; these transformations are expressed through utopian or dystopian visions of empowered knowledge workers or electronic sweatshops. Visions, however, do little to examine the evidence for and the nature of such transformations. In what ways do new computer-based technologies re-form and reshape the nature, stucture, and organization of work? In particular, how do these technologies affect a domain of work which is abstract in nature and consists of the evaluation and amalgamation of many diverse information sources?This dissertation reports on an empirical study of the impact of information technologies on a specific class of knowledge workers, classical scholars. My goal is to understand the phenomenon of change due to increased use of information technologies from the point of view of the members of this social world. In order to do this, I will follow the procedures for data collection and analysis of the grounded theory approach as developed by Anselm Strauss and his associates. I employ the social worlds perspective as an organizing framework.In subsequent chapters, I consider the diffusion of a particular set of computer-based research tools within the discipline and subsequent changes to individuals' work patterns, task definition and interactions within and without the discipline. I further evaluate changes in the accessibility of information and the attendent impact on social and organizational, structures. Finally, I describe the emergence of electronic communities and new domains of work as information and communication technologies become more prevalent

The Problematic of Privacy in the Namespace

In the twenty-first century, the issue of privacy--particularly the privacy of individuals with regard to their personal information and effects--has become highly contested terrain, producing a crisis that affects both national and global social formations. This crisis, or problematic, characterizes a particular historical conjuncture I term the namespace. Using cultural studies and the theory of articulation, I map the emergent ways that the namespace articulates economic, juridical, political, cultural, and technological forces, materials, practices and protocols. The cohesive articulation of the namespace requires that privacy be reframed in ways that make its diminution seem natural and inevitable. In the popular media, privacy is often depicted as the price we pay as citizens and consumers for security and convenience, respectively. This discursive ideological shift supports and underwrites the interests of state and corporate actors who leverage the ubiquitous network of digitally connected devices to engender a new regime of informational surveillance, or dataveillance. The widespread practice of dataveillance represents a strengthening of the hegemonic relations between these actors--each shares an interest in promoting an emerging surveillance society, a burgeoning security politics, and a growing information economy--that further empowers them to capture and store the personal information of citizens/consumers. In characterizing these shifts and the resulting crisis, I also identify points of articulation vulnerable to rearticulation and suggest strategies for transforming the namespace in ways that might empower stronger protections for privacy and related civil rights

IT Supported Construction Project Management Methodology Based on Process and Product Model and Quality Management

Computer Integrated Construction Project Management (CPM) supported by product and process models can be seen as a future type of integration structure facilitating the solution of various management problems in the fragmented Construction Industry. The key to success is directly correlated with the comprehensive integration of currently isolated IT applications. However, despite that a number of initiatives have been developed, no fully generic models have yet to be formally standardized. This topic has been the subject of intensive research during the last decades. In this thesis a Computer Integrated CPM approach, which is supported by IFC (Industry Foundation Classes) and ISO9001:2000 Quality Management System, is proposed. The main aim is to provide integration of product, process and organizational information to help achieve the interoperability of the involved actors and tools in a concurrent environment. According to implied requirements which are represented in the ‘state of the art’ section, the fundamental concepts are presented in two parts as: (1) realization of CPM in an IT concept and (2) formalization of IFC Views for software interoperability on the example of Bidding Preparation Phase. In order to realize a generic framework using a high-level process core model named Organizational Management Process (OMP) model, different aspects have been brought together into a consistent life cycle structure. These are: (1) a set of layered processes based on ISO procedural definitions, (2) software integration requirements based on Construction Management Phases, (3) application methods of the Procurement System and (4) Organizational data. This provides for synchronizing technical products, processes, documents, and actors in their inter-relationship. The framework is hierarchically structured in three layers Phases – Processes - Product data. The developed IT Management Processes (ITMP) which are used as a baseline for the IFC Views implementation are derived from the OMP. Moreover, in order to support completeness, a mapping structure between processes and scenarios based on the Procurement Systems was constituted. The representation of OMP and ITMP is provided by using the ARIS eEPC (extended event-driven process chain) modeling method. On the basis of a generalized representation of product data, a system-wide integration model for heterogeneous client applications which supports different CPM areas can be achieved. IFC Product Data Model integrates different domains thereby enabling coordination of bidding preparations. However, there is a need to realize individual model subsets. i.e. views of the product model. In this context, adaptable views were developed based on ITMP. The defined resources’ relevancies to IFC Objects are examined by realizing central information elements. These provide a mapping structure between process resources and IFC Classes. On that basis integration of process and product models can be accomplished. In order to realize IFC Views, IFC Concepts and IFC Instance Diagrams were developed based on IFC View Definition Format. The grouping of IFC Concepts enables the implementation of the adaptable IFC Views that are required for standardized system integration. This is achieved with the help of formal specification using the Generalized Subset Definition Schema. The validation has been made based on an alphanumerical comparison. The selected 3D full-model and the developed IFC View for Product Catalog models are compared in this context. There are two consequences observed. In the first case, which also addresses Unit Price Procurement systems, the desired results were obtained by filtering the required data. However, when the results were compared for Design & Build and Lump-sum Procurement Systems (contracts), an extension need was observed in the IFC Model. The solution is provided via formalization of cost data and material analysis information by an extension of IFC Concept namely ‘IfcConstructionResource’ with new classes and with new relations. Thereby a common information model based on the data schema of the IFC standard is constituted.Das von Produkt- und Prozessmodellen unterstützte computerintegrierte Bauprojektmanagement (CPM) kann als der zukünftige Typ der Integrationsstruktur angesehen werden, der die Lösung verschiedener Baumanagementprobleme in der fragmentierten Bauindustrie erleichtern kann. Der Schlüssel zum Erfolg steht in direkter Beziehung zu einer umfassenden Integration derzeit getrennter IT-Anwendungen. Trotz zahlreich entwickelter Ansätze, die zur Verfügung gestellt wurden, sind bisher noch keine vollständig generischen Modelle formell standardisiert worden, obwohl dies in den letzten Jahrzehnten ein Thema intensiver Forschung war. In dieser Promotionsschrift wird eine computerintegrierte CPM-Methode, die auf Basis der IFC (Industry Foundation Classes) und dem Qualitätsmanagement ISO 9001:2000 aufbaut, vorgeschlagen. Das Hauptziel besteht in der Schaffung der Integration von Produkt-, Prozess- und Organisationsinformationen, um die Interoperabilität der beteiligten Akteure und Tools in einer parallelen Umgebung erreichen zu können. Entsprechend den Anforderungen, die im Abschnitt „Stand der Technik“ aufgeführt sind, werden die vorgeschlagenen, grundlegenden Konzepte in zwei Bereiche aufgeteilt: (1) Umsetzung der CPM-Prozesse in ein IT-Konzept und (2) Formalisierung der IFC-Sichten für die Interoperabilität von Software, beispielhaft ausgeführt für die der Ausschreibungsphase. Um einen generischen Rahmen unter Verwendung eines hochrangigen Prozesskernmodells, das als organisatorischer Managementprozess (OMP) bezeichnet wird, zu realisieren, werden zuerst die verschiedenen Aspekte in einer konsistenten Lebenszyklenstruktur zusammengefügt. Diese sind: (1) eine Menge hierarchisch geschichteter Prozesse, erstellt auf der Grundlage der Verfahrensdefinitionen von ISO 9001, (2) die Softwareintegrationsanforderungen auf der Grundlage der Baumanagementphasen, (3) die Anwendungsmethoden des Beschaffungssystems und (4) die Organisationsdaten. Dadurch wird die Synchronisation der in Wechselbeziehung stehenden technischen Produkte, Prozesse, Dokumente und Akteure geschaffen. Das gesamte System ist hierarchisch in die drei Ebenen Phasen – Prozesse – Produktdaten strukturiert. Die entwickelten IT-Managementprozesse (ITMP), die als Grundlage für die IFC-Implementierungssichten dienen, werden aus dem OMP hergeleitet. Der Vollständigkeit halber, wird eine Abbildungsstruktur zwischen den Prozessen und den Szenarien, die die Beschaffungssysteme beschreiben, entwickelt. Die Darstellung der OMP und ITMP erfolgt unter Verwendung der erweiterten ereignisgesteuerten Prozessketten (eEPK) nach der ARIS-Modelliermethode. Auf der Grundlage einer verallgemeinerten Darstellung der Prozessdaten kann das systemweite Integrationsmodell für heterogene Client-Anwendungen, das verschiedene CPM-Bereiche unterstützt, erreicht werden. Das IFC-Produktdatenmodell integriert verschiedene Domänen und ermöglicht somit die Koordinierung der hier beispielhaft gewählten Ausschreibungsbearbeitungen. Hierzu ist es notwendig, Teilmodelle, d. h. Sichten des Produktmodells zu erzeugen. Entsprechend wurden anpassbare Sichten auf der Grundlage von ITMP entwickelt. Die Bedeutung der in diesem Zusammenhang identifizierten Informationsprozessressourcen in Bezug auf die IFC-Objekte wurde durch die Einführung zentraler Informationselemente, sog. IFC Concepts, untersucht. Diese stellen eine Abbildungsstruktur zwischen den Prozessressourcen und IFC-Klassen zur Verfügung. Auf dieser Grundlage konnte die Integration von Prozess- und Produktmodellen erreicht werden. Um die IFC-Sichten zu realisieren, wurden auf der Grundlage des IFC-Sichtendefinitionsformats IFC-Konzepte und IFC-Instanzendiagramme entwickelt. Die Gruppierung in IFC-Konzepten ermöglichte die Implementierung von anpassbaren IFC-Sichten, die für die standardisierte Systemintegration erforderlich sind. Diese wird mit Hilfe einer formellen Spezifikation unter Verwendung der verallgemeinerten Subset-Definitionsschema-Methode (GMSD) erreicht. Die Validierung erfolgte auf der Grundlage eines alphanumerischen Vergleichs, in dem ein ausgewähltes 3D-Produktmodell und die daraus entwickelte IFC-Sicht für das Produktkatalogmodell verglichen wurden. Es ergaben sich zwei Schlussfolgerungen. Im ersten Fall, der auch das Einheitspreisbeschaffungssystem betrifft, konnten die gewünschten Ergebnisse direkt durch Filterung der erforderlichen Daten erhalten werden. Beim Vergleich der Ergebnisse sowohl für Pauschal-, als auch für Entwurfs- und Baubeschaffungssysteme (Verträge) wurde jedoch festgestellt, dass für das IFC-Modell ein Erweiterungsbedarf besteht. Eine Lösung wurde über die Formalisierung der Kostendaten und Materialanalyseinformationen durch Erweiterung des IFC-Konzepts IfcBauRessource mit neuen Klassen und mit neuen Beziehungen erreicht. Somit erhält man ein allgemeines Informationsmodell auf der Grundlage des Datenschemas des IFC-Standards

Expanding Eco-Visualization: Sculpting Corn Production

This dissertation expands upon the definition of eco-visualization artwork. EV was originally defined in 2006 by Tiffany Holmes as a way to display the real time consumption statistics of key environmental resources for the goal of promoting ecological literacy. I assert that the final forms of EV artworks are not necessarily dependent on technology, and can differ in terms of media used, in that they can be sculptural, video-based, or static two-dimensional forms that communicate interpreted environmental information. There are two main categories of EV: one that is predominantly screen-based and another that employs a variety of modes of representation to visualize environmental information. EVs are political acts, situated in a charged climate of rising awareness, operating within the context of environmentalism and sustainability. I discuss a variety of EV works within the frame of ecopsychology, including EcoArtTech’s Eclipse and Keith Deverell’s Building Run; Andrea Polli’s Cloud Car and Particle Falls; Nathalie Miebach’s series, The Sandy Rides; and Natalie Jeremijenko’s Mussel Choir. The range of EV works provided models for my creative project, Sculpting Corn Production, and a foundation from which I developed a creative methodology. Working to defeat my experience of solastalgia, Sculpting Corn Production is a series of discrete paper sculptures focusing on American industrial corn farming. This EV also functions as a way for me to understand our devastated monoculture landscapes and the politics, economics, and related areas of ecology of our food production