EXPRESS: Resource-oriented and RESTful Semantic Web services

This thesis investigates an approach that simplifies the development of Semantic Web services (SWS) by removing the need for additional semantic descriptions.The most actively researched approaches to Semantic Web services introduce explicit semantic descriptions of services that are in addition to the existing semantic descriptions of the service domains. This increases their complexity and design overhead. The need for semantically describing the services in such approaches stems from their foundations in service-oriented computing, i.e. the extension of already existing service descriptions. This thesis demonstrates that adopting a resource-oriented approach based on REST will, in contrast to service-oriented approaches, eliminate the need for explicit semantic service descriptions and service vocabularies. This reduces the development efforts while retaining the significant functional capabilities.The approach proposed in this thesis, called EXPRESS (Expressing RESTful Semantic Services), utilises the similarities between REST and the Semantic Web, such as resource realisation, self-describing representations, and uniform interfaces. The semantics of a service is elicited from a resource’s semantic description in the domain ontology and the semantics of the uniform interface, hence eliminating the need for additional semantic descriptions. Moreover, stub-generation is a by-product of the mapping between entities in the domain ontology and resources.EXPRESS was developed to test the feasibility of eliminating explicit service descriptions and service vocabularies or ontologies, to explore the restrictions placed on domain ontologies as a result, to investigate the impact on the semantic quality of the description, and explore the benefits and costs to developers. To achieve this, an online demonstrator that allows users to generate stubs has been developed. In addition, a matchmaking experiment was conducted to show that the descriptions of the services are comparable to OWL-S in terms of their ability to be discovered, while improving the efficiency of discovery. Finally, an expert review was undertaken which provided evidence of EXPRESS’s simplicity and practicality when developing SWS from scratch

Feedback Systems: An Introduction for Scientists and Engineers

This book provides an introduction to the basic principles and tools for the design and analysis of feedback systems. It is intended to serve a diverse audience of scientists and engineers who are interested in understanding and utilizing feedback in physical, biological, information and social systems.We have attempted to keep the mathematical prerequisites to a minimum while being careful not to sacrifice rigor in the process. We have also attempted to make use of examples from a variety of disciplines, illustrating the generality of many of the tools while at the same time showing how they can be applied in specific application domains. A major goal of this book is to present a concise and insightful view of the current knowledge in feedback and control systems. The field of control started by teaching everything that was known at the time and, as new knowledge was acquired, additional courses were developed to cover new techniques. A consequence of this evolution is that introductory courses have remained the same for many years, and it is often necessary to take many individual courses in order to obtain a good perspective on the field. In developing this book, we have attempted to condense the current knowledge by emphasizing fundamental concepts. We believe that it is important to understand why feedback is useful, to know the language and basic mathematics of control and to grasp the key paradigms that have been developed over the past half century. It is also important to be able to solve simple feedback problems using back-of-the-envelope techniques, to recognize fundamental limitations and difficult control problems and to have a feel for available design methods. This book was originally developed for use in an experimental course at Caltech involving students from a wide set of backgrounds. The course was offered to undergraduates at the junior and senior levels in traditional engineering disciplines, as well as first- and second-year graduate students in engineering and science. This latter group included graduate students in biology, computer science and physics. Over the course of several years, the text has been classroom tested at Caltech and at Lund University, and the feedback from many students and colleagues has been incorporated to help improve the readability and accessibility of the material. Because of its intended audience, this book is organized in a slightly unusual fashion compared to many other books on feedback and control. In particular, we introduce a number of concepts in the text that are normally reserved for second-year courses on control and hence often not available to students who are not control systems majors. This has been done at the expense of certain traditional topics, which we felt that the astute student could learn independently and are often explored through the exercises. Examples of topics that we have included are nonlinear dynamics, Lyapunov stability analysis, the matrix exponential, reachability and observability, and fundamental limits of performance and robustness. Topics that we have deemphasized include root locus techniques, lead/lag compensation and detailed rules for generating Bode and Nyquist plots by hand. Several features of the book are designed to facilitate its dual function as a basic engineering text and as an introduction for researchers in natural, information and social sciences. The bulk of the material is intended to be used regardless of the audience and covers the core principles and tools in the analysis and design of feedback systems. Advanced sections, marked by the “dangerous bend” symbol shown here, contain material that requires a slightly more technical background, of the sort that would be expected of senior undergraduates in engineering. A few sections are marked by two dangerous bend symbols and are intended for readers with more specialized backgrounds, identified at the beginning of the section. To limit the length of the text, several standard results and extensions are given in the exercises, with appropriate hints toward their solutions. To further augment the printed material contained here, a companion web site has been developed and is available from the publisher’s web page: http://press.princeton.edu/titles/8701.html The web site contains a database of frequently asked questions, supplemental examples and exercises, and lecture material for courses based on this text. The material is organized by chapter and includes a summary of the major points in the text as well as links to external resources. The web site also contains the source code for many examples in the book, as well as utilities to implement the techniques described in the text. Most of the code was originally written using MATLAB M-files but was also tested with LabView MathScript to ensure compatibility with both packages. Many files can also be run using other scripting languages such as Octave, SciLab, SysQuake and Xmath. The first half of the book focuses almost exclusively on state space control systems. We begin in Chapter 2 with a description of modeling of physical, biological and information systems using ordinary differential equations and difference equations. Chapter 3 presents a number of examples in some detail, primarily as a reference for problems that will be used throughout the text. Following this, Chapter 4 looks at the dynamic behavior of models, including definitions of stability and more complicated nonlinear behavior. We provide advanced sections in this chapter on Lyapunov stability analysis because we find that it is useful in a broad array of applications and is frequently a topic that is not introduced until later in one’s studies. The remaining three chapters of the first half of the book focus on linear systems, beginning with a description of input/output behavior in Chapter 5. In Chapter 6, we formally introduce feedback systems by demonstrating how state space control laws can be designed. This is followed in Chapter 7 by material on output feedback and estimators. Chapters 6 and 7 introduce the key concepts of reachability and observability, which give tremendous insight into the choice of actuators and sensors, whether for engineered or natural systems. The second half of the book presents material that is often considered to be from the field of “classical control.” This includes the transfer function, introduced in Chapter 8, which is a fundamental tool for understanding feedback systems. Using transfer functions, one can begin to analyze the stability of feedback systems using frequency domain analysis, including the ability to reason about the closed loop behavior of a system from its open loop characteristics. This is the subject of Chapter 9, which revolves around the Nyquist stability criterion. In Chapters 10 and 11, we again look at the design problem, focusing first on proportional-integral-derivative (PID) controllers and then on the more general process of loop shaping. PID control is by far the most common design technique in control systems and a useful tool for any student. The chapter on frequency domain design introduces many of the ideas of modern control theory, including the sensitivity function. In Chapter 12, we combine the results from the second half of the book to analyze some of the fundamental trade-offs between robustness and performance. This is also a key chapter illustrating the power of the techniques that have been developed and serving as an introduction for more advanced studies. The book is designed for use in a 10- to 15-week course in feedback systems that provides many of the key concepts needed in a variety of disciplines. For a 10-week course, Chapters 1–2, 4–6 and 8–11 can each be covered in a week’s time, with the omission of some topics from the final chapters. A more leisurely course, spread out over 14–15 weeks, could cover the entire book, with 2 weeks on modeling (Chapters 2 and 3) — particularly for students without much background in ordinary differential equations — and 2 weeks on robust performance (Chapter 12). The mathematical prerequisites for the book are modest and in keeping with our goal of providing an introduction that serves a broad audience. We assume familiarity with the basic tools of linear algebra, including matrices, vectors and eigenvalues. These are typically covered in a sophomore-level course on the subject, and the textbooks by Apostol [10], Arnold [13] and Strang [187] can serve as good references. Similarly, we assume basic knowledge of differential equations, including the concepts of homogeneous and particular solutions for linear ordinary differential equations in one variable. Apostol [10] and Boyce and DiPrima [42] cover this material well. Finally, we also make use of complex numbers and functions and, in some of the advanced sections, more detailed concepts in complex variables that are typically covered in a junior-level engineering or physics course in mathematical methods. Apostol [9] or Stewart [186] can be used for the basic material, with Ahlfors [6], Marsden and Hoffman [146] or Saff and Snider [172] being good references for the more advanced material. We have chosen not to include appendices summarizing these various topics since there are a number of good books available. One additional choice that we felt was important was the decision not to rely on a knowledge of Laplace transforms in the book. While their use is by far the most common approach to teaching feedback systems in engineering, many students in the natural and information sciences may lack the necessary mathematical background. Since Laplace transforms are not required in any essential way, we have included them only in an advanced section intended to tie things together for students with that background. Of course, we make tremendous use of transfer functions, which we introduce through the notion of response to exponential inputs, an approach we feel is more accessible to a broad array of scientists and engineers. For classes in which students have already had Laplace transforms, it should be quite natural to build on this background in the appropriate sections of the text. Acknowledgments: The authors would like to thank the many people who helped during the preparation of this book. The idea for writing this book came in part from a report on future directions in control [155] to which Stephen Boyd, Roger Brockett, John Doyle and Gunter Stein were major contributors. Kristi Morgansen and Hideo Mabuchi helped teach early versions of the course at Caltech on which much of the text is based, and Steve Waydo served as the head TA for the course taught at Caltech in 2003–2004 and provided numerous comments and corrections. Charlotta Johnsson and Anton Cervin taught from early versions of the manuscript in Lund in 2003–2007 and gave very useful feedback. Other colleagues and students who provided feedback and advice include Leif Andersson, John Carson, K. Mani Chandy, Michel Charpentier, Domitilla Del Vecchio, Kate Galloway, Per Hagander, Toivo Henningsson Perby, Joseph Hellerstein, George Hines, Tore Hägglund, Cole Lepine, Anders Rantzer, Anders Robertsson, Dawn Tilbury and Francisco Zabala. The reviewers for Princeton University Press and Tom Robbins at NI Press also provided valuable comments that significantly improved the organization, layout and focus of the book. Our editor, Vickie Kearn, was a great source of encouragement and help throughout the publishing process. Finally, we would like to thank Caltech, Lund University and the University of California at Santa Barbara for providing many resources, stimulating colleagues and students, and pleasant working environments that greatly aided in the writing of this book

Development and application of software and algorithms for network approaches to proteomics data analysis

The cells making up all living organisms integrate external and internal signals to carry out the functions of life. Dysregulation of signaling can lead to a variety of grave diseases, including cancer [Slamon et al., 1987]. In order to understand signal transduction, one has to identify and characterize the main constituents of cellular signaling cascades. Proteins are involved in most cellular processes and form the major class of biomolecules responsible for signal transduction. Post-translational modifications (PTMs) of proteins can modulate their enzymatic activity and their protein-protein interactions (PPIs) which in turn can ultimately lead to changes in protein expression. Classical biochemistry has approached the study of proteins, PTMs and interaction from a reductionist view. The abundance, stability and localization of proteins was studied one protein at a time, following the one gene-one protein-one function paradigm [Beadle and Tatum, 1941]. Pathways were considered to be linear, where signals would be transmitted from a gene to proteins, eventually resulting in a specific phenotype. Establishing the crucial link between genotype and phenotype remains challenging despite great advances in omics technologies, such as liquid chromatography (LC)-mass spectrometry (MS) that allow for the system-wide interrogation of proteins. Systems and network biology [Barabási and Oltvai, 2004, Bensimon et al., 2012, Jørgensen and Locard-Paulet, 2012, Choudhary and Mann, 2010] aims to transform modern biology by utilizing omics technologies to understand and uncover the various complex networks that govern the cell. The first detected large-scale biological networks have been found to be highly structured and non-random [Albert and Barabási, 2002]. Furthermore, these are assembled from functional and topological modules. The smallest topological modules are formed by the direct physical interactions within protein-protein and protein-RNA complexes. These molecular machines are able to perform a diverse array of cellular functions, such as transcription and degradation [Alberts, 1998]. Members of functional modules are not required to have a direct physical interaction. Instead, such modules also include proteins with temporal co-regulation throughout the cell cycle [Olsen et al., 2010], or following the circadian day-night rhythm [Robles et al., 2014]. The signaling pathways that make up the cellular network [Jordan et al., 2000] are assembled from a hierarchy of these smaller modules [Barabási and Oltvai, 2004]. The regulation of these modules through dynamic rewiring enables the cell to respond to internal an external stimuli. The main challenge in network biology is to develop techniques to probe the topology of various biological networks, to identify topological and functional modules, and to understand their assembly and dynamic rewiring. LC-MS has become a powerful experimental platform that addresses all these challenges directly [Bensimon et al., 2012], and has long been used to study a wide range of biomolecules that participate in the cellular network. The field of proteomics in particular, which is concerned with the identification and characterization of the proteins in the cell, has been revolutionized by recent technological advances in MS. Proteomics experiments are used not only to quantify peptides and proteins, but also to uncover the edges of the cellular network, by screening for physical PPIs in a global [Hein et al., 2015] or condition specific manner [Kloet et al., 2016]. Crucial for the interpretation of the large-scale data generated by MS experiments is the development of software tools that aid researchers in translating raw measurements into biological insights. The MaxQuant and Perseus platforms were designed for this exact purpose. The aim of this thesis was to develop software tools for the analysis of MS-based proteomics data with a focus on network biology and apply the developed tools to study cellular signaling. The first step was the extension of the Perseus software with network data structures and activities. The new network module allows for the sideby-side analysis of matrices and networks inside an interactive workflow and is described in article 1. We subsequently apply the newly developed software to study the circadian phosphoproteome of cortical synapses (see article 2). In parallel we aimed to improve the analysis of large datasets by adapting the previously Windows-only MaxQuant software to the Linux operating system, which is more prevalent in high performance computing environments (see article 3)

Construction of a support tool for the design of the activity structures based computer system architectures

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel University.This thesis is a reapproachment of diverse design concepts, brought to bear upon the computer system engineering problem of identification and control of highly constrained multiprocessing (HCM) computer machines. It contributes to the area of meta/general systems methodology, and brings a new insight into the design formalisms, and results afforded by bringing together various design concepts that can be used for the construction of highly constrained computer system architectures. A unique point of view is taken by assuming the process of identification and control of HCM computer systems to be the process generated by the Activity Structures Methodology (ASM). The research in ASM has emerged from the Neuroscience research, aiming at providing the techniques for combining the diverse knowledge sources that capture the 'deep knowledge' of this application field in an effective formal and computer representable form. To apply the ASM design guidelines in the realm of the distributed computer system design, we provide new design definitions for the identification and control of such machines in terms of realisations. These realisation definitions characterise the various classes of the identification and control problem. The classes covered consist of: 1. the identification of the designer activities, 2. the identification and control of the machine's distributed structures of behaviour, 3. the identification and control of the conversational environment activities (i.e. the randomised/ adaptive activities and interactions of both the user and the machine environments), 4. the identification and control of the substrata needed for the realisation of the machine, and 5. the identification of the admissible design data, both user-oriented and machineoriented, that can force the conversational environment to act in a self-regulating manner. All extent results are considered in this context, allowing the development of both necessary conditions for machine identification in terms of their distributed behaviours as well as the substrata structures of the unknown machine and sufficient conditions in terms of experiments on the unknown machine to achieve the self-regulation behaviour. We provide a detailed description of the design and implementation of the support software tool which can be used for aiding the process of constructing effective, HCM computer systems, based on various classes of identification and control. The design data of a highly constrained system, the NUKE, are used to verify the tool logic as well as the various identification and control procedures. Possible extensions as well as future work implied by the results are considered.Government of Ira

Where is cognition? Towards an embodied, situated, and distributed interactionist theory of cognitive activity

In recent years researchers from a variety of cognitive science disciplines have begun to challenge some of the core assumptions of the dominant theoretical framework of cognitivism including the representation-computational view of cognition, the sense-model-plan-act understanding of cognitive architecture, and the use of a formal task description strategy for investigating the organisation of internal mental processes. Challenges to these assumptions are illustrated using empirical findings and theoretical arguments from the fields such as situated robotics, dynamical systems approaches to cognition, situated action and distributed cognition research, and sociohistorical studies of cognitive development. Several shared themes are extracted from the findings in these research programmes including: a focus on agent-environment systems as the primary unit of analysis; an attention to agent-environment interaction dynamics; a vision of the cognizer's internal mechanisms as essentially reactive and decentralised in nature; and a tendency for mutual definitions of agent, environment, and activity. It is argued that, taken together, these themes signal the emergence of a new approach to cognition called embodied, situated, and distributed interactionism. This interactionist alternative has many resonances with the dynamical systems approach to cognition. However, this approach does not provide a theory of the implementing substrate sufficient for an interactionist theoretical framework. It is suggested that such a theory can be found in a view of animals as autonomous systems coupled with a portrayal of the nervous system as a regulatory, coordinative, and integrative bodily subsystem. Although a number of recent simulations show connectionism's promise as a computational technique in simulating the role of the nervous system from an interactionist perspective, this embodied connectionist framework does not lend itself to understanding the advanced 'representation hungry' cognition we witness in much human behaviour. It is argued that this problem can be solved by understanding advanced cognition as the re-use of basic perception-action skills and structures that this feat is enabled by a general education within a social symbol-using environment

Large space structures and systems in the space station era: A bibliography with indexes (supplement 03)

Bibliographies and abstracts are listed for 1221 reports, articles, and other documents introduced into the NASA scientific and technical information system between January 1, 1991 and June 30, 1991. Topics covered include large space structures and systems, space stations, extravehicular activity, thermal environments and control, tethering, spacecraft power supplies, structural concepts and control systems, electronics, advanced materials, propulsion, policies and international cooperation, vibration and dynamic controls, robotics and remote operations, data and communication systems, electric power generation, space commercialization, orbital transfer, and human factors engineering

Generic semantics-based task-oriented dialogue system framework for human-machine interaction in industrial scenarios

285 p.En Industria 5.0, los trabajadores y su bienestar son cruciales en el proceso de producción. En estecontexto, los sistemas de diálogo orientados a tareas permiten que los operarios deleguen las tareas mássencillas a los sistemas industriales mientras trabajan en otras más complejas. Además, la posibilidad deinteractuar de forma natural con estos sistemas reduce la carga cognitiva para usarlos y genera aceptaciónpor parte de los usuarios. Sin embargo, la mayoría de las soluciones existentes no permiten unacomunicación natural, y las técnicas actuales para obtener dichos sistemas necesitan grandes cantidadesde datos para ser entrenados, que son escasos en este tipo de escenarios. Esto provoca que los sistemas dediálogo orientados a tareas en el ámbito industrial sean muy específicos, lo que limita su capacidad de sermodificados o reutilizados en otros escenarios, tareas que están ligadas a un gran esfuerzo en términos detiempo y costes. Dados estos retos, en esta tesis se combinan Tecnologías de la Web Semántica contécnicas de Procesamiento del Lenguaje Natural para desarrollar KIDE4I, un sistema de diálogo orientadoa tareas semántico para entornos industriales que permite una comunicación natural entre humanos ysistemas industriales. Los módulos de KIDE4I están diseñados para ser genéricos para una sencillaadaptación a nuevos casos de uso. La ontología modular TODO es el núcleo de KIDE4I, y se encarga demodelar el dominio y el proceso de diálogo, además de almacenar las trazas generadas. KIDE4I se haimplementado y adaptado para su uso en cuatro casos de uso industriales, demostrando que el proceso deadaptación para ello no es complejo y se beneficia del uso de recursos

Large space structures and systems in the space station era: A bibliography with indexes (supplement 05)

Bibliographies and abstracts are listed for 1363 reports, articles, and other documents introduced into the NASA scientific and technical information system between January 1, 1991 and July 31, 1992. Topics covered include technology development and mission design according to system, interactive analysis and design, structural and thermal analysis and design, structural concepts and control systems, electronics, advanced materials, assembly concepts, propulsion and solar power satellite systems