Investigation of spacecraft cluster autonomy through an acoustic imaging interferometric testbed

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1999.Includes bibliographical references (p. 169-173).The development and use of a novel testbed architecture is presented. Separated spacecraft interferometers have been proposed for applications in sparse aperture radar or astronomical observations. Modeled after these systems, an integrated hardware and software interferometry testbed is developed. Utilizing acoustic sources and sensors as a simplified analog to radio or optical systems, the Acoustic Imaging Testbed's simplest function is that of a Michelson interferometer. Robot arms control the motion of microphones. Through successive measurements an acoustic image can be formed. On top of this functionality, a layered software architecture is developed. This software creates a virtual environment that mimics the command, control and communications functions appropriate to a space interferometer. Autonomous spacecraft agents interact within this environment as the logical equivalent of distributed satellites. Optimal imaging configurations are validated. A scalable approach to cluster autonomy is discussed.by John Enright.S.M

Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

A flight software development and simulation framework for advanced space systems

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2002.Includes bibliographical references (p. 293-302).Distributed terrestrial computer systems employ middleware software to provide communications abstractions and reduce software interface complexity. Embedded applications are adopting the same approaches, but must make provisions to ensure that hard real-time temporal performance can be maintained. This thesis presents the development and validation of a middleware system tailored to spacecraft flight software development. Our middleware runs on the Generalized Flight Operations Processing Simulator (GFLOPS) and is called the GFLOPS Rapid Real-time Development Environment (GRRDE). GRRDE provides publish-subscribe communication services between software components. These services help to reduce the complexity of managing software interfaces. The hard real-time performance of these services has been verified with General Timed Automata modelling and extensive run-time testing. Several example applications illustrate the use of GRRDE to support advanced flight software development. Two technology-focused studies examine automatic code generation and autonomous fault protection within the GRRDE framework. A complex simulation of the TechSat 21 distributed spacebased radar mission highlights the utility of the approach for large-scale applications.by John Patrick Enright.Ph.D

Pattern operators for grid

The definition and programming of distributed applications has become a major research issue due to the increasing availability of (large scale) distributed platforms and the requirements posed by the economical globalization. However, such a task requires a huge effort due to the complexity of the distributed environments: large amount of users may communicate and share information across different authority domains; moreover, the “execution environment” or “computations” are dynamic since the number of users and the computational infrastructure change in time. Grid environments, in particular, promise to be an answer to deal with such complexity, by providing high performance execution support to large amount of users, and resource sharing across different organizations. Nevertheless, programming in Grid environments is still a difficult task. There is a lack of high level programming paradigms and support tools that may guide the application developer and allow reusability of state-of-the-art solutions. Specifically, the main goal of the work presented in this thesis is to contribute to the simplification of the development cycle of applications for Grid environments by bringing structure and flexibility to three stages of that cycle through a commonmodel. The stages are: the design phase, the execution phase, and the reconfiguration phase. The common model is based on the manipulation of patterns through pattern operators, and the division of both patterns and operators into two categories, namely structural and behavioural. Moreover, both structural and behavioural patterns are first class entities at each of the aforesaid stages. At the design phase, patterns can be manipulated like other first class entities such as components. This allows a more structured way to build applications by reusing and composing state-of-the-art patterns. At the execution phase, patterns are units of execution control: it is possible, for example, to start or stop and to resume the execution of a pattern as a single entity. At the reconfiguration phase, patterns can also be manipulated as single entities with the additional advantage that it is possible to perform a structural reconfiguration while keeping some of the behavioural constraints, and vice-versa. For example, it is possible to replace a behavioural pattern, which was applied to some structural pattern, with another behavioural pattern. In this thesis, besides the proposal of the methodology for distributed application development, as sketched above, a definition of a relevant set of pattern operators was made. The methodology and the expressivity of the pattern operators were assessed through the development of several representative distributed applications. To support this validation, a prototype was designed and implemented, encompassing some relevant patterns and a significant part of the patterns operators defined. This prototype was based in the Triana environment; Triana supports the development and deployment of distributed applications in the Grid through a dataflow-based programming model. Additionally, this thesis also presents the analysis of a mapping of some operators for execution control onto the Distributed Resource Management Application API (DRMAA). This assessment confirmed the suitability of the proposed model, as well as the generality and flexibility of the defined pattern operatorsDepartamento de Informática and Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa; Centro de Informática e Tecnologias da Informação of the FCT/UNL; Reitoria da Universidade Nova de Lisboa; Distributed Collaborative Computing Group, Cardiff University, United Kingdom; Fundação para a Ciência e Tecnologia; Instituto de Cooperação Científica e Tecnológica Internacional; French Embassy in Portugal; European Union Commission through the Agentcities.NET and Coordina projects; and the European Science Foundation, EURESCO

Pattern Operators for Grid Environments

The definition and programming of distributed applications has become a major research issue due to the increasing availability of (large scale) distributed platforms and the requirements posed by the economical globalization. However, such a task requires a huge effort due to the complexity of the distributed environments: large amount of users may communicate and share information across different authority domains; moreover, the “execution environment” or “computations” are dynamic since the number of users and the computational infrastructure change in time. Grid environments, in particular, promise to be an answer to deal with such complexity, by providing high performance execution support to large amount of users, and resource sharing across different organizations. Nevertheless, programming in Grid environments is still a difficult task. There is a lack of high level programming paradigms and support tools that may guide the application developer and allow reusability of state-of-the-art solutions. Specifically, the main goal of the work presented in this thesis is to contribute to the simplification of the development cycle of applications for Grid environments by bringing structure and flexibility to three stages of that cycle through a commonmodel. The stages are: the design phase, the execution phase, and the reconfiguration phase. The common model is based on the manipulation of patterns through pattern operators, and the division of both patterns and operators into two categories, namely structural and behavioural. Moreover, both structural and behavioural patterns are first class entities at each of the aforesaid stages. At the design phase, patterns can be manipulated like other first class entities such as components. This allows a more structured way to build applications by reusing and composing state-of-the-art patterns. At the execution phase, patterns are units of execution control: it is possible, for example, to start or stop and to resume the execution of a pattern as a single entity. At the reconfiguration phase, patterns can also be manipulated as single entities with the additional advantage that it is possible to perform a structural reconfiguration while keeping some of the behavioural constraints, and vice-versa. For example, it is possible to replace a behavioural pattern, which was applied to some structural pattern, with another behavioural pattern. In this thesis, besides the proposal of the methodology for distributed application development, as sketched above, a definition of a relevant set of pattern operators was made. The methodology and the expressivity of the pattern operators were assessed through the development of several representative distributed applications. To support this validation, a prototype was designed and implemented, encompassing some relevant patterns and a significant part of the patterns operators defined. This prototype was based in the Triana environment; Triana supports the development and deployment of distributed applications in the Grid through a dataflow-based programming model. Additionally, this thesis also presents the analysis of a mapping of some operators for execution control onto the Distributed Resource Management Application API (DRMAA). This assessment confirmed the suitability of the proposed model, as well as the generality and flexibility of the defined pattern operatorsDepartamento de Informática and Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa; Centro de Informática e Tecnologias da Informação of the FCT/UNL; Reitoria da Universidade Nova de Lisboa; Distributed Collaborative Computing Group, Cardiff University, United Kingdom; Fundação para a Ciência e Tecnologia; Instituto de Cooperação Científica e Tecnológica Internacional; French Embassy in Portugal; European Union Commission through the Agentcities.NET and Coordina projects; and the European Science Foundation, EURESCO

The SEMAINE API : a component integration framework for a naturally interacting and emotionally competent embodied conversational agent

The present thesis addresses the topic area of Embodied Conversational Agents (ECAs) with capabilities for natural interaction with a human user and emotional competence with respect to the perception and generation of emotional expressivity. The focus is on the technological underpinnings that facilitate the implementation of a real-time system with these capabilities, built from re-usable components. The thesis comprises three main contributions. First, it describes a new component integration framework, the SEMAINE API, which makes it easy to build emotion-oriented systems from components which interact with one another using standard and pre-standard XML representations. Second, it presents a prepare-and-trigger system architecture which substantially speeds up the time to animation for system utterances that can be pre-planned. Third, it reports on the W3C Emotion Markup Language, an upcoming web standard for representing emotions in technological systems. We assess critical aspects of system performance, showing that the framework provides a good basis for implementing real-time interactive ECA systems, and illustrate by means of three examples that the SEMAINE API makes it is easy to build new emotion-oriented systems from new and existing components.Die vorliegende Dissertation behandelt das Thema der virtuellen Agenten mit Fähigkeiten zur natürlichen Benutzer-Interaktion sowie emotionaler Kompetenz bzgl. der Wahrnehmung und Generierung emotionalen Ausdrucks. Der Schwerpunkt der Arbeit liegt auf den technologischen Grundlagen für die Implementierung eines echtzeitfähigen Systems mit diesen Fähigkeiten, das aus wiederverwendbaren Komponenten erstellt werden kann. Die Arbeit umfasst drei Kernaspekte. Zum Einen beschreibt sie ein neues Framework zur Komponenten-Integration, die SEMAINE API: Diese erleichtert die Erstellung von Emotions-orientierten Systemen aus Komponenten, die untereinander mittels Standard- oder Prä-Standard-Repräsentationen kommunizieren. Zweitens wird eine Systemarchitektur vorgestellt, welche Vorbereitung und Auslösung von Systemverhalten entkoppelt und so zu einer substanziellen Beschleunigung der Generierungszeit führt, wenn Systemäußerungen im Voraus geplant werden können. Drittens beschreibt die Arbeit die W3C Emotion Markup Language, einen werdenden Web-Standard zur Repräsentation von Emotionen in technologischen Systemen. Es werden kritische Aspekte der Systemperformanz untersucht, wodurch gezeigt wird, dass das Framework eine gute Basis für die Implementierung echtzeitfähiger interaktiver Agentensysteme darstellt. Anhand von drei Beispielen wird illustriert, dass mit der SEMAINE API leicht neue Emotions-orientierte Systeme aus neuen und existierenden Komponenten erstellt werden können

Technology 2003: The Fourth National Technology Transfer Conference and Exposition, volume 2

Proceedings from symposia of the Technology 2003 Conference and Exposition, Dec. 7-9, 1993, Anaheim, CA, are presented. Volume 2 features papers on artificial intelligence, CAD&E, computer hardware, computer software, information management, photonics, robotics, test and measurement, video and imaging, and virtual reality/simulation