A predição de estruturas de proteínas é um campo de pesquisa que busca simular o enovelamento de cadeias de aminoácidos de forma a descobrir as funções das proteínas na natureza, um processo altamente dispendioso por meio de métodos in vivo. Inserida no contexto da Bioinformática, é uma das tarefas mais computacionalmente custosas e desafiadoras da atualidade. Devido à complexidade, muitas pesquisas se utilizam de gateways científicos para disponibilização de ferramentas de execução e análise desses experimentos, aliado ao uso de workflows científicos para organização de tarefas e disponibilização de informações. No entanto, esses gateways podem enfrentar gargalos de desempenho e falhas estruturais, produzindo resultados de baixa qualidade. Para atuar nesse contexto multifacetado e oferecer alternativas para algumas das limitações, esta tese propõe uma arquitetura modular baseada nos conceitos de Service Oriented Architecture (SOA) para oferta de recursos computacionais em gateways científicos, com foco nos experimentos de Protein Structure Prediction (PSP). A Arquitetura Modular Distribuída para auxílio à Predição de Estruturas de Proteínas (MDAPSP) é descrita conceitualmente e validada em um modelo de simulação computacional, no qual se pode identificar suas capacidades, detalhar o funcionamento de seus módulos e destacar seu potencial. A avaliação experimental demonstra a qualidade dos algoritmos propostos, ampliando a capacidade de atendimento de um gateway científico, reduzindo o tempo necessário para experimentos de predição e lançando as bases para o protótipo de uma arquitetura funcional. Os módulos desenvolvidos alcançam boa capacidade de otimização de experimentos de PSP em ambientes distribuídos e constituem uma novidade no modelo de provisionamento de recursos para gateways científicos. / PSP is a scientific process that simulates the folding of amino acid chains to discover the function of a protein in live organisms, considering that its an expensive process to be done by in vivo methods. PSP is a computationally demanding and challenging effort in the Bioinformatics stateof- the-art. Many works use scientific gateways to provide tools for execution and analysis of such experiments, along with scientific workflows to organize tasks and to share information. However, these gateways can suffer performance bottlenecks and structural failures, producing low quality results. With the goal of offering alternatives to some of the limitations and considering the complexity of the topics involved, this thesis proposes a modular architecture based on SOA concepts to provide computing resources to scientific gateways, with focus on PSP experiments. The Modular Distributed Architecture to support Protein Structure Prediction (MDAPSP) is described conceptually and validated in a computer simulation model that explain its capabilities, detail the modules operation and highlight its potential. The performance evaluation presents the quality of the proposed algorithms, a reduction of response time in PSP experiments and prove the benefits of the novel algorithms, establishing the basis for a prototype. The new modules can optmize the PSP experiments in distributed environments and are a innovation in the resource provisioning model for scientific gateways.

A predição de estruturas de proteínas é um campo de pesquisa que busca simular o enovelamento de cadeias de aminoácidos de forma a descobrir as funções das proteínas na natureza, um processo altamente dispendioso por meio de métodos in vivo. Inserida no contexto da Bioinformática, é uma das tarefas mais computacionalmente custosas e desafiadoras da atualidade. Devido à complexidade, muitas pesquisas se utilizam de gateways científicos para disponibilização de ferramentas de execução e análise desses experimentos, aliado ao uso de workflows científicos para organização de tarefas e disponibilização de informações. No entanto, esses gateways podem enfrentar gargalos de desempenho e falhas estruturais, produzindo resultados de baixa qualidade. Para atuar nesse contexto multifacetado e oferecer alternativas para algumas das limitações, esta tese propõe uma arquitetura modular baseada nos conceitos de Service Oriented Architecture (SOA) para oferta de recursos computacionais em gateways científicos, com foco nos experimentos de Protein Structure Prediction (PSP). A Arquitetura Modular Distribuída para auxílio à Predição de Estruturas de Proteínas (MDAPSP) é descrita conceitualmente e validada em um modelo de simulação computacional, no qual se pode identificar suas capacidades, detalhar o funcionamento de seus módulos e destacar seu potencial. A avaliação experimental demonstra a qualidade dos algoritmos propostos, ampliando a capacidade de atendimento de um gateway científico, reduzindo o tempo necessário para experimentos de predição e lançando as bases para o protótipo de uma arquitetura funcional. Os módulos desenvolvidos alcançam boa capacidade de otimização de experimentos de PSP em ambientes distribuídos e constituem uma novidade no modelo de provisionamento de recursos para gateways científicos. / PSP is a scientific process that simulates the folding of amino acid chains to discover the function of a protein in live organisms, considering that its an expensive process to be done by in vivo methods. PSP is a computationally demanding and challenging effort in the Bioinformatics stateof- the-art. Many works use scientific gateways to provide tools for execution and analysis of such experiments, along with scientific workflows to organize tasks and to share information. However, these gateways can suffer performance bottlenecks and structural failures, producing low quality results. With the goal of offering alternatives to some of the limitations and considering the complexity of the topics involved, this thesis proposes a modular architecture based on SOA concepts to provide computing resources to scientific gateways, with focus on PSP experiments. The Modular Distributed Architecture to support Protein Structure Prediction (MDAPSP) is described conceptually and validated in a computer simulation model that explain its capabilities, detail the modules operation and highlight its potential. The performance evaluation presents the quality of the proposed algorithms, a reduction of response time in PSP experiments and prove the benefits of the novel algorithms, establishing the basis for a prototype. The new modules can optmize the PSP experiments in distributed environments and are a innovation in the resource provisioning model for scientific gateways.

ITC/USA 2015 Conference Proceedings / The Fifty-First Annual International Telemetering Conference and Technical Exhibition / October 26-29, 2015 / Bally's Hotel & Convention Center, Las Vegas, NV / Northrop Grumman Corporation's B-2 Flight Test Instrumentation team is revamping its entire Data Acquisition System (DAS) to be an Ethernet based network (EBN) system that will provide simplified wiring, higher speeds, greater capacity, and control over the data. The old system became obsolete in terms of capability and maintainability. New on-board avionic systems also demand that the Flight Test Instrumentation group (INSTR) accommodate fiber and high speed Ethernet data. In addition, the footprint and location for INSTR systems and components will be moved to remote areas. INSTR engineering selected the Teletronics Technology Corporation's Ethernet networked Data Acquisition Units (DAUs), known as MnDAUs, as the core system. Prior to the first flight utilization of the new INSTR DAS will undergo extensive lab and field testing to assure flight test effectiveness and the accuracy of all necessary data products. The goal is to acquire and employ the best system available while avoiding costly lessons.

Distributed Computing Infrastructures (DCIs) have emerged as a viable and affordable solution to the computing needs of communities of practice that may require the need to improve system performance or enhance the availability of their scientific applications. According to the literature, the ease of access and several other issues which relate to the interoperability among different resources are the biggest challenges surrounding the use of these infrastructures. The traditional method of using a Command Line Interface (CLI) to access these resources is difficult and can make the learning curve quite steep. This approach can result in the low uptake of DCIs as it prevents potential users of the infrastructures from adopting the technology. Science Gateways have emerged as a viable option that are used to realise the high-level scientific domain-specific user interfaces that hide all the details of the underlying infrastructures and expose only the science-specific aspects of the scientific applications to be executed in the various DCIs. A Science Gateway is a digital interface to advanced technologies which is used to provide adequate support for science and engineering research and education. The focus of this study therefore is to propose and implement a Methodology for dEveloping Scientific Software Applications in science GatEways (MESSAGE). This will be achieved by testing an approach which is considered to be appropriate for developing applications in Science Gateways. In the course of this study, several Science Gateway functionalities obtained from the review of literature which may be utilised to provide services for different communities of practice are highlighted. To implement the identified functionalities, this study utilises the methodology for developing scientific software applications in Science Gateways. In order to achieve this purpose, this research therefore adopts the Catania Science Gateway Framework (CSGF) and the Future Gateway approach to implement the methods and ideas described in the proposed methodology, as well the essential services of Science Gateways discussed throughout the thesis. In addition, three different set of scientific software applications are utilised for the implementation of the proposed methodology. While the first application primarily serves as the case study for implementing the methodology discussed in this thesis, a second application is used to evaluate the entire process. Furthermore, several other real-life scientific applications developed (using two distinctly different Science Gateway frameworks) are also utilised for the purpose of evaluation. Subsequently, a revised MESSAGE methodology for developing scientific software applications in Science Gateways is discussed in the latter Chapter of this thesis. Following from the implementation of both scientific software applications which sees the use of portlets to execute single experiments, a study was also conducted to investigate ways in which Science Gateways may be utilised for the execution of multiple experiments in a distributed environment. Finally, similar to making different scientific software applications accessible and available (worldwide) to the communities that need them, the processes involved in making their associated research outputs (such as data, software and results) easily accessible and readily available are also discussed. The main contribution of this thesis is the MESSAGE methodology for developing scientific software applications in Science Gateways. Other contributions which are also made in different aspects of this research include a framework of the essential services required in generic Science Gateways and an approach to developing and executing multiple experiments (via Science Gateway interfaces) within a distributed environment. To a lesser extent, this study also utilises the Open Access Document Repository (OADR) (and other related technologies) to demonstrate accessibility and availability of research outputs associated with specific scientific software applications, thereby introducing the concept (and thus laying the foundation) of an Open Science research.

Les systèmes de stockage actuels font face à une explosion des données à gérer. A l'échelle actuelle, il serait illusoire d'imaginer une unique entité centralisée capable de stocker et de restituer les données de tous ses utilisateurs. Bien que du point de vue de l'utilisateur, le système de stockage apparaît tel un unique interlocuteur, son architecture sous-jacente est nécessairement devenue distribuée. En d'autres termes, le stockage n'est plus assigné à un équipement centralisé, mais est maintenant distribué parmi de multiples entités de stockage indépendantes, connectées via un réseau. Par conséquent, la bande passante inhérente à ce réseau devient une ressource à prendre en compte dans le design d'un système de stockage distribué. En effet, la bande passante d'un système est intrinsèquement une ressource limitée, qui doit être convenablement gérée de manière à éviter toute congestion du système. Cette thèse se propose d'optimiser l'utilisation de la bande passante dans les systèmes de stockage distribués, en limitant l'impact du churn et des défaillances. L'objectif est double, le but est d'une part, de maximiser la bande passante disponible pour les échanges de données, et d'une autre part de réduire la consommation de bande passante inhérente aux opérations de maintenance. Pour ce faire, nous présentons trois contributions distinctes. La première contribution présente une architecture pair-à-pair hybride qui tient compte de la topologie bas-niveau du réseau, c'est à dire la présence de gateways entre les utilisateurs et le système. La seconde contribution propose un mécanisme de timeout adaptatif au niveau utilisateur, basé sur une approche Bayésienne. La troisième contribution décrit un protocole permettant la réparation efficace de données encodées via des codes à effacement. Enfin, cette thèse se conclut sur la possibilité d'utiliser des techniques d'alignement d'interférence, communément utilisées en communication numérique afin d’accroître l'efficacité des protocoles de réparation de données encodées. / Modern storage systems have to face the surge of the amount of data to handle. At the current scale, it would be an illusion to believe that a single centralized storage device is able to store and retrieve all its users' data. While from the user's viewpoint the storage system remains a single interlocutor, its underlying architecture has become necessarily distributed. In others words, storage is no longer assigned to a centralized storage equipment, but is now distributed between multiple independent storage devices, connected via a network. Therefore, when designing networked storage systems, bandwidth should now be taken into account as a critical resource. In fact, the bandwidth of a system is intrinsically a limited resource which should be handled with care to avoid congestion. The focus of this thesis is to optimize the available bandwidth of distributed storage systems, lowering the impact of churn and failures. The objective is twofold, on the one hand the purpose is to increase the available bandwidth for data exchanges and on the other hand, to decrease the amount of bandwidth consumed by maintenance. We present three distinct contributions in this manuscript. The first contribution of this thesis presents an hybrid peer-to-peer architecture taking into account the low level topology of the network i.e., the presence of gateways between the system and the users. The second contribution proposes an adaptive and user-level timeout mechanism, based on a Bayesian approach. The third contribution describes a repair protocol especially designed for erasure-coded stored data. Finally, this thesis concludes on the possibility of employing interference alignment techniques in order to increase the efficiency of repair protocols especially designed for encoded data.

No description available.

Les systèmes de stockage actuels font face à une explosion des données à gérer. A l'échelle actuelle, il serait illusoire d'imaginer une unique entité centralisée capable de stocker et de restituer les données de tous ses utilisateurs. Bien que du point de vue de l'utilisateur, le système de stockage apparaît tel un unique interlocuteur, son architecture sous-jacente est nécessairement devenue distribuée. En d'autres termes, le stockage n'est plus assigné à un équipement centralisé, mais est maintenant distribué parmi de multiples entités de stockage indépendantes, connectées via un réseau. Par conséquent, la bande passante inhérente à ce réseau devient une ressource à prendre en compte dans le design d'un système de stockage distribué. En effet, la bande passante d'un système est intrinsèquement une ressource limitée, qui doit être convenablement gérée de manière à éviter toute congestion du système. Cette thèse se propose d'optimiser l'utilisation de la bande passante dans les systèmes de stockage distribués, en limitant l'impact du churn et des défaillances. L'objectif est double, le but est d'une part, de maximiser la bande passante disponible pour les échanges de données, et d'une autre part de réduire la consommation de bande passante inhérente aux opérations de maintenance. Pour ce faire, nous présentons trois contributions distinctes. La première contribution présente une architecture pair-à-pair hybride qui tient compte de la topologie bas-niveau du réseau, c'est à dire la présence de gateways entre les utilisateurs et le système. La seconde contribution propose un mécanisme de timeout adaptatif au niveau utilisateur, basé sur une approche Bayésienne. La troisième contribution décrit un protocole permettant la réparation efficace de données encodées via des codes à effacement. Enfin, cette thèse se conclut sur la possibilité d'utiliser des techniques d'alignement d'interférence, communément utilisées en communication numérique afin d'accroître l'efficacité des protocoles de réparation de données encodées.

Modifications of footers in title page, page-2 and page-3.

An online payment system allows a customer to make a payment to an online merchant or a service provider. Payment gateways, a channel between customers and payment processors, use various security tools to secure a customer’s payment information, usually debit or credit card information, during an online payment. However, the security provided by a payment gateway cannot completely protect a customer’s payment information when a merchant also has the ability to obtain the payment information in some form. Furthermore, not all merchants provide a secure payment environment to their customers and, despite having a standard payment policy, adhere to it. Consequently, this exposes a customer’s payment information to risks of being compromised or misused by merchants or stolen by hackers and spammers. In this thesis we propose a new approach to payment systems in which a customer’s payment information cannot be obtained by a merchant. A customer sends his payment information directly to a payment gateway and a payment gateway, upon verifying the transaction, sends a payment to the appropriate merchant. We use the Pedersen commitment scheme along with dual signatures to securely transfer funds to a merchant and protect a customer’s payment information from any Internet vulnerabilities.

Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographical references (p. 44-48).