Efficient, Dependable Storage of Human Genome Sequencing Data

A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são críticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivíduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessíveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensíveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de $1/Genoma/Ano), integrando os mecanismos propostos a configurações de armazenamento apropriadasThe understanding of human genome impacts several areas of human life. Data from human genomes is massive because there are millions of samples to be sequenced, and each sequenced human genome may size hundreds of gigabytes. Human genomes are critical because they are extremely valuable to research and may provide hints on individuals’ health status, identify their donors, or reveal information about donors’ relatives. Their size and criticality, plus the amount of data being produced by medical and life-sciences institutions, require systems to scale while being secure, dependable, auditable, and affordable. Current storage infrastructures are too expensive to ignore cost efficiency in storing human genomes, and they lack the proper knowledge and mechanisms to protect the privacy of sample donors. This thesis proposes an efficient storage system for human genomes that medical and lifesciences institutions may trust and afford. It enhances traditional storage ecosystems with privacy-aware, data-reduction, and auditability techniques to enable the efficient, dependable use of multi-tenant infrastructures to store human genomes. Contributions from this thesis include (1) a study on the privacy-sensitivity of human genomes; (2) to detect genomes’ privacy-sensitive portions systematically; (3) specialised data reduction algorithms for sequencing data; (4) an independent auditability scheme for secure dispersed storage; and (5) a complete storage pipeline that obtains reasonable privacy protection, security, and dependability guarantees at modest costs (e.g., less than$1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations

Assuring virtual network reliability and resilience

A framework developed that uses reliability block diagrams and continuous-time Markov chains to model and analyse the reliability and availability of a Virtual Network Environment (VNE). In addition, to minimize the unpredicted failures and reduce the impact of failure on a virtual network, a dynamic solution proposed for detecting a failure before it occurs in the VNE. Moreover, to predict failure and establish a tolerable maintenance plan before failure occurs in the VNE, a failure prediction method for VNE can be used to minimise the unpredicted failures, reduce backup redundancy and maximise system performance

Partitioning workflow applications over federated clouds to meet non-functional requirements

PhD ThesisWith cloud computing, users can acquire computer resources when they need them on a pay-as-you-go business model. Because of this, many applications are now being deployed in the cloud, and there are many di erent cloud providers worldwide. Importantly, all these various infrastructure providers o er services with di erent levels of quality. For example, cloud data centres are governed by the privacy and security policies of the country where the centre is located, while many organisations have created their own internal \private cloud" to meet security needs. With all this varieties and uncertainties, application developers who decide to host their system in the cloud face the issue of which cloud to choose to get the best operational conditions in terms of price, reliability and security. And the decision becomes even more complicated if their application consists of a number of distributed components, each with slightly di erent requirements. Rather than trying to identify the single best cloud for an application, this thesis considers an alternative approach, that is, combining di erent clouds to meet users' non-functional requirements. Cloud federation o ers the ability to distribute a single application across two or more clouds, so that the application can bene t from the advantages of each one of them. The key challenge for this approach is how to nd the distribution (or deployment) of application components, which can yield the greatest bene ts. In this thesis, we tackle this problem and propose a set of algorithms, and a framework, to partition a work ow-based application over federated clouds in order to exploit the strengths of each cloud. The speci c goal is to split a distributed application structured as a work ow such that the security and reliability requirements of each component are met, whilst the overall cost of execution is minimised. To achieve this, we propose and evaluate a cloud broker for partitioning a work ow application over federated clouds. The broker integrates with the e-Science Central cloud platform to automatically deploy a work ow over public and private clouds. We developed a deployment planning algorithm to partition a large work ow appli- - i - cation across federated clouds so as to meet security requirements and minimise the monetary cost. A more generic framework is then proposed to model, quantify and guide the partitioning and deployment of work ows over federated clouds. This framework considers the situation where changes in cloud availability (including cloud failure) arise during work ow execution

New Waves of IoT Technologies Research – Transcending Intelligence and Senses at the Edge to Create Multi Experience Environments

The next wave of Internet of Things (IoT) and Industrial Internet of Things (IIoT) brings new technological developments that incorporate radical advances in Artificial Intelligence (AI), edge computing processing, new sensing capabilities, more security protection and autonomous functions accelerating progress towards the ability for IoT systems to self-develop, self-maintain and self-optimise. The emergence of hyper autonomous IoT applications with enhanced sensing, distributed intelligence, edge processing and connectivity, combined with human augmentation, has the potential to power the transformation and optimisation of industrial sectors and to change the innovation landscape. This chapter is reviewing the most recent advances in the next wave of the IoT by looking not only at the technology enabling the IoT but also at the platforms and smart data aspects that will bring intelligence, sustainability, dependability, autonomy, and will support human-centric solutions.acceptedVersio

An overview of VANET vehicular networks

Today, with the development of intercity and metropolitan roadways and with various cars moving in various directions, there is a greater need than ever for a network to coordinate commutes. Nowadays, people spend a lot of time in their vehicles. Smart automobiles have developed to make that time safer, more effective, more fun, pollution-free, and affordable. However, maintaining the optimum use of resources and addressing rising needs continues to be a challenge given the popularity of vehicle users and the growing diversity of requests for various services. As a result, VANET will require modernized working practices in the future. Modern intelligent transportation management and driver assistance systems are created using cutting-edge communication technology. Vehicular Ad-hoc networks promise to increase transportation effectiveness, accident prevention, and pedestrian comfort by allowing automobiles and road infrastructure to communicate entertainment and traffic information. By constructing thorough frameworks, workflow patterns, and update procedures, including block-chain, artificial intelligence, and SDN (Software Defined Networking), this paper addresses VANET-related technologies, future advances, and related challenges. An overview of the VANET upgrade solution is given in this document in order to handle potential future problems

A pattern-based framework for the design of secure and dependable SDN/NFV-enabled networks

As the world becomes an interconnected network where objects and humans interact, cyber and physical networks appear to play an important role in smart ecosystems due to their increasing use on critical infrastructure and smart cities. Software Defined Networking (SDN) and Network Function Virtualisation (NFV) are a promising combination for programmable connectivity, rapid service provisioning and service chaining as they offer the necessary end-to-end optimisations. However, with the actual exponential growth of connected devices, future networks, such as SDN and NFV, require open architectures, facilitated by standards and a strong ecosystem.In this thesis, a model-based approach is proposed to support the design and verification of secure and dependable SDN/NFV-enabled networks. The model is based on the development of a pattern-based approach to design executable patterns as solutions for reusable designs and interactions of objects, encoded in a rule based reasoning system, able to guarantee security and dependability (S&D) properties in SDN/NFV enabled networks. To execute S&D patterns, a pattern based framework is implemented for the insertion of patterns at design and at runtime level. The developed pattern framework highlights also the benefit of leveraging the flexibility of SDN/NFV-enabled networks to deploy enhanced reactive security mechanisms for the protection of the industrial network via the use of service function chaining (SFC). To prove the importance of this approach and the functionality of the pattern framework, different pattern instances are implemented to guarantee S&D in network infrastructures. The developed design patterns are able to design network topologies, guarantee network properties and offer security service provisioning and chaining. Finally, in order to evaluate the developed patterns in the pattern framework, three different use cases are described, where a number of usage scenarios are deployed and evaluated experimentally

Service Quality and Profit Control in Utility Computing Service Life Cycles

Utility Computing is one of the most discussed business models in the context of Cloud Computing. Service providers are more and more pushed into the role of utilities by their customer's expectations. Subsequently, the demand for predictable service availability and pay-per-use pricing models increases. Furthermore, for providers, a new opportunity to optimise resource usage offers arises, resulting from new virtualisation techniques. In this context, the control of service quality and profit depends on a deep understanding of the representation of the relationship between business and technique. This research analyses the relationship between the business model of Utility Computing and Service-oriented Computing architectures hosted in Cloud environments. The relations are clarified in detail for the entire service life cycle and throughout all architectural layers. Based on the elaborated relations, an approach to a delivery framework is evolved, in order to enable the optimisation of the relation attributes, while the service implementation passes through business planning, development, and operations. Related work from academic literature does not cover the collected requirements on service offers in this context. This finding is revealed by a critical review of approaches in the fields of Cloud Computing, Grid Computing, and Application Clusters. The related work is analysed regarding appropriate provision architectures and quality assurance approaches. The main concepts of the delivery framework are evaluated based on a simulation model. To demonstrate the ability of the framework to model complex pay-per-use service cascades in Cloud environments, several experiments have been conducted. First outcomes proof that the contributions of this research undoubtedly enable the optimisation of service quality and profit in Cloud-based Service-oriented Computing architectures

Improving shared access to Cloud of Things resources.

Cloud of Things (CoT) is an emerging paradigm that integrates Cloud Computing and Internet of Things (IoT) to support a wide range of real-world applications. Resource allocation plays a vital role in CoT, especially when allocating IoT physical resources to Cloud-based applications to ensure seamless application execution. Due to the heterogeneity and the constrained capacities of IoT resources, resource allocation is a challenge. This complexity leads to missing/limiting shared access to the IoT physical resources and consequently lessen the reusability of the resources across multiple applications. This issue results in, 1) replicating IoT deployments making them expensive and not feasible for many prospective users, 2) existing IoT infrastructures are over-provisioned to meet the unpredictable application requirements in which resources may be significantly underutilised, and 3) the adoption of CoT is slowed. Improving shared access to CoT resources can provide efficient resource allocation, improve resource utilisation and likely to reduce the cost of IoT deployments. Existing solutions include small-scale, hardware and platform-dependent mechanisms to enable or improve shared access to IoT resources. The research presented in this thesis considers trading CoT resources in a marketplace as an approach to improve shared access to CoT resources. It proposes a solution to Cot resource allocation that re-imagines CoT resources as commodities that can be provided and consumed by the marketplace participants. The novel contributions of the research presented in this thesis are summarised as follows: 1) a model to describe and quantify the value of CoT resources, 2) a resource sharing and allocation strategy called Exclusive Shared Access (ESA) to CoT resources, 3) a QoS-aware optimisation model for trading CoT resources as a single and multipleobjective optimisation problem, and 4) a marketplace architecture and experimental evaluation to verify its performance and scalability