The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

Enabling Context-Aware Web Services: A Middleware Approach for Ubiquitous Environments

In ubiquitous environments, mobile applications should sense and react to environmental changes to provide a better user experience. In order to deal with these concerns, Service-Oriented Architectures (SOA) provide a solution allowing applications to interact with the services available in their surroundings. In particular, context-aware Web Services can adapt their behavior considering the user context. However, the limited resources of mobile devices restrict the adaptation degree. Furthermore, the diverse nature of context information makes difficult its retrieval, processing and distribution. To tackle these challenges, we present the CAPPUCINO platform for executing context-aware Web Services in ubiquitous environments. In particular, in this chapter we focus on the middleware part that is built as an autonomic control loop that deals with dynamic adaptation. In this autonomic loop we use FraSCAti, an implementation of the Service Component Architecture (SCA) specification, as the execution kernel for Web Services. The context distribution is achieved with SPACES, a flexible solution based on REST (REpresentational State Transfer ) principles and benefiting from the COSMOS (COntext entitieS coMpositiOn and Sharing ) context manage- ment framework. The application of our platform is illustrated with a mobile commerce application scenario that combines context-aware Web Services and social networks

POLICY-BASED MIDDLEWARE FOR MOBILE CLOUD COMPUTING

Mobile devices are the dominant interface for interacting with online services as well as an efficient platform for cloud data consumption. Cloud computing allows the delivery of applications/functionalities as services over the internet and provides the software/hardware infrastructure to host these services in a scalable manner. In mobile cloud computing, the apps running on the mobile device use cloud hosted services to overcome resource constraints of the host device. This approach allows mobile devices to outsource the resource-consuming tasks. Furthermore, as the number of devices owned by a single user increases, there is the growing demand for cross-platform application deployment to ensure a consistent user experience. However, the mobile devices communicate through unstable wireless networks, to access the data and services hosted in the cloud. The major challenges that mobile clients face when accessing services hosted in the cloud, are network latency and synchronization of data. To address the above mentioned challenges, this research proposed an architecture which introduced a policy-based middleware that supports user to access cloud hosted digital assets and services via an application across multiple mobile devices in a seamless manner. The major contribution of this thesis is identifying different information, used to configure the behavior of the middleware towards reliable and consistent communication among mobile clients and the cloud hosted services. Finally, the advantages of the using policy-based middleware architecture are illustrated by experiments conducted on a proof-of-concept prototype

Improving Information Flow within the Production Management System with Web Services

The efficiency of the production planning and control process in construction depends significantly on the reliability and timely availability of resource information. The Last Planner system for production control mandates that a construction task should not be started unless all the seven resource prerequisites are in satisfactory condition. Failure to do so results in wasteful processes. However, this information is not readily available due to the lack of systems integration that prevails within the industry. Current implementations of the last planner system mostly rely on the team leaders‘ and foreman‘s ability to gather the required information for the weekly planning meetings and also for the look-ahead planning. However, much time is wasted chasing relevant information due to the above-mentioned problems. Also, the reliability of planning could be much improved if there is a system available, which aggregates resource information from various project stakeholders in one place. In such a situation, web services could provide an ideal platform for integration as they provide a flexible way to integrate disparate systems, with choreography based on identified business processes drawn from Last Planner and implemented using BPMN/BPEL. With the improvement in connectivity as a result of better availability of high speed Internet through mobile and fixed networks, there is a better opportunity for information integration through web services. A conceptual framework based on web services is put forward which aims to improve the information flow within the industry and provide the right information at the right time to enable better planning and control within the production system

Scientific Workflows for Metabolic Flux Analysis

Metabolic engineering is a highly interdisciplinary research domain that interfaces biology, mathematics, computer science, and engineering. Metabolic flux analysis with carbon tracer experiments (13 C-MFA) is a particularly challenging metabolic engineering application that consists of several tightly interwoven building blocks such as modeling, simulation, and experimental design. While several general-purpose workflow solutions have emerged in recent years to support the realization of complex scientific applications, the transferability of these approaches are only partially applicable to 13C-MFA workflows. While problems in other research fields (e.g., bioinformatics) are primarily centered around scientific data processing, 13C-MFA workflows have more in common with business workflows. For instance, many bioinformatics workflows are designed to identify, compare, and annotate genomic sequences by "pipelining" them through standard tools like BLAST. Typically, the next workflow task in the pipeline can be automatically determined by the outcome of the previous step. Five computational challenges have been identified in the endeavor of conducting 13 C-MFA studies: organization of heterogeneous data, standardization of processes and the unification of tools and data, interactive workflow steering, distributed computing, and service orientation. The outcome of this thesis is a scientific workflow framework (SWF) that is custom-tailored for the specific requirements of 13 C-MFA applications. The proposed approach – namely, designing the SWF as a collection of loosely-coupled modules that are glued together with web services – alleviates the realization of 13C-MFA workflows by offering several features. By design, existing tools are integrated into the SWF using web service interfaces and foreign programming language bindings (e.g., Java or Python). Although the attributes "easy-to-use" and "general-purpose" are rarely associated with distributed computing software, the presented use cases show that the proposed Hadoop MapReduce framework eases the deployment of computationally demanding simulations on cloud and cluster computing resources. An important building block for allowing interactive researcher-driven workflows is the ability to track all data that is needed to understand and reproduce a workflow. The standardization of 13 C-MFA studies using a folder structure template and the corresponding services and web interfaces improves the exchange of information for a group of researchers. Finally, several auxiliary tools are developed in the course of this work to complement the SWF modules, i.e., ranging from simple helper scripts to visualization or data conversion programs. This solution distinguishes itself from other scientific workflow approaches by offering a system of loosely-coupled components that are flexibly arranged to match the typical requirements in the metabolic engineering domain. Being a modern and service-oriented software framework, new applications are easily composed by reusing existing components

Service-oriented architecture for device lifecycle support in industrial automation

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores Especialidade: Robótica e Manufactura IntegradaThis thesis addresses the device lifecycle support thematic in the scope of service oriented industrial automation domain. This domain is known for its plethora of heterogeneous equipment encompassing distinct functions, form factors, network interfaces, or I/O specifications supported by dissimilar software and hardware platforms. There is then an evident and crescent need to take every device into account and improve the agility performance during setup, control, management, monitoring and diagnosis phases. Service-oriented Architecture (SOA) paradigm is currently a widely endorsed approach for both business and enterprise systems integration. SOA concepts and technology are continuously spreading along the layers of the enterprise organization envisioning a unified interoperability solution. SOA promotes discoverability, loose coupling, abstraction, autonomy and composition of services relying on open web standards – features that can provide an important contribution to the industrial automation domain. The present work seized industrial automation device level requirements, constraints and needs to determine how and where can SOA be employed to solve some of the existent difficulties. Supported by these outcomes, a reference architecture shaped by distributed, adaptive and composable modules is proposed. This architecture will assist and ease the role of systems integrators during reengineering-related interventions throughout system lifecycle. In a converging direction, the present work also proposes a serviceoriented device model to support previous architecture vision and goals by including embedded added-value in terms of service-oriented peer-to-peer discovery and identification, configuration, management, as well as agile customization of device resources. In this context, the implementation and validation work proved not simply the feasibility and fitness of the proposed solution to two distinct test-benches but also its relevance to the expanding domain of SOA applications to support device lifecycle in the industrial automation domain