Standardisation of Provenance Systems in Service Oriented Architectures --- White Paper

This White Paper presents provenance in computer systems as a mechanism by which business and e-science can undertake compliance validation and analysis of their past processes. We discuss an open approach that can bring benefits to application owners, IT providers, auditors and reviewers. In order to capitalise on such benefits, we make specific recommendations to move forward a standardisation activity in this domain

Work flows in life science

The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab experiments. Various tools, such as databases, web applications and scripting languages, are used to design and run in-silico experiments. As the size and complexity of these experiments grow, new types of tools are required to design and execute the experiments and to analyse the results. Workflow systems promise to fulfill this role. The bioinformatician composes an experiment by using tools and web services as building blocks, and connecting them, often through a graphical user interface. Workflow systems, such as Taverna, provide access to up to a few thousand resources in a uniform way. Although workflow systems are intended to make the bioinformaticians' work easier, bioinformaticians experience difficulties in using them. This thesis is devoted to find out which problems bioinformaticians experience using workflow systems and to provide solutions for these problems.\u

The architecture of discovery net : towards grid-based discovery services

Imperial Users onl

Enacting the Semantic Web: Ontological Orderings, Negotiated Standards, and Human-machine Translations

Artificial intelligence (AI) that is based upon semantic search has become one of the dominant means for accessing information in recent years. This is particularly the case in mobile contexts, as search based AI are embedded in each of the major mobile operating systems. The implications are such that information is becoming less a matter of choosing between different sets of results, and more of a presentation of a single answer, limiting both the availability of, and exposure to, alternate sources of information. Thus, it is essential to understand how that information comes to be structured and how deterministic systems like search based AI come to understand the indeterminate worlds they are tasked with interrogating. The semantic web, one of the technologies underpinning these systems, creates machine-readable data from the existing web of text and formalizes those machine-readable understandings in ontologies. This study investigates the ways that those semantic assemblages structure, and thus define, the world. In accordance with assemblage theory, it is necessary to study the interactions between the components that make up such data assemblages. As yet, the social sciences have been slow to systematically investigate data assemblages, the semantic web, and the components of these important socio-technical systems. This study investigates one major ontology, Schema.org. It uses netnographic methods to study the construction and use of Schema.org to determine how ontological states are declared and how human-machine translations occur in those development and use processes. This study has two main findings that bear on the relevant literature. First, I find that development and use of the ontology is a product of negotiations with technical standards such that ontologists and users must work around, with, and through the affordances and constraints of standards. Second, these groups adopt a pragmatic and generalizable approach to data modeling and semantic markup that determines ontological context in local and global ways. This first finding is significant in that past work has largely focused on how people work around standards’ limitations, whereas this shows that practitioners also strategically engage with standards to achieve their aims. Second, the particular approach that these groups use in translating human knowledge to machines, differs from the formalized and positivistic approaches described in past work. At a larger level, this study fills a lacuna in the collective understanding of how data assemblages are constructed and operate

Active provenance for data intensive research

The role of provenance information in data-intensive research is a significant topic of discussion among technical experts and scientists. Typical use cases addressing traceability, versioning and reproducibility of the research findings are extended with more interactive scenarios in support, for instance, of computational steering and results management. In this thesis we investigate the impact that lineage records can have on the early phases of the analysis, for instance performed through near-real-time systems and Virtual Research Environments (VREs) tailored to the requirements of a specific community. By positioning provenance at the centre of the computational research cycle, we highlight the importance of having mechanisms at the data-scientists’ side that, by integrating with the abstractions offered by the processing technologies, such as scientific workflows and data-intensive tools, facilitate the experts’ contribution to the lineage at runtime. Ultimately, by encouraging tuning and use of provenance for rapid feedback, the thesis aims at improving the synergy between different user groups to increase productivity and understanding of their processes. We present a model of provenance, called S-PROV, that uses and further extends PROV and ProvONE. The relationships and properties characterising the workflow’s abstractions and their concrete executions are re-elaborated to include aspects related to delegation, distribution and steering of stateful streaming operators. The model is supported by the Active framework for tuneable and actionable lineage ensuring the user’s engagement by fostering rapid exploitation. Here, concepts such as provenance types, configuration and explicit state management allow users to capture complex provenance scenarios and activate selective controls based on domain and user-defined metadata. We outline how the traces are recorded in a new comprehensive system, called S-ProvFlow, enabling different classes of consumers to explore the provenance data with services and tools for monitoring, in-depth validation and comprehensive visual-analytics. The work of this thesis will be discussed in the context of an existing computational framework and the experience matured in implementing provenance-aware tools for seismology and climate VREs. It will continue to evolve through newly funded projects, thereby providing generic and user-centred solutions for data-intensive research

A virtual imaging platform for multi-modality medical image simulation.

International audienceThis paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011

A formal architecture-centric and model driven approach for the engineering of science gateways

From n-Tier client/server applications, to more complex academic Grids, or even the most recent and promising industrial Clouds, the last decade has witnessed significant developments in distributed computing. In spite of this conceptual heterogeneity, Service-Oriented Architecture (SOA) seems to have emerged as the common and underlying abstraction paradigm, even though different standards and technologies are applied across application domains. Suitable access to data and algorithms resident in SOAs via so-called ‘Science Gateways’ has thus become a pressing need in order to realize the benefits of distributed computing infrastructures.In an attempt to inform service-oriented systems design and developments in Grid-based biomedical research infrastructures, the applicant has consolidated work from three complementary experiences in European projects, which have developed and deployed large-scale production quality infrastructures and more recently Science Gateways to support research in breast cancer, pediatric diseases and neurodegenerative pathologies respectively. In analyzing the requirements from these biomedical applications the applicant was able to elaborate on commonly faced issues in Grid development and deployment, while proposing an adapted and extensible engineering framework. Grids implement a number of protocols, applications, standards and attempt to virtualize and harmonize accesses to them. Most Grid implementations therefore are instantiated as superposed software layers, often resulting in a low quality of services and quality of applications, thus making design and development increasingly complex, and rendering classical software engineering approaches unsuitable for Grid developments.The applicant proposes the application of a formal Model-Driven Engineering (MDE) approach to service-oriented developments, making it possible to define Grid-based architectures and Science Gateways that satisfy quality of service requirements, execution platform and distribution criteria at design time. An novel investigation is thus presented on the applicability of the resulting grid MDE (gMDE) to specific examples and conclusions are drawn on the benefits of this approach and its possible application to other areas, in particular that of Distributed Computing Infrastructures (DCI) interoperability, Science Gateways and Cloud architectures developments