Alastair Hume

Introduction to OGSA-DAI services

In todays large collaborative environments, potentially composed of multiple distinct organisations, uniform controlled access to data has become a key requirement if these organisations are to work together as Virtual Organisations. We refer to such an integrated set of data resources as a virtual data warehouse. The Open Grid Services Architecture – Data Access and Integration (OGSA-DAI) project was established to produce a common middleware solution, aligned with the Global Grid Forums (GGF) OGSA vision [OGSA] to allow uniform access to data resources using a service based architecture. In this paper the service infrastructure provided by OGSA-DAI is presented providing a snapshot of its current state, in an evolutionary process, which is attempting to build infrastructure to allow easy integration and access to distributed data using grids or web services. More information about OGSA-DAI is available from the project web site: www.ogsadai.org.

BonFIRE: A Multi-cloud Test Facility for Internet of Services Experimentation

BonFIRE offers a Future Internet, multi-site, cloud testbed, targeted at the Internet of Services community, that supports large scale testing of applications, services and systems over multiple, geographically distributed, heterogeneous cloud testbeds. The aim of BonFIRE is to provide an infrastructure that gives experimenters the ability to control and monitor the execution of their experiments to a degree that is not found in traditional cloud facilities.

The design and implementation of OGSA-DQP: A service-based distributed query processor

Service-based approaches are rising to prominence because of their potential to meet the requirements for distributed application development in e-business and e-science. The emergence of a service-oriented view of hardware and software resources raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. This paper explores one aspect of service-based computing and data management, viz., how to integrate query processing technology with a service-based architecture suitable for a Grid environment. The paper addresses this by describing in detail the design and implementation of a service-based distributed query processor. The query processor is service-based in two orthogonal senses: firstly, it supports querying over data storage and analysis resources that are made available as services, and, secondly, its internal architecture factors out as services the functionalities related to the construction and execution of distributed query plans. The resulting system both provides a declarative approach to service orchestration, and demonstrates how query processing can benefit from a service-based architecture. As well as describing and motivating the architecture used, the paper also describes usage scenarios, and, using a bioinformatics application, presents performance results that benchmark the system and illustrate the benefits provided by the service-based architecture.

Integrating distributed data sources with OGSA–DAI DQP and Views

OGSA-DAI (Open Grid Services Architecture Data Access and Integration) is a framework for building distributed data access and integration systems. Until recently, it lacked the built-in functionality that would allow easy creation of federations of distributed data sources. The latest release of the OGSA-DAI framework introduced the OGSA-DAI DQP (Distributed Query Processing) resource. The new resource encapsulates a distributed query processor, that is able to orchestrate distributed data sources when answering declarative user queries. The query processor has many extensibility points, making it easy to customize. We have also introduced a new OGSA-DAI Views resource that provides a flexible method for defining views over relational data. The interoperability of the two new resources, together with the flexibility of the OGSA-DAI framework, allows the building of highly customized data integration solutions.

BonFIRE: The Clouds and Services Testbed

BonFIRE is a multi-site test bed that supports testing of Cloud-based and distributed applications. BonFIRE breaks the mould of commercial Cloud offerings by providing unique functionality in terms of observability, control, advanced Cloud features and ease of use for experimentation. A number of successful use cases have been executed on BonFIRE, involving industrial and academic users and delivering impact in diverse areas, such as media, e-health, environment and manufacturing. The BonFIRE user-base is expanding through its free, Open Access scheme, daily carrying out important research, while the consortium is working to sustain the facility beyond 2014.

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell−1) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell−1) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.

Building Bridges between Islands of Data - An Investigation into Distributed Data Management in the Humanities

Ancient documents represent a primary source for research in the humanities. A substantial body of digital material has evolved containing information about these documents. Unfortunately these digital resources are often held within myriad locations, owned by a range of groups or individuals, are held within a diverse range of formats and are either unavailable or are available only in isolation. This paper describes a successful investigation into using the OGSA-DAI distributed data management software to build bridges between these islands of data and so to facilitate navigation across a larger data space than is otherwise achievable. An overview of a proof-of-concept that was developed is given along with the technical challenges encountered. Discussion from researchers in the humanities about such an architecture reveals the possibility of creating virtual data centres for the coordinated sharing of such resources. It also raises important questions as to how distributed data resources can be meaningfully federated and queried.

Security and performance enhancements to OGSA-DAI for Grid data virtualization

In this paper we describe our work on enabling dynamic access control and secure management over federated data resources, such as relational or XML databases exposed to public network infrastructures via OGSA‐DAI middleware. We have proposed some extensions to the OGSA‐DAI architecture and successfully implemented new mechanisms enabling secure communication and distributed data integrity along with fine‐grain authorization and policy enforcement to minimize the complexity of the security right management. As a proof of concept some preliminary results of various performance tests of our solutions are also presented in this paper. We then analyze our achievements and describe future work and research. Copyright

Cloud and Network Facilities Federation in BonFIRE

In recent years we have seen how Cloud Computing is changing the way of doing businesses and how services are delivered over the Internet. This disruption is a major challenge for Service Providers and Independent Software Vendors when creating new services and software applications for the Cloud. BonFIRE offers a federated, multi-site cloud testbed to support large-scale testing of applications, services and systems. This is achieved by federating geographically distributed, heterogeneous clouds testbeds where each exposes unique configuration and/or features while giving to the experimenters (users) an homogeneous way to interact with the facility. All those testbeds are controlled by a central set of services commonly denominated “Broker”. Additionally, BonFIRE is federated with different network facilities like the Virtual Wall, FEDERICA and AutoBAHN to provide high-level interfaces to network control functionality, in order to simulate diverse network QoS scenarios, enabling vertical federation.

Applying Grid Technologies to Distributed Data Mining

The Grid promises improvements in the effectiveness with which global businesses are managed if it enables distributed expertise to be efficiently applied to the analysis of distributed data. We report an ESRC-funded collaboration between EPCC in Edinburgh and Curtin University of Technology in Perth, Australia, that is applying public-domain Grid technologies to secure data mining within a commercial environment. We describe this Grid infrastructure and discuss its strengths and weaknesses.