UK e-Science Research Articles

1st INCF Workshop on Global Portal Services for Neuroscience

INCF was established by definition to coordinate activities in neuroinformatics, i.e., coordination and promotion of databasing/sharing, analytical tools and computational models. Portals were considered to be basic tools not only in neuroinformatics activities in the field but also for the INCF mission itself. As the amount of neuroscience data explodes, so do the numbers of databases and associated portals, and the relations, often overlapping, between them. It is urgent that these activities be coordinated to make them accessible and useful to the neuroscience community. The committee determined that it is essential that the INCF take a lead role in this coordination. INCF should be proactive in establishing a list of maintained and developing neuroscience portals/databases. This list should include links to development sites and descriptions of the objectives of the project. The level of disclosure of any new development project should be regulated by the developer. INCF should: i) act as a broker to bring together individuals with expertise in particular areas of development, ii) provide guidance on the availability of development resources, and iii) advise on current “best practice”, including infrastructure recommendations, design processes, and scalable source control. This “best practice” should be conducted to enable interoperability via improved and pervasive ontology, have accessible API/scriptable interface, and have exposed database schemas. INCF should generate a policy statement on open source and accessibility of projects in development. INCF could provide a repository or library for the code base, data, etc., of projects no longer in development which might be reused in developing new resources. INCF representatives should be observers at NSF, NIH, DOD, Creative Commons, UK e-Science All Hands, and other meetings on core technologies related to cyberinfrastructure, and pass appropriate information on to developers. INCF should play a role in identifying and facilitating the development of unique value-added projects, such as an international database of neuronal connectivity. INCF should identify and coordinate requirements (standards) that assist in the acquisition of data, metadata, and development of databases. In addition, there needs to be a standard practice/policy on the release of statements and information. Methods and routes for dissemination vary between internal documents within nodes and those for external consumption. How do you measure/ evaluate success and how are people to be held accountable? Success measures must be considered in the context of on-going funding/support from the National Nodes. Annual reports can fulfill some of these requirements both in the preparation and its dissemination. This could include summaries of node activity, which will help with good practice. Last but not least, opportunities for running undergraduate courses in neuroinformatics should be considered as well as including neuroinformatics in medical training. Educational material could also be made available via the portal.

E-Science–towards the cloud: infrastructures, applications and research

The 2011 e-Science All Hands Meeting (AHM) marked the tenth annual gathering of technologists and scientists first brought together by the UK e-Science Programme—the £250 million research venture funded by the UK Research Councils. In the decade since the founding of this programme in 2001, e-science research has evolved from fundamental research focused on computational grids into work involving research from a wide variety of domains, such as bioinformatics, computing, astronomy, physics and medicine. The AHM community is now multinational, interdisciplinary and dynamic, and has recently moved towards addressing the issues and challenges raised by the increasing emergence of cloud computing in daily life. This continuing popularity and success has been highlighted by AHM 2011, hosted at the University of York by the EPSRC White Rose Grid e-Science Centre and attended by over 200 delegates. This Theme Issue provides a snapshot of the community's vibrant diversity, featuring the best papers presented at the conference, peer-reviewed for this issue, written by researchers from many different countries and backgrounds. The first paper in this issue, ‘The application of cloud computing to scientific workflows: a study of cost and performance’ by Berriman et al. [1], discusses a key factor in the use of cloud computing—is it economically beneficial for scientists to use a third-party cloud provider? Following this, Turilli et al. [2], writing in ‘Flexible services for the support of research’, focus on the adoption of the cloud by higher education institutions and address both flexible on-demand access to storage resources and scalability across a heterogeneous set of cloud infrastructures. Turner et al. [3] write of their experiences in developing secure virtual research environments to integrate multidisciplinary research in ‘Secure data sharing across portals: experiences from OneVRE’. Next, Tablan et al. [4] present ‘GATECloud.net: a platform for large-scale, open-source text processing on the cloud’, a paper discussing the authors' cloud-based platform's ability to perform large-scale data-intensive natural language processing experiments by harnessing the computing power of the Amazon Cloud. Additionally, the paper includes a cost–benefit analysis and usage evaluation. Moving away from the cloud, Yang et al. [5] discuss philosophical issues concerning data quality, identify actual user needs on data quality, review current standards and specifications, and propose an integrated model for data quality in the field of Earth observation in ‘An integrated view of data quality in Earth observation’. Service orientation is another interest of the AHM community, and Weeks et al. [6] present a developmental overview of the CARMEN virtual laboratory platform for integrating scientific code through a service-oriented infrastructure in ‘The CARMEN software as a service infrastructure’. In ‘Enhancing research publications using Rich Interactive Narratives’, Takeda et al. [7] describe a mechanism that provides an interactive framework for research publications in the fields of archaeology and chemistry. Following this, Colling et al. [8] discuss the highly important work of the UK's gridPP project in providing the grid infrastructure needed by experiments at the Large Hadron Collider at CERN in the paper ‘Processing LHC data in the UK’. Returning to the cloud, the work undertaken within the RAPPORT project to investigate the running of a group of multi-domain scientific applications on cloud resources is presented by Cohen et al. [9] in ‘RAPPORT: running scientific high-performance computing applications on the cloud’. Djemame et al. [10] then present their approach to risk management as applied to cloud computing, with a particular emphasis on legal issues, in the paper ‘Legal issues in clouds: towards a risk inventory’. In ‘Developing cloud applications using e-Science Central’, Hiden et al. [11] present an overview of the e-Science Central (e-SC) cloud processing system and its application to a number of e-science projects. Finally, Suresh et al. [12] discuss how cloud computing has the potential for enabling a new technique for using queuing theory to meet specified response-time targets against fluctuating event arrival rates in their paper ‘Scalable and responsive event processing in the cloud’. As can be seen from the above descriptions, the variety, scope and standard of submissions to AHM 2011 was very high; in order to help focus the conference, we are indebted to the Conference Programme Committee, featuring 36 international experts and leaders in their respective fields. Owing to space constraints, many high-quality pieces of research presented at the conference cannot be published in this Theme Issue, but we are confident that the whole body of work presented at the conference will help to continue to drive e-science and digital research both in the UK and abroad.

The Taverna Workbench: Integrating and analysing biological and clinical data with computerised workflows

Katy Wolstencroft is a Research Fellow in the School of Computer Science, University of Manchester and a visiting researcher in the Molecular Cell Physiology group at the Vrije Universiteit, Amsterdam. She has a PhD and MSc in Bioinformatics from the University of Manchester, and a BSc in Biochemistry from the University of Leeds. Katy’s work is primarily in the area of data and knowledge integration, where she leads the bioinformatics research activities in the myGrid consortium. myGrid is a UK e-Science initiative that has produced, amongst other things, the Taverna workflows workbench (http://www.taverna.org.uk/), the myExperiment workflow repository (http://www.myexperiment.org) and the BioCatalogue service catalogue (http://www.biocatalogue.org). Currently, her main focus is on the BBSRC funded SysMO SEEK project, to develop a data exchange and modelling environment for Systems Biology consortia in Europe (http://www.sysmo-db.org/). It was designed for the SysMO consortium, (Systems Biology of Micro-Organisms), but it has now been adopted by many other consortia, providing a common platform for hundreds of research labs in Europe. Katy also coordinates the training and outreach activities in myGrid. As such, she has been involved in teaching scientific workflows and related technologies in over 50 workshops, summer schools and conferences throughout the world. In this tutorial, she will provide an introduction to designing and reusing workflows for high-throughput bioinformatics data analysis, using Taverna and myExperiment. Scientific workflows enable the chaining together of distributed analysis resources and databases to construct complex analysis pipelines that are ideal for high throughput omics data analysis. These workflows are reusable experimental methods that can be shared and rerun for other data, or for experimental validation.

Towards a virtual research environment for language and literature researchers

Language and literature researchers often use a variety of data resources in order to conduct their day-to-day research. Such resources include dictionaries, thesauri, corpora, images, audio and video collections. These resources are typically distributed, and comprise non-interoperable repositories of data that are often licence protected. In this context, researchers typically conduct their research through direct access to individual web-based resources. This form of research is non-scalable, time consuming and often frustrating to the researchers. The JISC funded project Enhancing Repositories for Language and Literature Researchers (ENROLLER, http://www.gla.ac.uk/enroller/) aims to address this by provision of an interactive, research infrastructure providing seamless access to a range of major language and literature repositories. This paper describes this infrastructure and the services that have been developed to overcome the issues in access and use of digital resources in humanities. In particular, we describe how high performance computing facilities including the UK e-Science National Grid Service (NGS, http://www.ngs.ac.uk) have been exploited to support advanced, bulk search capabilities, implemented using Google’s MapReduce algorithm. We also describe our experiences in the use of the resource brokering Workload Management System (WMS) and the Virtual Organization Membership Service (VOMS) solutions in this space. Finally we outline the experiences from the arts and humanities community on the usage of this infrastructure.

E-Science: past, present and future II

The All Hands Meeting (AHM) has become the annual event at which computational scientists and technologists come together to share, discuss and advance the exciting research that has grown out of the UK e-Science Programme. Since 2001, the UK Research Councils have funded over £250 million worth of

Engineering design optimization using services and workflows

Multi-disciplinary design optimization (MDO) is the process whereby the often conflicting requirements of the different disciplines to the engineering design process attempts to converge upon a description that represents an acceptable compromise in the design space. We present a simple demonstrator of a flexible workflow framework for engineering design optimization using an e-Science tool. This paper provides a concise introduction to MDO, complemented by a summary of the related tools and techniques developed under the umbrella of the UK e-Science programme that we have explored in support of the engineering process. The main contributions of this paper are: (i) a description of the optimization workflow that has been developed in the Taverna workbench, (ii) a demonstrator of a structural optimization process with a range of tool options using common benchmark problems, (iii) some reflections on the experience of software engineering meeting mechanical engineering, and (iv) an indicative discussion on the feasibility of a 'plug-and-play' engineering environment for analysis and design.

Crossing boundaries: computational science, e-Science and global e-Infrastructure

This is the second of two theme issues of Phil. Trans. R. Soc. A , which together contain selected papers from the UK e-Science All Hands Meeting 2008. The conference was held in Edinburgh between 8 and 11 September 2008 ( ). The papers that appear here have been

Data and Information Access in E-Research: Results from a 2008 Survey Among UK E-Science Project Participants

Questions concerning the actual extent of 'openness' of research processes identified with contemporary e-science should address at least two main sets of issues pertaining to the conduct of 'open science.' The first set concerns the terms on which individuals may enter and leave research projects. Who is permitted to join the collaboration? Are all of the participating researchers able to gain full access to the project's databases and other key research resources? How easy or hard is it for members and new entrants to develop distinct agendas of enquiry within the context of the ongoing project, and how much control do they retain over the communication of their findings? What restrictions are placed (formally or informally) on the uses they may make of data, information and knowledge in their possession after they exit from the research collaboration?

CARMEN: A Neuroscience Portal for Collaboration via Tools and Data sharing

CARMEN: A Neuroscience Portal for Collaboration via Tools and Data sharing

Report from the UK e-Science All Hands Meeting, September 10-13, 2007, Nottingham, UK

This is a report from the UK e-Science All Hands Meeting held at the East Midlands Conference Centre, Nottingham on September 10-13, 2007. This event was the 5th annual All Hands Meeting. The proceedings of the meeting are available from the UK e-Science 2007 All Hands Meeting Website.

User Priorities for Data: Results from SUPER

SUPER, a Study of User Priorities for e-infrastructure for Research, was a six-month effort funded by the UK e-Science Core Programme and JISC. Its aim was to inform investment in order to provide a usable, useful, and accessible e-infrastructure for all researchers and a coherent set of e-infrastructure services that would increase usage by at least a factor of ten by 2010. Through a series of unstructured face-to-face interviews with over 45 participants from 30 different projects, an online survey, together with a day-long workshop at NeSC, we have observed recurring issues relating to the provision of e-infrastructure. In this article we focus on the data-related issues identified during these interactions. We conclude with a prioritised list of future activities for research, development, and adoption in the data space.

CARMEN: Distributed Search and Data-Mining in Complex Neurophysiology Data

Event Abstract Back to Event CARMEN: Distributed Search and Data-Mining in Complex Neurophysiology Data Bojian Liang1*, Tom Jackson1, Martyn Fletcher1, Mark Jessop1 and Jim Austin1 1 University of York, United Kingdom We describe research within the UK CARMEN [1] e-Science project which is addressing the challenge of creating and managing experimental data and methods within the context of Neuroscience research. The traditional research approach of testing a hypothesis and publishing the results is hampered in situations where others need to build on the results and need access to the data or original methods. CARMEN addresses this issue by allowing scientists to share data & methods within a collaborative Grid environment. The CARMEN platform (a CAIRN) is a Grid-based, shared data and services repository. Central to the data management challenge is providing visualisation and search capabilities across the stored, high-volume, time-series, spike train data from nerve cell recordings. A prior UK e-Science project, DAME[2], developed a distributed signal search engine, called Signal Data Explorer (SDE) [3]. Interoperability between SDE and other neuroscience software services is being investigated within CARMEN, to provide a centralised capability for visualisation and search. The SDE provides data visualisation, transformations and real-time search capabilities for complex time-series signal data. The interactive search capability is provided by the SDE via distributed Grid data repositories which use: • Distributed data management - SDE interfaces directly to the Storage Resource Broker (SRB) from San Diego Supercomputer Center (SDSC); • The pattern matching architecture consisting of Pattern Match Controller (PMC) and Pattern Match Engine (PME) components. The raw data to be stored by the CARMEN CAIRN nodes consists of spatiotemporal signals expressed, either as time-series recordings (collected by single electrodes or MEAs), or as image files. Querying of the data at the “signal” level is provided via a highly intuitive and interactive SDE GUI. This GUI allows users to formulate queries by simple selection of regions of interest in time-series signals, or via libraries of templates queries, built up over the course of prior experiments. The SDE GUI also supports complex visualisation requirements, permitting users to explore data events and features in detail or in a broad overview, as required. Auxiliary viewing windows permit users to arrange collated views on data signals, and support additional functionality such as signal superimposition, filtering and spike sorting. The talk will provide a demonstration of progress on the development of the search and visualisation capabilities, working on experimental MEA data, and will show how additional analysis functionality, such as spike sorting or correlation functions, can be supported within the tool. User feedback is an important aspect of the development iteration and we will conclude with examples of how SDE is supporting laboratory experiments within the CARMEN consortium.

Managing Semantic Metadata for Web/Grid Services

Web/Grid services’ metadata and semantics are becoming increasing important for service sharing and effective reuse. In this paper we present a generic framework for engineering and managing services’ Semantic Metadata (SMD) with the ultimate purpose of facilitating interoperability, automation, and knowledgeable reuse of services for problem solving. The framework addresses fundamental issues, approaches, and tools for the whole lifecycle of SMD management, in other words, those of acquiring, modeling, representing, publishing, and reusing services’ SMD. It adopts ontologies and the Semantic Web technologies as the enabling technologies by which services’ metadata are semantically enriched and made interoperable, understandable, and accessible on the Web/Grid for both humans and machines. In particular, mechanisms are proposed to make use of service SMD for service discovery and composition. The paper also describes a service SMD management system in the context of the UK e-Science project GEODISE. A suite of tools are developed, which forms the core of the SMD management infrastructure. We demonstrate the added value of the use of SMD through the integration of SMD management with GEODISE application systems.

Decision support system on the grid

Aero-engines are extremely reliable machines and operational failures are rare. However, currently great effort is being put into reducing the number of in-flight engine shutdowns, aborted take-offs and flight delays through the use of advanced engine health monitoring technology. This represents a benefit to society through reduced delays, reduced anxiety and reduced cost of ownership of aircraft. This is reflected in a change of emphasis within aero-engine companies where, instead of selling engines to customers, there is a fundamental shift to adoption of power-by-the-hour contracts. In these contracts, airlines make fixed regular payments based on the hours flown and the engine manufacturer retains responsibility for maintaining the engine. To support this new approach, improvements in in-flight monitoring of engines are being introduced with the collection of much more detailed data on the operation of the engine. At the same time advances have been made in Internet technologies providing a worldwide network of computers that can be used to access and process that data. The explosion of available knowledge within those large datasets also presents its own problems and here it is necessary to work on advanced decision support systems to identify the useful information in the data and provide knowledge-based advice between individual aircraft, airline repair and overhaul bases, world-wide data warehouses and the engine manufacturer. This paper presents a practical framework in which to build such a system that is inherent in the emerging Grid computing paradigm that provides the necessary computing resources. A demonstrator system already developed and implemented in the UK E-Science Grid project, DAME, is introduced.

Genomics research in the UK—the social science agenda

We sketch the development of UK genetics and genomics research, and emphasize the UK's key role in the international genetics and genomics research community. We highlight in particular the part played by the UK's Research Councils and other funders. With the move from genomics to post-genomics research, the field is diversifying, and interdisciplinarity becomes increasingly important, as traditional disciplinary boundaries become blurred, or break down, in the face of newly emerging sciences. We consider the changing nature of health and ill health in the developed and developing world, and questions about the complex nature of the relationships between genes and the environment, and their future implications for human health and human populations. We describe the ESRC's activities, stressing the importance of both the social, ethical and legal issues raised by these emerging disciplines, and of public engagement. Finally, we link the data handling and analysis issues raised by these emerging sciences, with other new research areas, in particular the UK's e-Science programme.

Improving scientists' interaction with complex computational–visualization environments based on a distributed grid infrastructure

The grid has the potential to transform collaborative scientific investigations through the use of closely coupled computational and visualization resources, which may be geographically distributed, in order to harness greater power than is available at a single site. Scientific applications to benefit from the grid include visualization, computational science, environmental modelling and medical imaging. Unfortunately, the diversity, scale and location of the required resources can present a dilemma for the scientific worker because of the complexity of the underlying technology. As the scale of the scientific problem under investigation increases so does the nature of the scientist's interaction with the supporting infrastructure. The increased distribution of people and resources within a grid-based environment can make resource sharing and collaborative interaction a critical factor to their success. Unless the technological barriers affecting user accessibility are reduced, there is a danger that the only scientists to benefit will be those with reasonably high levels of computer literacy. This paper examines a number of important human factors of user interaction with the grid and expresses this in the context of the science undertaken by RealityGrid, a project funded by the UK e-Science programme. Critical user interaction issues will also be highlighted by comparing grid computational steering with supervisory control systems for local and remote access to the scientific environment. Finally, implications for future grid developers will be discussed with a particular emphasis on how to improve the scientists' access to what will be an increasingly important resource.

Modelling biological complexity: a physical scientist's perspective.

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter. The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.

SEMANTICS‐ASSISTED PROBLEM SOLVING ON THE SEMANTIC GRID

In this paper we propose a distributed knowledge management framework for semantics and knowledge creation, population, and reuse on the grid. Its objective is to evolve the Grid toward the Semantic Grid with the ultimate purpose of facilitating problem solving in e‐Science. The framework uses ontology as the conceptual backbone and adopts the service‐oriented computing paradigm for information‐ and knowledge‐level computation. We further present a semantics‐based approach to problem solving, which exploits the rich semantic information of grid resource descriptions for resource discovery, instantiation, and composition. The framework and approach has been applied to a UK e‐Science project—Grid Enabled Engineering Design Search and Optimisation in Engineering (GEODISE). An ontology‐enabled problem solving environment (PSE) has been developed in GEODISE to leverage the semantic content of GEODISE resources and the Semantic Grid infrastructure for engineering design. Implementation and initial experimental results are reported.

Digital Mammography: A World without Film?

eDiaMoND is a next generation Internet ("Grid") multidisciplinary research project funded by the UK e-Science Programme with the following objectives; the development of a next generation Internet enabled prototype to demonstrate the potential benefits of a national infrastructure to support digital mammography; the exploration of potential benefits for digital mammography systems, with particular emphasis being placed on selected applications, namely, screening, training, computer-aided detection and appropriate support for epidemiological studies. EDiaMoND has worked in conjunction with selected clinical partners to enable the collection of valuable mammography information and the design of applications based upon extensive requirements gathering exercises. The clinical partners validated both the immediate needs and assisted with defining future needs of such an architecture to support the UK Health Service. The project has succeeded in invoking the interest of clinical partners and representatives of the UK NHS Breast Screening Programme in our vision of a world without film, albeit a long way off. The project has also succeeded in identifying the barriers to adopting this approach with the current limitations within the NHS, and has developed a blueprint for working towards this strategy. A UK national digital mammography archive has the potential to provide major benefits for the UK. For example, such an archive could: ensure that previous mammograms are always available, and could link up seamlessly the screening, assessment and symptomatic clinics; it could provide a huge teaching and training resource; it could be a huge resource for epidemiological studies.

UK e-Science Programme: Next Generation Grid Applications

In November 2000, the government announced a new e-Science initiative in the UK with some £120m funding. In this paper we describe a range of the applications that are now on-going within the e-Science Programme and we detail one of the focuses of the e-Science Core Programme, that of building a UK e-Science Grid. We briefly discuss some of the middleware development activities in the UK and indicate where they sit in the international scene.