BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

'BioNessie(G) - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

Aggregating assessment tools in a service orientated architecture

Until recently assessment and other eLearning systems have tended to adopt monolithic architectures and this has restricted integration with other tools. The ELearning Framework (ELF) sets out to address this problem by creating an eLearning environment within which components with discrete purposes communicate via webservices. In order to help co-ordinate the design of the ELF, JISC has recently sponsored a number of Framework Reference Model Projects, and FReMa is the Framework Reference Model for Assessment. In this paper we examine how FReMA is facilitating a common understanding of the components of assessment and their interfaces, and we explain how this information is being elicited from the community by reference to tools which are already contributing to the model. We also present our approach to the adaptive website by which the emerging model is being disseminated to a range of stakeholders

Geographic information system algorithms to locate prospective sites for pumped hydro energy storage

Pumped hydro energy storage is capable of large-scale energy time shifting and a range of ancillary services, which can facilitate high levels of photovoltaics and wind integration in electricity grids. This study aims to develop a series of advanced Geographic Information System algorithms to locate prospective sites for off-river pumped hydro across a large land area such as a state or a country. Two typical types of sites, dry-gully and turkey’s nest, are modelled and a sequence of Geographic Information System-based procedures are developed for an automated site search. A case study is conducted for South Australia, where 168 dry-gully sites and 22 turkey’s nest sites have been identified with a total water storage capacity of 441 gigalitres, equivalent to 276 gigawatt-hours of energy storage. This demonstrates the site searching algorithms can work efficiently in the identification of off-river pumped hydro sites, allowing high-resolution assessments of pumped hydro energy storage to be quickly conducted on a broad scale. The sensitivity analysis shows the significant influences of maximum dam wall heights on the number of sites and the total storage capacity. It is noted that the novel models developed in this study are also applicable to the deployments of other types of pumped hydro such as the locations of dry-gully and turkey’s nest sites adjacent to existing water bodies, old mining pits and oceans

Using Provenance to support Good Laboratory Practice in Grid Environments

Conducting experiments and documenting results is daily business of scientists. Good and traceable documentation enables other scientists to confirm procedures and results for increased credibility. Documentation and scientific conduct are regulated and termed as "good laboratory practice." Laboratory notebooks are used to record each step in conducting an experiment and processing data. Originally, these notebooks were paper based. Due to computerised research systems, acquired data became more elaborate, thus increasing the need for electronic notebooks with data storage, computational features and reliable electronic documentation. As a new approach to this, a scientific data management system (DataFinder) is enhanced with features for traceable documentation. Provenance recording is used to meet requirements of traceability, and this information can later be queried for further analysis. DataFinder has further important features for scientific documentation: It employs a heterogeneous and distributed data storage concept. This enables access to different types of data storage systems (e. g. Grid data infrastructure, file servers). In this chapter we describe a number of building blocks that are available or close to finished development. These components are intended for assembling an electronic laboratory notebook for use in Grid environments, while retaining maximal flexibility on usage scenarios as well as maximal compatibility overlap towards each other. Through the usage of such a system, provenance can successfully be used to trace the scientific workflow of preparation, execution, evaluation, interpretation and archiving of research data. The reliability of research results increases and the research process remains transparent to remote research partners.Comment: Book Chapter for "Data Provenance and Data Management for eScience," of Studies in Computational Intelligence series, Springer. 25 pages, 8 figure

CC-interop : COPAC/Clumps Continuing Technical Cooperation. Final Project Report

As far as is known, CC-interop was the first project of its kind anywhere in the world and still is. Its basic aim was to test the feasibility of cross-searching between physical and virtual union catalogues, using COPAC and the three functioning "clumps" or virtual union catalogues (CAIRNS, InforM25, and RIDING), all funded or part-funded by JISC in recent years. The key issues investigated were technical interoperability of catalogues, use of collection level descriptions to search union catalogues dynamically, quality of standards in cataloguing and indexing practices, and usability of union catalogues for real users. The conclusions of the project were expected to, and indeed do, contribute to the development of the JISC Information Environment and to the ongoing debate as to the feasibility and desirability of creating a national UK catalogue. They also inhabit the territory of collection level descriptions (CLDs) and the wider services of JISC's Information Environment Services Registry (IESR). The results of this project will also have applicability for the common information environment, particularly through the landscaping work done via SCONE/CAIRNS. This work is relevant not just to HE and not just to digital materials, but encompasses other sectors and domains and caters for print resources as well. Key findings are thematically grouped as follows: System performance when inter-linking COPAC and the Z39.50 clumps. The various individual Z39.50 configurations permit technical interoperability relatively easily but only limited semantic interoperability is possible. Disparate cataloguing and indexing practices are an impairment to semantic interoperability, not just for catalogues but also for CLDs and descriptions of services (like those constituting JISC's IESR). Creating dynamic landscaping through CLDs: routines can be written to allow collection description databases to be output in formats that other UK users of CLDs, including developers of the JISC information environment. Searching a distributed (virtual) catalogue or clump via Z39.50: use of Z39.50 to Z39.50 middleware permits a distributed catalogue to be searched via Z39.50 from such disparate user services as another virtual union catalogue or clump, a physical union catalogue like COPAC, an individual Z client and other IE services. The breakthrough in this Z39.50 to Z39.50 conundrum came with the discovery that the JISC-funded JAFER software (a result of the 5/99 programme) meets many of the requirements and can be used by the current clumps services. It is technically possible for the user to select all or a sub-set of available end destination Z39.50 servers (we call this "landscaping") within this middleware. Comparing results processing between COPAC and clumps. Most distributed services (clumps) do not bring back complete results sets from associated Z servers (in order to save time for users). COPAC on-the-fly routines could feasibly be applied to the clumps services. An automated search set up to repeat its query of 17 catalogues in a clump (InforM25) hourly over nearly 3 months returned surprisingly good results; for example, over 90% of responses were received in less than one second, and no servers showed slower response times in periods of traditionally heavy OPAC use (mid-morning to early evening). User behaviour when cross-searching catalogues: the importance to users of a number of on-screen features, including the ability to refine a search and clear indication that a search is processing. The importance to users of information about the availability of an item as well as the holdings data. The impact of search tools such as Google and Amazon on user behaviour and the expectations of more information than is normally available from a library catalogue. The distrust of some librarians interviewed of the data sources in virtual union catalogues, thinking that there was not true interoperability

A framework for P2P application development

Although Peer-to-Peer (P2P) computing has become increasingly popular over recent years, there still exist only a very small number of application domains that have exploited it on a large scale. This can be attributed to a number of reasons including the rapid evolution of P2P technologies, coupled with their often-complex nature. This paper describes an implemented abstraction framework that seeks to aid developers in building P2P applications. A selection of example P2P applications that have been developed using this framework are also presented

Enterprise engineering using semantic technologies

Modern Enterprises are facing unprecedented challenges in every aspect of their businesses: from marketing research, invention of products, prototyping, production, sales to billing. Innovation is the key to enhancing enterprise performances and knowledge is the main driving force in creating innovation. The identification and effective management of valuable knowledge, however, remains an illusive topic. Knowledge management (KM) techniques, such as enterprise process modelling, have long been recognised for their value and practiced as part of normal business. There are plentiful of KM techniques. However, what is still lacking is a holistic KM approach that enables one to fully connect KM efforts with existing business knowledge and practices already in IT systems, such as organisational memories. To address this problem, we present an integrated three-dimensional KM approach that supports innovative semantics technologies. Its automated formal methods allow us to tap into modern business practices and capitalise on existing knowledge. It closes the knowledge management cycle with user feedback loops. Since we are making use of reliable existing knowledge and methods, new knowledge can be extracted with less effort comparing with another method where new information has to be created from scratch

BCAS: A Web-enabled and GIS-based Decision Support System for the Diagnosis and Treatment of Breast Cancer

For decades, geographical variations in cancer rates have been observed but the precise determinants of such geographic differences in breast cancer development are unclear. Various statistical models have been proposed. Applications of these models, however, require that the data be assembled from a variety of sources, converted into the statistical models’ parameters and delivered effectively to researchers and policy makers. A web-enabled and GIS-based system can be developed to provide the needed functionality. This article overviews the conceptual web-enabled and GIS-based system (BCAS), illustrates the system’s use in diagnosing and treating breast cancer and examines the potential benefits and implications for breast cancer research and practice