@inproceedings{bachler2004-collaborative, author = {Bachler, M. and Buckingham Shum, S. and Chen-Burger, J. and Dalton, J. and De Roure, D. and Eisenstadt, M. and Komzak, J. and Michaelides, D. and Page, K. and Potter, S. and Shadbolt, N. and Tate, A.}, title = {Collaborative Tools in the Semantic Grid}, booktitle = {GGF11 - The Eleventh Global Grid Forum}, editor = {Moreau, Luc}, publisher = {Global Grid Forum}, } @inproceedings{bachler2004-chain, author = {Bachler, M. and Buckingham-Shum, S. and Chen-Burger, J. and Dalton, J. and Roure, D. De and Eisenstadt, M. and Frey, J. and Komzak, J. and Michaelides, D. and Page, K. and Potter, S. and Shadbolt, N. and Tate, A.}, title = {Chain ReAKTing: Collaborative Advanced Knowledge Technologies in the CombeChem Grid}, booktitle = {UK e-Science All Hands Meeting}, } @inproceedings{bachler2004-1, author = {Bachler, Michelle and Shum, Simon Buckingham and Chen-Burger, Yun-Heh and Dalton, Jeff and De Roure, David and Eisenstadt, Marc and Frey, Jeremy and Komzak, Jiri and Michaelides, Danius and Page, Kevin and Potter, Stephen and Shadbolt, Nigel and Tate, Austin}, title = {Collaboration in the Semantic Grid: a Basis for e-Learning}, booktitle = {Grid Learning Services (GLS'2004) at the 7th International Conference on Intelligent Tutoring Systems Workshop (ITS'2004)}, pages = {1-12}, } @misc{bandara2008-pragmatic, author = {Bandara, Ayomi and Payne, Terry and De Roure, David and Gibbins, Nicholas and Lewis, Tim}, title = {A Pragmatic Approach for the Semantic Description and Matching of Pervasive Resources}, abstract = {The increasing popularity of personal wireless devices has raised new demands for the efficient discovery of heterogeneous devices and services in pervasive environments. With the advancement of the electronic world, the diversity of available services is increasing rapidly. %This raises new demands for the efficient discovery and location of heterogeneous services and resources in dynamically changing environments. Traditional approaches for service discovery describe services at a syntactic level and the matching mechanisms available for these approaches are limited to syntactic comparisons based on attributes or interfaces. In order to overcome these limitations, there has been an increased interest in the use of semantic description and matching techniques to support effective service discovery. In this paper, we present a semantic matching approach to facilitate the discovery of device-based services in pervasive environments. The approach includes a ranking mechanism that orders services according to their suitability and also considers priorities placed on individual requirements in a request during the matching process. The solution has been systematically evaluated for its retrieval effectiveness and the results have shown that the matcher results agree reasonably well with human judgement. Another important practical concern is the efficiency and the scalability of the semantic matching solution. Therefore, we have evaluated the scalability of the proposed solution by investigating the variation in matching time in response to increasing numbers of advertisements and increasing request sizes, and have presented the empirical results.}, keywords = {Semantic Matching, Pervasive Computing}, year = {2008} } @article{bandara2010-19, author = {Bandara, Ayomi and Payne, Terry and De Roure, David and Gibbins, Nicholas and Lewis, Tim}, title = {A pragmatic approach for the semantic description and matching of pervasive resources}, journal = {International Journal of Pervasive Computing and Communication}, volume = {6}, number = {1}, pages = {19-46}, abstract = {There has been an increased interest in the use of semantic description and matching techniques, to support service discovery and to overcome the limitations in the traditional syntactic approaches. However, the existing semantic matching approaches lack certain desirable properties that must be present in an effective solution to support service discovery. We present a semantic description and matching approach to facilitate resource discovery in pervasive environments; the approach includes a ranking mechanism that orders services according to their suitability and also considers priorities placed on individual requirements in a request. The solution has been evaluated for its effectiveness and the results have shown that the matcher results agree reasonably well with human judgement. The solution was also evaluated for its efficiency/scalability and from the experimental results obtained; we can observe that for most practical situations, matching time can be considered acceptable for reasonable numbers of advertisements and request sizes. The proposed approach improves existing semantic matching solutions in several key aspects. Specifically; it presents an effective approximate matching and ranking criterion and incorporates priority consideration in the matching process. As shown in the evaluation experiments, these features significantly improves the effectiveness of semantic matching.}, year = {2010} } @misc{bandara2007-semantic, author = {Bandara, Ayomi and Payne, Terry and De Roure, David and Lewis, Tim}, title = {A Semantic Approach for Description and Ranked Matching of Services in Pervasive Environments}, abstract = {With the recent developments in technology, new and diverse devices are being introduced into the pervasive world. This has raised new challenges for the discovery of devices and their services in dynamic environments. The existing approaches such as Jini [AOSJ99], UPnP [UPnP06], etc., describe services at a syntactic level and the matching mechanisms in these approaches are limited to syntactic comparisons based on attributes or interfaces. In order to overcome the limitations of these approaches, there has been an increasing interest in the use of Semantic Web technologies to support the description and matching of services. This paper proposes a semantic matching framework to facilitate effective discovery of device based services in pervasive environments. This offers a ranking mechanism that will order the available services in the order of their suitability; the evaluation of the experimental results have indicated that the results correlate well with human perception.}, keywords = {service matching, semantic web, pervasive computing}, year = {2007} } @article{barillari2007-2577, author = {Barillari, Caterina and Taylor, Justine and Viner, Russell and Essex, Jonathan W.}, title = {Classification of water molecules in protein binding sites}, journal = {Journal of the American Chemical Society}, volume = {129}, number = {9}, pages = {2577-2587}, abstract = {Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.}, keywords = {novo ligand design, free-energy, rational design, am1-bcc model, potent, factor xa, generation, efficient, complexes, selective inhibitors, drug design}, year = {2007} } @misc{bently2010-driving, author = {Bently, L. and Cook, N. and Frey, J. and Derclaye, E. and Donkin, R. and Egan, G. and Holderness, M. and Hudson, L.J. and Kelani, R. and Korn, N. and Mateer, M. and Neylon, C. and Roberts, D. and Smith, V.}, title = {Driving UK Research. Is copyright a help or a hindrance}, year = {2010} } @techreport{bicarregui2006-vision, author = {Bicarregui, Juan and Boulderstone, Richard and Estelle, Lorraine and Frey, Jeremy and Jacobs, Neil and Kilbride, William and Matthews, Brian and McGreevy, Robert}, title = {20/20 Vision: an e-Infrastructure for the next decade. Report of the Data and Information Creation Working Group to the e-Infrastructure Steering Group}, type = {Other}, abstract = {We cover 5 aspects of data creation: 1. The nature of the data itself 2. The creation of data by physical research 3. The creation of data by e-research 4. The creation of data by digitization or repurposing from other sources 5. The integration and certification of data Throughout the document by data we mean information and data. For each topic we give current issues and discuss the functionality to be provided by the future e-infrastructure. We then give outline of some new aspects of the programme of work required to achieve it. We conclude with some general comments on implementing the programme work and some “don’t needs” .}, year = {2006} } @techreport{biedermann2009-optimal, author = {Biedermann, Stefanie and Woods, David C.}, title = {Optimal designs for generalised nonlinear models with application to second harmonic generation experiments}, type = {Working Paper}, year = {2009} } @misc{blower2010-blogmydata, author = {Blower, J. and Santokhee, A. and Frey, J. and Milsted, A.}, title = {BlogMyData: A Virtual Research Environment for collobaroative visualization of environmental data}, year = {2010} } @techreport{borda2006-report, author = {Borda, Ann and Careless, Jason and Dimitrova, Maia and Fraser, Michael and Frey, Jeremy and Hubbard, Paul and Goldstein, Stéphane and Pung, Caroline and Shoebridge, Michele and Wiseman, Norman}, title = {Report of the Working Group on Virtual Research Communities for the OST e-Infrastructure Steering Group}, note = {VRC final report}, type = {Other}, abstract = {Virtual Research Communities (VRC) are a new concept but early research suggests that they have the potential to open exciting new opportunities to collaborate in research and thus realise significant gains at institutional, national and international levels. International comparisons have revealed that the UK is well advanced in its understanding of the area and has the world’s best structured programme of developments under way. Further programmes to develop their full potential need to examine issues of human behaviour, the role of government and other policy makers and closer links with commercial organisations, as well as continuing to pursue development of technology and standards. Five inter-related programmes of work are recommended to maintain the UK’s leading position in this area, and retain our ability to carry out world-class research: 1.Establish a major programme of activities to understand the behavioural and social issues associated with greater take-up and transferability of developments in VRCs. The importance of reflecting the real needs, habits, preferences and aspirations of researchers themselves cannot be underestimated (see 6.1). 2.Continue and enhance current VRE development programmes to explore and understand concepts, techniques and their applications to e-Science and research, using opportunities for joint international programmes where possible (see 6.2). 3.Extend the e-framework activities of the JISC to encompass the full range of requirements of a VRC and establish whether a single, generic framework is possible or whether several, discipline-based frameworks are necessary (see 6.3) 4.Encourage greater cooperation between research and the commercial sector to ensure good practice in computer-based collaboration in business enterprises can be transferred into e-Science, to provide a vehicle for developing user-friendly commercial VRE applications and to enhance knowledge transfer activities (see 6.4). 5.Establish a task force to monitor developments in VRCs and similar activities in e-Science to recommend to government and funding organisations how policies and reward mechanisms can be shaped to promote take-up of opportunities, and to encourage the development of young researchers able to use the full capabilities of e-Science when they enter their field (see 6.5).}, year = {2006} } @misc{borkum2010-integration, author = {Borkum, M. and Coles, S. and Frey, J.}, title = {Integration of oreChem with e-Crystals Repository for Crystal Structures}, year = {2010} } @inproceedings{borkum2010 (accepted)-semantic-bad1, author = {Borkum, M. and Coles, S. and Frey, J. and Lagoze, C.}, title = {A Semantic eScience Platform for Chemistry}, } @inproceedings{borkum2010-using, author = {Borkum, M. and Coles, S. and Lagoze, C. and Frey, J.}, title = {Using oreChemexperiments ontology: Planning and enacting chemistry}, booktitle = {ACS RDF Symposium}, } @inproceedings{borkum2010 (accepted)-orechem-bad2, author = {Borkum, M. and Lagoze, C. and Coles, S. and Frey, J.}, title = {oreChem: Planning and Enacting Chemsitry on the Semantic Web}, booktitle = {Microsoft e-Science}, } @inproceedings{buckinghamshum2002-coakting, author = {Buckingham Shum, S. and De Roure, D. and Eisenstadt, M. and Shadbolt, N. and Tate, A.}, title = {CoAKTinG: Collaborative Advanced Knowledge Technologies in the Grid}, booktitle = {Second Workshop on Advanced Collaborative Environments}, } @article{christensen2003-286, author = {Christensen, Stefan W.}, title = {Ensemble Construction via Designed Output Distortion}, journal = {Lecture Notes in Computer Science}, volume = {2709}, pages = {286-295}, note = {Proc. 4th Int. Workshop Multiple Classifier Systems, Guildford, Surrey, UK, June 11-13 2003}, abstract = {A new technique for generating regression ensembles is introduced in the present paper. The technique is based on earlier work on promoting model diversity through injection of noise into the outputs; it differs from the earlier methods in its rigorous requirement that the mean displacements applied to any data points output value be exactly zero. It is illustrated how even the introduction of extremely large displacements may lead to prediction accuracy superior to that achieved by bagging. It is demonstrated how ensembles of models with very high bias may have much better prediction accuracy than single models of the same bias-defying the conventional belief that ensembling high bias models is not purposeful. Finally is outlined how the technique may be applied to classification.}, year = {2003} } @article{christensen2004-39, author = {Christensen, Stefan W. and Sinclair, Ian and Reed, Philippa A. S.}, title = {Designing committees of models through deliberate weighting of data points}, journal = {Journal of Machine Learning Research}, volume = {4}, number = {1}, pages = {39-66}, year = {2004} } @misc{coles2008-experiences, author = {Coles, Simon and Carr, Leslie and Frey, Jeremy}, title = {Experiences with repositories and blogs in laboratories}, keywords = {scientific data repositories, e-science, cyberinfrastructure, preservation}, year = {2008} } @misc{coles2006-185, author = {Coles, Simon and Frey, Jeremy and Milsted, Andrew}, title = {Curation of chemistry from laboratory to publication: “The curation of laboratory experimental data as part of the overall data lifecycle”}, publisher = {National e-Science Centre}, pages = {185-192}, abstract = {The paper will illustrate the “CombeChem Project” experience of supporting the chemical data lifecycle, from inception in the laboratory to organization of the data from the chemical literature. The paper will follow the different parts of the data lifecycle, beginning with a discussion of how the laboratory data could (or should) be recorded, and enriched with appropriate metadata, so as to ensure that curated data can be understood within its original context when subsequently accessed, as it is generated (the ideal of “Autonomic Annotation@Source”). Intrinsic to our argument is the recording of the context as well as the data, and maintaining access to the data in the most flexible form for potential future re-use for purposes that are not recognised when the data was collected. This is likely to involve many routes to dissemination, with data and ideas being treated by parallel but linked methods, which will influence traditional approaches to publication and dissemination, giving rise to a Grid style access to the information working across several administrative domains summarized by the concept of “Publication@Source”.}, keywords = {eprints, data, crystalography, provenance, dissemination, semantic web}, year = {2006} } @misc{coles2008-ecrystals, author = {Coles, Simon and Lyon, Liz}, title = {The eCrystals Federation}, publisher = {OR08}, abstract = {This paper presents the eCrystals Federation project, which represents an entire community engagement in a deployment of the 'open data repository' model supporting the research data lifecycle. The project is establishing a number of open data repositories across a variety of crystallography laboratories around the world, based on the concepts proved by the eBank-UK project and the Southampton eCrystals data repository. This whole community involvement involves a collaboration between crystallographers, archivists, librarians, subject repositories, data centres, publishers and information providers. Building on this data repository federation we present an analysis of the surrounding issues which primarily include community interactions, interoperability, advocacy, sustainability and curation.}, year = {2008} } @misc{coles2007-repository, author = {Coles, Simon J.}, title = {A repository based framework for capture, management, curation and dissemination of research data}, publisher = {University of Southampton, UK}, abstract = {Based on the e-Bank-UK (http://www.ukoln.ac.uk/projects/ebank-uk) and Repository for the Laboratory, R4L (http://r4l.eprints.org) projects, a working model for a scientific data capture, management, curation and dissemination framework will be presented. The eCrystals repository has been constructed on an institutional repository platform and has been configured to ingest small molecule crystallographic data generated by the UK National Crystallography Service, whilst the R4L repository supports a range of different types of analytical chemistry data. This model addresses the current escalating ‘data deluge’ problem through integration of digital libraries technologies with both the research laboratory and also with established publication and dissemination routes. The institutional model provides a potential mechanism for the long term archival and availability of information in a manner that enables the capture of its research data output through integration into the laboratory environment. The repository ingest process ensures full capture of laboratory data and effective metadata creation at the point it is generated. A private archive provides effective management of the data, whilst an embargo procedure allows dissemination of results through a public archive in a timely manner. A schema for the dissemination of crystallographic data has been devised through consultation with the community which enables effective harvesting by data centres and third party aggregator services. The use of persistent identifiers provides a mechanism to permanently link the conventional scholarly article with its associated underlying dataset. Current work is investigating the issues associated with the construction of a federation of data repositories (institutional and subject based) operating on different software platforms and its long term integration into the publishing and chemical information provision processes.}, year = {2007} } @article{coles2007-3, author = {Coles, S.J.}, title = {The Repository for the Laboratory (R4L) Project}, journal = {DLib Magazine}, volume = {13}, pages = {3-4}, year = {2007} } @article{coles2006-science, author = {Coles, S. J. and Frey, J.G. and Hursthouse, M.B. and Light, M.E. and Milsted, A.J. and Carr, L.A. and De Roure, D. and Gutteridge, C.J. and Mills, H.R. and Meacham, K.E. and Surridge, M. and Lyon, E. and Heery, R. and Duke, M. and Day, M.}, title = {An E-Science Environment for Service Crystallographys from Submission to Dissemination}, journal = {Journal of Chemical Information and Modeling}, year = {2006} } @article{coles2006-1006, author = {Coles, Simon J. and Frey, Jeremy G. and Hursthouse, Michel B. and Light, Mark E. and Milsted, Andrew J. and Carr, Leslie A. and De Roure, David and Gutteridge, Christopher J. and Mills, Hogo R. and Meacham, Ken E. and Surridge, Michael and Lyon, Elizabeth and Heery, Rachel and Duke, Monica and Day, Michael}, title = {An e-science environment for service crystallographysfrom submission to dissemination}, journal = {Journal of Chemical Information and Modeling}, volume = {46}, number = {3}, pages = {1006-1016}, abstract = {The U.K. National Crystallography Service (NCS) has developed a prototype e-science infrastructure for the provision of a small molecule crystallography service from sample receipt to results dissemination. This paper outlines the two strands of this service, which (a) enable a user to contribute in the conduction of an experiment and (b) provide an effective route for the archival and dissemination of the arising results. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure, which seamlessly provides instantaneous feedback and the ability to remotely monitor and guide diffraction experiments and stage the diffraction data to a securely accessible location. Publication of all the data and results generated during the course of the experiment, from processed data to analyzed structures, is then enabled by means of an open access data repository. The repository publishes its content through established digital libraries' protocols, which enable harvester and aggregator services to make the data searchable and accessible.}, year = {2006} } @inproceedings{coles2002-grid, author = {Coles, S.J. and Frey, J.G. and Hursthouse, M.B. and Light, M.E. and Surridge, M. and Meacham, K.E. and Marvin, D.J. and De Roure, D.C. and Mills, H. R.}, title = {Grid/Web enhancements to the National Crystallographic Service: experiences with an interactive e-Science demonstrator}, booktitle = {Euroweb 2002 - the Web and the GRID: from e-Science to e-Business}, editor = {Hopgood, F. R. A. and Matthews, B. and Wilson, M. D.}, series = {ElectronicWorkshops in Computing}, publisher = {British Computer Society}, } @misc{coles2006-ecrystals, author = {Coles, Simon J. and Hursthouse, Michael B. and Frey, Jeremy G. and Milsted, Andrew J. and Carr, Leslie A. and Koch, Traugott and Lyon, Elizabeth and Duke, Monica}, title = {eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data}, abstract = {Recently the funding councils in the UK stated that ‘the data underpinning the published results of publically-funded research should be made available as widely and rapidly as possible’. Thirty years ago a research student would present about five crystal structures as their PhD thesis, however with modern technologies and good crystals this can now be achieved in the timespan of a single morning. This increase in pace of generation further exacerbates a problem in the communication of the results. Additionally, the general route for the publication of a crystal structure report is coupled with and often governed by the underlying chemistry and is therefore subject to the lengthy peer review process and tied to the timing of the publication as a whole. This bottleneck in the dissemination of crystal structure data hinders the potential growth of databases and the data mining studies that are reliant on these collections. Just 500,000 small unit cell crystal structures are available in the CSD, ICSD & CRYSMET databases, while it is estimated that at least twice this number have been determined in research laboratories and are likely to remain unpublished. In addition, publication in the mainstream literature still offers only indirect (and often subscription controlled) access to this data. The work of the eBank-UK project (http://www.ukoln.ac.uk/projects/ebank-uk/) has addressed this problem by establishing an institutional data repository that supports, manages and disseminates metadata relating to the crystal structure data it contains (i.e. all the files generated during a crystal structure determination). This process alters the traditional method of peer review by openly providing crystal structure data where the reader or user may directly check correctness and validity. The repository (http://ecrystals.chem.soton.ac.uk) makes available all the raw, derived and results data from a crystallographic experiment with little further researcher effort after the creation of a normal completed structure in a laboratory archive. Not only does this approach allow rapid release of crystal structure data into the public domain, but it can also provide mechanisms for value added services that allow rapid discovery of the data for further studies and reuse, whilst ownership of the data is retained by the creator. The details of the preparation of data, upload process, files supported and automatic report generation will be presented. Additionally, the process whereby metadata relating to each archive entry is disseminated, using current Digital Libraries technologies, for discovery and reuse by will be summarised. Strategies for the installation of archives at new sites, the construction of harvesting and aggregator services and the interaction with crystallographic data holding bodies, such as IUCr and CCDC, will also be outlined. Additionally links to educational tools, specifically the Schools eMalaria project (http://emalaria.soton.ac.uk), will also be presented.}, keywords = {electronic publishing, crystallographic databases, computer networking}, year = {2006} } @article{deoliveirabranco2008-775, author = {de Oliveira Branco, Miguel and Zaluska, Ed and De Roure, David}, title = {Managing very-large distributed datasets}, journal = {Lecture Notes in Computer Science}, volume = {5331}, pages = {775-792}, abstract = {In this paper, we introduce a system for handling very large datasets, which need to be stored across multiple computing sites. Data distribution introduces complex management issues, particularly as computing sites may make use of different storage systems with different internal organizations. The motivation for our work is the ATLAS Experiment for the Large Hadron Collider (LHC) at CERN, where the authors are involved in developing the data management middleware. This middleware, called DQ2, is charged with shipping petabytes of data every month to research centers and universities worldwide and has achieved aggregate throughputs in excess of 1.5 Gbytes/sec over the wide-area network. We describe DQ2’s design and implementation, which builds upon previous work on distributed file systems, peer-to-peer systems and Data Grids. We discuss its fault tolerance and scalability properties and briefly describe results from its daily usage for the ATLAS Experiment.}, year = {2008} } @article{deroure2003-77, author = {De Roure, David}, title = {On Self-Organization and the Semantic Grid}, journal = {IEEE Intelligent Systems}, volume = {18}, number = {4}, pages = {77-79}, note = {Trends & Controversies}, month = {July-August 2003}, year = {2003} } @inproceedings{deroure2003-70, author = {De Roure, David}, title = {Semantic Grid and Pervasive Computing}, booktitle = {GGF9 Semantic Grid Workshop}, editor = {Roure, David De and Goble, Carole and Fox, Geoffrey}, pages = {70-76}, } @article{deroure2009-science, author = {De Roure, David}, title = {e-Science and the Web}, journal = {IEEE Computer}, year = {2009} } @inbook{deroure2003-65, author = {De Roure, D. and Baker, M.A. and Jennings, N.R. and Shadbolt, N.R.}, title = {The evolution of the Grid}, booktitle = {Grid computing - making the global infrastructure a reality}, editor = {Berman, F. and Fox, G. and Hey, A. J. G.}, publisher = {John Wiley and Sons Ltd}, pages = {65-100}, year = {2003} } @misc{deroure2007-three, author = {De Roure, David and Frey, Jeremy}, title = {Three Perspectives on Collaborative Knowledge Acquisition in e-Science}, abstract = {Through a series of e-Science projects we have explored the creation of a complete digital chain of knowledge from the scientific laboratory through to scholarly research output. In this paper we describe this experience and we discuss three perspectives on collaborative knowledge acquisition within the context of this cyberinfrastructure: Publication at Source, Record and Reuse, and Annotation.}, year = {2007} } @article{deroure2004-science, author = {De Roure, David and Gil, Yolanda and Hendler, Jim}, title = {E-Science Special Issue}, journal = {IEEE Intelligent Systems}, volume = {19}, number = {1}, year = {2004} } @inbook{deroure2005-building, author = {De Roure, David and Goble, Carole}, title = {Building the Semantic Grid}, booktitle = {Engineering the Grid: status and perspective}, editor = {Dongarra, J. and Zima, H. and Hoisie, A. and Yang, L. and Martino, B. Di}, publisher = {American Scientific Publishers}, year = {2005} } @misc{deroure2008-201, author = {De Roure, David and Goble, Carole}, title = {Re-evaluating the Grid: the social life of programs}, publisher = {Springer-Verlag New York Inc.}, pages = {201-212}, abstract = {This paper discusses programming the Grid in the space between the Grid infrastructure and those using it to conduct scientific research. Rather than looking at any particular grid programming model, we consider the need to address ‘usability’ of programming solutions in this space. As a case study we consider a popular solution; i.e. scientific workflows, and we reflect on Web 2.0 approaches. We suggest that broad adoption of Grid infrastructure is dependent on ease of programming in this space.}, keywords = {Grid, Scientific Workflow, Web 2.0}, year = {2008} } @misc{deroure2010-anchors, author = {De Roure, David and Goble, Carole}, title = {Anchors in Shifting Sand: the Primacy of Method in the Web of Data}, abstract = {Is the Linkded Data Web ready for people to use open government data or scientific datasets to do reproducible research? For one thing, practice and support for versioning have not yet emerged. In this paper we propose that we also need the "methods" by which results are obtained to be first class citizens in the Web of Data, so that they can be shared and discussed and so that results can be explained, interpreted and reused. We discuss our experience of the myExperiment.org Web Site, a social network of people sharing reusable methods for processing research data, with mechanisms for discovering, sharing, enacting, versioning and curation.}, keywords = {linked data, myExperiment, versioning}, year = {2010} } @article{deroure2004-65, author = {De Roure, D. and Hendler, J.A.}, title = {E-Science: the Grid and the Semantic Web}, journal = {IEEE Intelligent Systems}, volume = {19}, number = {1}, pages = {65-71}, year = {2004} } @techreport{deroure2001-research, author = {De Roure, D. and Jennings, N. R. and Shadbolt, N. R.}, title = {Research Agenda for the Semantic Grid - A Future e-Science Infrastructure}, institution = {National e-Science Centre}, number = {UKeS-2002-02}, month = {December}, year = {2001} } @inbook{deroure2003-437, author = {De Roure, D. and Jennings, N.R. and Shadbolt, N.R.}, title = {The Semantic Grid - A future e-Science infrastructure}, booktitle = {Grid Computing - Making the Global Infrastructure a Reality}, editor = {Berman, F. and Fox, G. and Hey, A. J. G.}, publisher = {John Wiley and Sons Ltd.}, pages = {437-470}, year = {2003} } @article{deroure2005-669, author = {De Roure, D. and Jennings, N.R. and Shadbolt, N.R.}, title = {The Semantic Grid: Past, Present, and Future}, journal = {Proceedings of the IEEE}, volume = {93}, number = {3}, pages = {669-681}, year = {2005} } @inproceedings{dialani2002-889, author = {Dialani, V. and Miles, S. and Moreau, L. and Roure, D. De and Luck, M.}, title = {Transparent, fault tolerance for web services based architectures, Lecture Notes in Computer Science,Springer-Verlag, 2002}, booktitle = {Euro-Par 2002. 8th International Euro-Par Conference}, editor = {Monien, B. and Feldman, R.}, publisher = {Springer-Verlag GmbH}, volume = {2400}, pages = {889-898}, } @misc{duke2005-46, author = {Duke, Monica and Day, Michael and Heery, Rachel and Carr, Leslie A. and Coles, Simon J.}, title = {Enhancing access to research data: the challenge of crystallography}, publisher = {ACM}, pages = {46-55}, year = {2005} } @article{fey2006-912, author = {Fey, N. and Harris, S. E. and Harvey, J. N. and Orpen, A. G.}, title = {Adding Value to Crystallographically-Derived Ligand Knowledge Bases}, journal = {J. Chem. Inf. Model.}, volume = {46}, pages = {912-929}, year = {2006} } @article{fey2005-291, author = {Fey, Natalie and Tsipis, Athanassios C. and Harris, Stephanie E. and Harvey, Jeremy N. and Orpen, A. Guy and Manson, Ralph A.}, title = {Development of a Ligand Knowldege Base, Part 1: Computational Descriptors for Phosphorus Donor Ligands}, journal = {Chemistry - A European Journal}, volume = {12}, number = {1}, pages = {291 - 302}, year = {2005} } @article{frey2008-curation, author = {Frey, Jeremy}, title = {Curation of laboratory experimental data as part of the overall data lifecycle}, journal = {International Journal of Digital Curation}, volume = {3}, number = {1}, abstract = {The explosion in the production of scientific data in recent years is placing strains upon conventional systems supporting integration, analysis, interpretation and dissemination of data and thus constraining the whole scientific process. Support for handling large quantities of diverse information can be provided by e-Science methodologies and the cyber-infrastructure that enables collaborative handling of such data. Regard needs to be taken of the whole process involved in scientific discovery. This includes the consideration of the requirements of the users and consumers further down the information chain and what they might ideally prefer to impose on the generators of those data. As the degree of digital capture in the laboratory increases, it is possible to improve the automatic acquisition of the ‘context of the data’ as well as the data themselves. This process provides an opportunity for the data creators to ensure that many of the problems they often encounter in later stages are avoided. We wish to elevate curation to an operation to be considered by the laboratory scientist as part of good laboratory practice, not a procedure of concern merely to the few specialising in archival processes. Designing curation into experiments is an effective solution to the provision of high-quality metadata that leads to better, more re-usable data and to better science.}, keywords = {laboratory data, curation, escience, data life cycle}, year = {2008} } @inbook{frey2006-270, author = {Frey, Jeremy and De Roure, David and Taylor, Kieron and Essex, Jonathan and Mills, Hugo and Zaluska, Ed}, title = {CombeChem: a case study in provenance and annotation using the Semantic Web}, booktitle = {Provenance and Annotation of Data}, editor = {Moreau, Luc and Foster, Ian}, publisher = {Springer}, volume = {4145/2006}, pages = {270-277}, abstract = {The CombeChem e-Science project has demonstrated the advantages of using Semantic Web technology, in particular RDF and triplestores, to describe and link diverse and complex chemical information, covering the whole process of the generation of chemical knowledge from inception in the synthetic chemistry laboratory, through analysis of the materials made which generates physical measurements, computations based on this data to develop interpretations, and the subsequent dissemination of the knowledge gained. The project successfully adopted a strategy of capturing semantic annotations ‘at source’ and establishing schema and ontologies based closely on current operational practice in order to facilitate implementation and adoption. The resulting ‘Semantic Data Grid’ comprises around 45 million RDF triples across multiple stores.}, year = {2006} } @inbook{frey2003-395, author = {Frey, Jeremy G.}, title = {Comb-e-Chem - an e-science research project}, booktitle = {EuroQSAR 2002 Designing Drugs and Crop Protectants: processes, problems and solutions}, editor = {Ford, Martyn and Livingstone, David and Dearden, John and Van der Waterbeemd, Han}, publisher = {Blackwell}, address = {Oxford, UK}, pages = {395-398}, year = {2003} } @article{frey2004-1024, author = {Frey, J. G.}, title = {Dark Lab or Smart Lab: The Challenges for 21st Century Laboratory Software}, journal = {Org. Proc. Res. Dev.}, volume = {8}, number = {6}, pages = {1024-1035}, year = {2004} } @misc{frey2006-combechem, author = {Frey, Jeremy G.}, title = {CombeChem: semantic support for the chemical information life cycle}, publisher = {American Chemical Society}, note = {CombeChem output}, abstract = {“CombeChem” provided experience of e-science semantic support for the chemical data lifecycle, from inception in the laboratory to dissemination of data, showing how laboratory data should be recorded, using electronic laboratory notebooks, enriched with appropriate metadata, to ensure information can be correctly understood when subsequently accessed, (“Annotation@Source”). Chemical information results from a chain of analysis & data integration. Current chemical data storage methodologies place restrictions on the use of this data; absence of sufficient high-quality metadata, particularly in a computer readable form, prevents automated access to the data without significant human intervention. The Semantic web approach enhances the data by making use of unique identifiers and relationships described with RDF. This informs new routes to dissemination, with data and ideas being treated by parallel but linked methods; a Grid style access to information spread across several administrative domains - individual laboratories to national repositories - the concept of “Publication@Source”.}, keywords = {CombeChem, e-science, RDF, ELN, grid, cyber-infrastructure, crystallography, e-print, dissemination, end-to-end, publication@source, repositories, semantics}, year = {2006} } @misc{frey2006-curation, author = {Frey, Jeremy G.}, title = {The curation of laboratory experimental data as part of the overall data lifecycle}, publisher = {Digital Curation Centre}, abstract = {The explosion in the production of scientific data in recent years is straining the conventional systems for integration, analysis, interpretation and dissemination of the data and constraining the whole scientific process. Support for handling the large quantities of diverse information can be provided by the e-science methodologies and the cyber-infrastructure that enables collaborative handling of this data. Regard needs to be taken of the whole process involved in the scientific discovery including consideration of the requirements of the users and consumers further down the information chain might ideally like to impose on the early stage generators of the data. As the degree of digital capture in the laboratory increases it is possible to improve the automatic acquisition of the ‘context of the data’ as well as the data itself. This provides an opportunity the data creators to ensure that many of the problems often encountered by data curators at later stages are avoided. We wish to elevate curation to something to be considered by the laboratory scientist as part of good laboratory practice, not something to be something only of concern to the few specialising in archival processes.}, keywords = {digital curation, chemistry, laboratory notebooks, semantics, comebchem, metadata, blogs}, year = {2006} } @misc{frey2006-future, author = {Frey, Jeremy G.}, title = {Future Lab - "Smart not Dark"}, publisher = {International Quality and Productivity Center (IQPC)}, note = {CombeChem Output}, abstract = {Discussion of the role of Electronic Laboratory Notebooks (ELN) is the future chemistry laboratories}, keywords = {Smart Lab, ELN, Semantic, RDF, Grid, e-Science, HCI, lab journal, context}, year = {2006} } @misc{frey2007-science, author = {Frey, Jeremy G.}, title = {Science as a collaborative process - the Scholarly Knowledge Cycle and Blogging the Laboratory (Smartlab 2.5?)}, publisher = {Open Grid Forum}, abstract = {Science as a collaborative process - the Scholarly Knowledge Cycle and Blogging the Laboratory (Smartlab 2.5?)}, year = {2007} } @misc{frey2008-blogs, author = {Frey, J. G.}, title = {Blogs, logs and pods}, year = {2008} } @inbook{frey2009-malaria, author = {Frey, Jeremy G.}, title = {e-Malaria}, booktitle = {Research in a Connected World}, editor = {Voss, A. and Vander Meer, E. and Ferguson, D.}, publisher = {Conexions Web site}, year = {2009} } @article{frey2009-522, author = {Frey, Jeremy G.}, title = {The value of the semantic web in the laboratory}, journal = {Drug Discovery Today}, volume = {14}, number = {11-12}, pages = {522-561}, abstract = {The Semantic Web is beginning to impact on the wider chemical and physical sciences, beyond the earlier adopted bio-informatics. While useful in large-scale data driven science with automated processing, these technologies can also help integrate the work of smaller scale laboratories producing diverse data. The semantics aid the discovery, reliable re-use of data, provide improved provenance and facilitate automated processing by increased resilience to changes in presentation and reduced ambiguity. The Semantic Web, its tools and collections are not yet competitive with well-established solutions to current problems. It is in the reduced cost of instituting solutions to new problems that the versatility of Semantic Web-enabled data and resources will make their mark once the more general-purpose tools are more available.}, keywords = {semantic web, chemistry laboratory, electronic laboratory notebooks}, year = {2009} } @inbook{frey2003-945, author = {Frey, J. G. and Bradley, M. and Essex, J.W. and Hursthouse, M.B. and Lewis, S.M. and Luck, M.M. and Moreau, L. and De Roure, D.C. and Surridge, M. and Welsh, A.H.}, title = {Combinatorial chemistry and the Grid}, booktitle = {Grid computing: making the global infrastructure a reality}, editor = {Berman, Fran and Hey, Anthony J. G. and Fox, Geoffrey C.}, series = {Wiley Series in Communications Networking and Distributed Systems}, publisher = {John Wiley & Sons Ltd.}, address = {Chichester, UK}, pages = {945-962}, year = {2003} } @inproceedings{frey2002-publication, author = {Frey, J.G. and De Roure, D. and Carr, L.A.}, title = {Publication At Source: Scientific Communication from a Publication Web to a Data Grid}, booktitle = {Euroweb 2002 Conference, The Web and the GRID: from e-science to e-business}, publisher = {BCS}, } @inproceedings{frey2003-context, author = {Frey, J. G. and De Roure, D. and schraefel, m. c. and Mills, H. and Fu, H. and Peppe, S. and Hughes, G. and Smith, G. and Payne, T. R.}, title = {Context Slicing the Chemical Aether}, booktitle = {First International Workshop on Hypermedia and the Semantic Web}, editor = {Millard, D.}, } @misc{frey2006-computer, author = {Frey, Jeremy G. and Gledhill, Robert J. and Milsted, Andrew and Kent, Sarah and Essex, Jon W. and Richards, G.W.}, title = {A computer-aided drug discovery system for chemistry teaching}, publisher = {American Chemical Society}, abstract = {The e-Malaria Project is designed to teach aspects of chemistry through exposure to drug design concepts. Initially it was a way to bring together school students with university researchers in the hunt for a new antimalaria drug. The design challenge offered is to use a distributed drug search and selection system to design potential antimalaria drugs accessed via an accessible Web interface. This e-science project displays the results of the trials in an accessible manner, giving students an opportunity for discussion and debate both with peers and with university contacts. The project was implemented using distributed computing techniques. This provides access to greater computing power and allows a much more complex and detailed formulation of the drug design problem to be tackled for research, teaching, and learning. The project is useful in undergraduate teaching where the system was used to support investigations of drug modeling and QSAR approaches.}, keywords = {malaria, grid, e-science, e-learning}, year = {2006} } @inproceedings{frey2004-less, author = {Frey, J. G. and Hughes, G. V. and Mills, H. R. and schraefel, m. c. and Smith, G. M. and De Roure, D.}, title = {Less is More: Lightweight Ontologies and User Interfaces for Smart Labs}, booktitle = {UK eScience All Hands Meeting}, } @inproceedings{fu2004-140, author = {Fu, H and Frey, J G}, title = {Semantic description and tracking of analysis of chemical data}, booktitle = {Second International Workshop on the Knowledge Grid and Grid Intelligence}, editor = {Zhuge, H. and Cheung, W. K. and Liu, J.}, pages = {140-149}, } @article{gelbrich2005-324, author = {Gelbrich, T. and Hursthouse, M.B.}, title = {A versatile procedure for the identification, description and quantification of structural similarity in molecular crystals}, journal = {Cryst. Eng. Comm}, volume = {7}, pages = {324-336}, year = {2005} } @article{gelbrich2004-1451, author = {Gelbrich, Thomas and Threlfall, Terence L. and Huth, Susanne and Seeger, Eva and Hursthouse, Michael B.}, title = {Investigation of Structural Relationships between Racemic Alkali and Ammonium Hydrogen Tartrates and their Chiral Counterparts}, journal = {Zeitschrift für anorganische und allgemeine Chemie}, volume = {630}, number = {10}, pages = {1451-1458}, year = {2004} } @article{geldhill2008-225, author = {Geldhill, Robert and Kent, Sarah and Milsted, Andrew and Chapman, Richard and Essex, Jonathan. W. and Frey, Jeremy. G.}, title = {e-Malaria: the schools Malaria project}, journal = {Concurrency and Computation: Practice & Experience}, volume = {20}, number = {3}, pages = {225-238}, abstract = {e-Malaria (http://emalaria.soton.ac.uk/) aims to bring together 16-18 year old school students with university researchers to explain aspects of computational drug design using the example of the hunt for a new anti-Malaria drug. Malaria kills a child every 30 seconds, and 40% of the world's population lives in countries where the disease is endemic. Resistance to existing drugs is increasing and there is a growing need for new compounds. This challenge is being offered to school students who will use a distributed drug search and selection system via a Web interface to design potential drugs. The project makes use of industrial code for the docking study (GOLD) and as such presents valuable lessons in how to achieve the integration of industrial programs into a free outreach environment. The results of the trials are displayed in an accessible manner, giving students an opportunity for discussion and debate both with peers and with university contacts. The initial project has been extended to provide a similar challenge for undergraduate chemists as part of a chemical informatics course at a level relevant to more advances chemical skills.}, keywords = {sites, malaria, grid, genetic algorithm, e-learning, docking, docking, recognition}, year = {2008} } @article{gerber2004-1427, author = {Gerber, Stefan and Krautscheid, Harald and Gelbrich, Thomas and Vollmer, Heike}, title = {Synthesis and Crystal Structures of Heterometallic AgI/FeII Coordination Polymers: (Me3PhN)2[Ag2Fe(SCN)6], (Me3PhN)6[Ag6Fe3(ECN)18] (E = S, Se) und (Me3PhN)4[Ag2Fe(SCN)8]}, journal = {Zeitschrift für anorganische und allgemeine Chemie}, volume = {630}, number = {10}, pages = {1427 - 1432}, note = {10.1002/zaac.200400138}, year = {2004} } @article{gledhill2006-960, author = {Gledhill, R. and Kent, S. and Hudson, B. and Richards, W. G. and Essex, J. W. and Frey, J. G.}, title = {A Computer-Aided Drug Discovery System for Chemistry Teaching}, journal = {J. Chem. Inf & Mod}, volume = {46}, number = {3}, pages = {960-970}, year = {2006} } @article{gledhill2006-960, author = {Gledhill, Robert and Kent, Sarah and Hudson, Brian and Richards, W. Graham and Essex, Jonathan W. and Frey, Jeremy G.}, title = {A computer-aided drug discovery system for chemistry teaching}, journal = {Journal of Chemical Information and Modeling}, volume = {46}, number = {3}, pages = {960-970}, abstract = {The Schools Malaria Project ( http://emalaria.soton.ac.uk/) brings together school students with university researchers in the hunt for a new antimalaria drug. The design challenge being offered to students is to use a distributed drug search and selection system to design potential antimalaria drugs. The system is accessed via a Web interface. This e-science project displays the results of the trials in an accessible manner, giving students an opportunity for discussion and debate both with peers and with the university contacts. The project has been implemented by using distributed computing techniques, spreading computer load over a network of machines that cross institutional boundaries, forming a grid. This provides access to greater computing power and allows a much more complex and detailed formulation of the drug design problem to be tackled for research, teaching, and learning.}, keywords = {docking}, year = {2006} } @misc{goble2006-1, author = {Goble, Carole and Corcho, Oscar and Alper, Pinar and De Roure, David}, title = {e-science and the semantic web: A symbiotic relationship}, publisher = {Springer-Verlag}, volume = {LNAI 4}, pages = {1-12}, abstract = {e-Science is scientific investigation performed through distributed global collaborations between scientists and their resources, and the computing infrastructure that enables this. Scientific progress increasingly depends on pooling know-how and results; making connections between ideas, people, and data; and finding and reusing knowledge and resources generated by others in perhaps unintended ways. It is about harvesting and harnessing the “collective intelligence” of the scientific community. The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation. Applying the Semantic Web paradigm to e-Science has the potential to bring significant benefits to scientific discovery. We identify the benefits of lightweight and heavyweight approaches, based on our experiences in the Life Sciences.}, year = {2006} } @inbook{goble2002-semantic, author = {Goble, C. and De Roure, D.}, title = {The Semantic Web and Grid Computing}, booktitle = {Real World Semantic Web Applications}, editor = {Kashyap, V. and Shklar, L.}, series = {Frontiers in Artificial Intelligence and Applications}, publisher = {IOS Press}, volume = {92}, year = {2002} } @inproceedings{goble2004-1129, author = {Goble, CA and De Roure, D.}, title = {The Semantic Grid: Myth Busting and Bridge Building}, booktitle = {16th European Conference on Artificial Intelligence (ECAI-2004)}, pages = {1129-1135}, } @article{goble2002-65, author = {Goble, C.A. and De Roure, D.}, title = {The Grid: an application of the semantic web}, journal = {ACM SIGMOD Record}, volume = {31}, number = {4}, pages = {65-70}, year = {2002} } @inbook{goble2004-431, author = {Goble, C.A. and De Roure, D. and Shadbolt, N.R. and Fernandes, A.A.A.}, title = {Enhancing Services and Applications with Knowledge and Semantics}, booktitle = {The Grid: Blueprint for a New Computing Infrastructure (2nd. ed)}, editor = {Foster, I. and Kesselman, C.}, publisher = {Morgan-Kaufmann}, pages = {431-458}, year = {2004} } @misc{greenhalgh2008-combining, author = {Greenhalgh, Chris and Glover, Kevin and Humble, Jan and Robinson, Jamie and Wilson, Steve and Frey, Jeremy and Page, Kevin and De Roure, David}, title = {Combining System Introspection with User-Provided Description to Support Configuration and Understanding of Pervasive systems}, abstract = {Pervasive computing systems such as smart spaces typically combine multiple embedded and/or mobile sensing, computing and interaction devices. A variety of distributed computing approaches are used to integrate these devices to support coordinated applications. This paper describes how simple user descriptions of (primarily) physical aspects of such a system can be combined with information from system introspection to make the system and its log recordings more understandable to potential users, as well as supporting easier configuration and monitoring, and allowing the expression of certain kinds of system behaviour that are otherwise hard to achieve.}, keywords = {Pervasive Computing, Semantic Web}, year = {2008} } @techreport{euexpertgroup2003-next, author = {Group, EU Expert}, title = {Next Generation Grid(s) 2005 – 2010}, institution = {European Commission}, month = {June}, year = {2003} } @article{guan2008-autonomic, author = {Guan, Tao and Zaluska, Ed and De Roure, David}, title = {An Autonomic Service Discovery Mechanism to Support Pervasive Device Accessing Semantic Grid}, journal = {International Journal of Autonomic Computing}, year = {2008} } @misc{guan2006-extending, author = {Guan, Tao and Zaluska, Ed and Roure, David}, title = {Extending Pervasive Devices with the Semantic Grid: A Service Infrastructure Approach}, year = {2006} } @misc{guan2007-autonomic, author = {Guan, Tao and Zaluska, Ed and Roure, David}, title = {An Autonomic Service Discovery Mechanism to Support Pervasive Device Accessing Semantic Grid}, year = {2007} } @article{hall2009-991, author = {Hall, Wendy and De Roure, David and Shadbolt, Nigel}, title = {The evolution of the Web and implications for eResearch}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {991-1001}, abstract = {The hypertext visionaries foresaw the potential of richly interlinked global information systems for advancing human knowledge. The Web provided the infrastructure to enable those ideas to become a reality, and it quickly became a platform for collaborative research and data sharing. As the Web has evolved, new ways of using it for eResearch have emerged, such as the social networking facilities enabled by Web 2.0 technologies. The next generation of the Web-the so-called Semantic Web-is now on the horizon, which will again enable new types of collaborative research to emerge. If we are to understand and anticipate these new modes of collaboration, we need a discipline that studies the Web as a whole. Web science is this discipline.}, year = {2009} } @inproceedings{heery2004-135, author = {Heery, Rachel and Duke, Monica and Day, Michael and Lyon, Liz and Coles, Simon and Frey, Jeremy and Hursthouse, Michael and Carr, Leslie and Gutteridge, Christopher}, title = {Integrating research data into the publication workflow: eBank experience}, booktitle = {PV-2004: Ensuring the Long-Term Preservation and Adding Value to the Scientific and Technical Data}, pages = {135-142}, } @article{hughes2004-1, author = {Hughes, Gareth and Mills, Hugo and Roure, David De and Frey, Jeremy G and Moreau, Luc and schraefel, mc and Smith, Graham and Zaluska, Ed}, title = {The Semantic Smart Laboratory: A system for supporting the chemical eScientist}, journal = {Org. Biomol. Chem.}, volume = {2}, pages = {1-10}, note = {DOI: 10.1039/b410075a}, year = {2004} } @article{hursthouse2004-85, author = {Hursthouse, Mike}, title = {High-throughput chemical crystallography (HTCC): meeting and greeting the combichem challenge}, journal = {Crystallography Reviews}, volume = {10}, pages = {85-96}, year = {2004} } @article{luck2004-203, author = {Luck, M. and McBurney, P. and Preist, C.}, title = {A Manifesto for Agent Technology: Towards Next Generation Computing}, journal = {Journal of Autonomous Agents and Multi-Agent Systems}, volume = {9}, number = {3}, pages = {203-252}, year = {2004} } @inproceedings{lyon2004-61, author = {Lyon, L. and Coles, S. and Carr, L. and Heery, R. and Hursthouse, M. and Gutteridge, C. and Duke, M. and Frey, J. and De Roure, D.}, title = {eBank UK Linking Research Data, Scholarly Communications and Learning}, booktitle = {GGF11 Workshop on Semantic Grid Applications}, editor = {Michaelides, Danius and Moreau, Luc}, publisher = {GGF}, pages = {61-70}, } @inproceedings{lyon2004-ebank, author = {Lyon, L. and Heery, R. and Duke, M. and Coles, S. and Frey, J. and Hursthouse, M. and Carr, L. and Gutteridge, C.}, title = {eBank UK: linking research data, scholarly communication and learning}, booktitle = {UK e-Science All Hands Meeting}, } @article{mansson2005-1791, author = {Mansson, RA and Frey, JG and Essex, JW and Welsh, AH}, title = {Prediction of properties from simulations: A re-examination with modern statistical methods}, journal = {Journal of Chemical Information and Modelling}, volume = {45}, number = {6}, pages = {1791 - 1803}, year = {2005} } @article{mansson?-statistical-bad3, author = {Mansson, R. A. and Welsh, A. H. and Fey, Natalie and Orpen, A. G.}, title = {"Statistical Modelling of a Ligand Knowledge Base"}, journal = {J. Chem. Inf. Model.}, volume = {submitted}, } @article{matthews2009-171, author = {Matthews, Brian and Duncan, Alastair and Jones, Catherine and Neylon, Cameron and Borkum, Mark and Coles, Simon and Hunter, Philip}, title = {A Protocol for Exchanging Scientific Citations}, journal = {e-Science and Grid Computing, International Conference on}, volume = {0}, pages = {171-177}, year = {2009} } @inproceedings{milsted2010 (accepted)-myexperimentalscience-bad4, author = {Milsted, A. and Frey, J. and Michaelides, D. and De Roure, D.}, title = {"MyExperimentalScience, extending the 'workflow'"}, booktitle = {Microsoft e-Science}, } @inproceedings{milsted2010 (accepted)-blogmydata-bad5, author = {Milsted, A. and Santokhee, A. and Frey, J. and Blower, J.}, title = {BlogMyData: A Virtual Research Environment for collobaorative visualization of environmental data}, booktitle = {Microsoft e-Science}, } @inproceedings{moreau2002-220, author = {Moreau, Luc}, title = {Agents for the Grid: A Comparison with Web Services (Part 1: the transport layer)}, booktitle = {Second IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID 2002)}, editor = {Bal, Henri E. and Lohr, Klaus-Peter and Reinefeld, Alexander}, publisher = {IEEE Computer Society}, pages = {220-228}, } @inproceedings{moreau2002-52, author = {Moreau, L and Avila-Rosas, A and Dialani, V and Miles, S and Liu, X}, title = {Agents for the Grid: A Comparison with Web Services (part II: Service Discovery)}, booktitle = {Workshop on Challenges in Open Agent Systems}, pages = {52-56}, } @misc{newman2009-myexperiment, author = {Newman, David and Bechhofer, Sean and De Roure, David}, title = {myExperiment: An ontology for e-Research}, abstract = {myExperiment describes itself as a "Social Virtual Research Environment" that provides the ability to share Research Objects (ROs) over a social infrastructure to facilitate actioning of research. The myExperiment Ontology is a logical representation of the data model used by this environment, allowing its data to to be published in a standard RDF format, whilst providing a generic extensible framework that can be reused by similar projects. ROs are data structures designed to semantically enhance research publications by capturing and preserving the research method so that it can be reproduced in the future. This paper provides some motivation for an RO speci�cation and briefly considers how existing domain-specifi�c ontologies might be integrated. It concludes by discussing the future direction of the myExperiment Ontology and how it will best support these ROs.}, year = {2009} } @article{patel2009-132, author = {Patel, Manjula and Coles, Simon and Giaretta, David and Rankin, Stephen and McIlwrath, Brian}, title = {The Role of OAIS Representation Information in the Digital Curation of Crystallography Data}, journal = {e-Science and Grid Computing, International Conference on}, volume = {0}, pages = {132-139}, year = {2009} } @misc{pickering2009-networked, author = {Pickering, Adrian and Gutteridge, Christopher and De Roure, David}, title = {A networked registration scheme to support open science}, abstract = {The Open Source and Open Science movements have demonstrated the success of distributed collaborative experimentation and intellectual property (IP) development. While those contributing to the effort may do so without seeking to secure IP rights, it is clear that credit and attribution are crucial to the scholarly lifecycle because they underpin reputation – when IP is created it is only fair that ‘credit is given where credit is due’. We propose that there need to be systems in place, independent of the project, where the evidence of ‘prior art’ can be registered.}, year = {2009} } @inbook{robinson2006-393, author = {Robinson, Jamie M. and Frey, Jeremy G. and De Roure, D. C. and Stanford-Clark, Andrew J. and Reynolds, Andrew D. and Bedi, Bharat V. and Conway-Jones, D.}, title = {The Combechem MQTT LEGO microscope: a grid enabled scientific apparatus demonstrator}, booktitle = {Proceedings of the Fifth All Hands Meeting}, publisher = {National eScience Center}, pages = {393-396}, abstract = {Grid computing impacts directly on the experimental scientific laboratory in the areas of monitoring and remote control of experiments, and the storage, processing and dissemination of the resulting data. We highlight some of the issues in extending the use of an MQ Telemetry Transport (MQTT) broker from facilitating the remote monitoring of an experiment and its environment to the remote control of an apparatus. To demonstrate these techniques, an Intel-Play QX3 microscope has been "grid-enabled" using a combination of software to control the microscope imaging, and sample handling hardware built from LEGO Mindstorms. The whole system is controlled remotely by passing messages using an IBM WebSphere Message Broker.}, keywords = {grid, message queueing telemetry transport, ibm, broker, publish-subscribe}, year = {2006} } @article{rousay2005-grid, author = {Rousay, Esther R. and Fu, Hongchen and Robinson, Jamie M. and Essex, Jonathan W. and Frey, Jeremy G.}, title = {Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface}, journal = {Phil. Trans, Royal Soc.}, year = {2005} } @article{russell2009-81, author = {Russell, K. G. and Eccleston, J. A. and Lewis, S. M. and Woods, D. C.}, title = {Design considerations for small experiments and simple logistic regression}, journal = {Journal of Statistical Computation and Simulation}, volume = {79}, number = {1}, pages = {81 - 91}, year = {2009} } @article{russell2009-721, author = {Russell, K.G. and Woods, D.C. and Lewis, S.M. and Eccleston, J.A. and Hall, Wendy and De Roure, David and Shadbolt, Nigel}, title = {D-optimal designs for Poisson regression models The evolution of the Web and implications for eResearch}, journal = {Statistica Sinica}, volume = {19}, number = {2}, pages = {721-730}, abstract = {We consider the problem of finding an optimal design under a Poisson regression model with a log link, any number of independent variables, and an additive linear predictor. Local D-optimality of a class of designs is established through use of a canonical form of the problem and a general equivalence theorem. The results are applied in conjunction with clustering techniques to obtain a fast method of finding designs that are robust to wide ranges of model parameter values. The methods are illustrated through examples. The hypertext visionaries foresaw the potential of richly interlinked global information systems for advancing human knowledge. The Web provided the infrastructure to enable those ideas to become a reality, and it quickly became a platform for collaborative research and data sharing. As the Web has evolved, new ways of using it for eResearch have emerged, such as the social networking facilities enabled by Web 2.0 technologies. The next generation of the Web-the so-called Semantic Web-is now on the horizon, which will again enable new types of collaborative research to emerge. If we are to understand and anticipate these new modes of collaboration, we need a discipline that studies the Web as a whole. Web science is this discipline.}, keywords = {clustering, locally optimal design, log-linear models, robust design}, year = {2009} } @inproceedings{schraefel2004-49, author = {schraefel, m. c. and Hughes, G. and Mills, H. and Smith, G. and Frey, J.}, title = {Making Tea: Iterative Design through Analogy. In Proceedings of Designing Interactive Systems}, booktitle = {2004 conference on Designing interactive systems: processes, practices, methods, and techniques}, publisher = {ACM Press}, pages = {49-58}, } @inproceedings{schraefel2004-25, author = {schraefel, m. c. and Hughes, G. and Mills, H. and Smith, G. and Payne, T. and Frey, J.}, title = {Breaking the Book: Translating the Chemistry Lab Book into a Pervasive Computing Lab Environment}, booktitle = {Conference on Human Factors in Computing Systems (CHI)}, publisher = {ACM Press}, pages = {25-32}, } @inproceedings{smith2004-53, author = {Smith, G. M. and schraefel, m. c.}, title = {The Radial Scroll Tool: Scrolling Support for Stylus- or Touch-Based Document Interaction}, booktitle = {17th annual ACM symposium on User interface software and technology (UIST)}, pages = {53-56}, } @misc{stephen2009-second, author = {Stephen, Wilson and Frey, Jeremy G. and Coles, Simon J.}, title = {Second Life: The next virtual laboratory?}, abstract = {A virtual world is a computer based environment, typically in three dimensions, where a person can interact and manipulate objects and communicate with others. Users are represented in the virtual world as avatars, although these are typically 'humans', they can have any shape and size. Virtual worlds have been used for a number of applications including research, commerce and education. In this paper we will focus on research-led education. There have been a number of virtual worlds developed specically for education, such as Active Worlds Educational Universe (AWEDU)[1], Media Grid[8] and EduSim[5]. Each of these virtual worlds are aimed at dierent age groups and attempt to simulate dierent aspects of real world teaching within their environment, such as lectures, demonstrations and group tasks. Virtual worlds can benet the learning environment as they oer visualisation not available through traditional simulation techniques and can promote discussion among students who are located across the globe. Second Life[9] has become the most popular of these virtual worlds with over 1.3 million users. Its success has come from its easy to use interface, global media coverage and its free-to-use policy. Second Life also allows, assuming you have the correct permissions, to build objects within its environment and develop scripts to run within them. It is this functionality that is used to develop its educational areas, such as virtual lecture theatres (with streamed media), interactive (and dynamic) models and virtual presentations. Second Life is closely linked to other online information stores, for example links to websites can be given to the user by exhibits as note cards, allowing users to expand the learning experience as they wish. The Virtual Chemistry Experience (ViCE) project[11], funded by Learning and Teaching Enhance- ment Unit (LATEU)[10], have generated a number of Second Life exhibits designed to promote teach- ing of chemistry to a wide range of ages. These exhibits focused mainly on drug docking in protein structures. The Second Life exhibit parallels the e-Malaria[3] web site, developed at the University of Southampton. A potential anti-malaria drug is generated and submitted to docking simulation software through a web interface. A docking score is generate which represents how well the candidate molecule would bind with the dihydrofolate reductase (DHFR) and therefore how good a possible drug candidate it is.}, year = {2009} } @inproceedings{szomszor2003-603, author = {Szomszor, Martin and Moreau, Luc}, title = {Recording and reasoning over data provenance in web and grid services}, booktitle = {International Conference on Ontologies, Databases and Applications of SEmantics (ODBASE'03)}, series = {Lecture Notes in Computer Science}, volume = {2888}, pages = {603-620}, } @inproceedings{taylor2005-148, author = {Taylor, K. Gledhill, R. Essex, J.W. and Frey, J.G. and Harris, S.W. and De Roure, D.}, title = {A Semantic Datagrid for Combinatorial Chemistry}, booktitle = {The 6th IEEE/ACM International Workshop}, pages = {148 - 155}, } @misc{taylor2006-semantic, author = {Taylor, K.R.}, title = {Semantic Units for Scientific Data Exchange}, year = {2006} } @misc{taylor2009-blogging, author = {Taylor, K.R.}, title = {Blogging Meets Computational Chemistry}, year = {2009} } @article{taylor2006-84, author = {Taylor, K.R. and Essex, J.W. and Frey, J.G. and Mills, H.R. and Hughes, G. and Zaluska, E.J.}, title = {The semantic grid and chemistry: experiences with CombeChem}, journal = {Web Semantics: Science, Services and Agents on the World Wide Web}, volume = {4}, number = {2}, pages = {84-101}, abstract = {The CombeChem e-Science project has demonstrated the advantages of using Semantic Web technology, in particular RDF and the associated triplestores, to describe and link diverse and complex chemical information, covering the whole process of the generation of chemical knowledge from inception in the synthetic chemistry laboratory, through analysis of the materials made which generates physical measurements, computations based on this data to develop interpretations, and the subsequent dissemination of the knowledge gained. The RDF descriptions employed allow for a uniform description of chemical data in a wide variety of forms including multimedia, and of the chemical processes both in the laboratory and in model building. The project successfully adopted a strategy of capturing semantic annotations ‘at source’ and establishing schema and ontologies based closely on current operational practice in order to facilitate implementation and adoption. We illustrate this in the contexts of the synthetic organic chemistry laboratory with chemists at the bench, computational chemistry for modelling data, and the linking of chemical publications to the underlying results and data to provide the appropriate provenance. The resulting ‘Semantic Data Grid’ comprises tens of millions of RDF triples across multiple stores representing complex chains of derived data with associated provenance.}, keywords = {chemical markup, web, xml, communities, triplestores, e-science, units, dissemination, research, chemistry, publication@ source, chemical data, laboratory notebooks}, year = {2006} } @article{taylor2006-939, author = {Taylor, Kieron R. and Gledhill, Robert and Essex, Jonathan W. and Frey, Jeremy G. and Harris, S.W. and De Roure, Dave C.}, title = {Bringing chemical data onto the semantic web}, journal = {Journal of Chemical Information and Modeling}, volume = {46}, number = {3}, pages = {939-952}, note = {comebchem project output}, abstract = {Present chemical data storage methodologies place many restrictions on the use of the stored data. The absence of sufficient high-quality metadata prevents intelligent computer access to the data without human intervention. This creates barriers to the automation of data mining in activities such as quantitative structure-activity relationship modelling. The application of Semantic Web technologies to chemical data is shown to reduce these limitations. The use of unique identifiers and relationships (represented as uniform resource identifiers, URIs, and resource description framework, RDF) held in a triplestore provides for greater detail and flexibility in the sharing and storage of molecular structures and properties.}, keywords = {CombeChem, e-Science, semantic web, RDF, schema}, year = {2006} } @article{taylor2006-939, author = {Taylor, K. R. and Gledhill, R. J. and Essex, J. R. and Frey, J. G. and Harris, S. W. and De Roure, D. C.}, title = {Bringing Chemical Data onto the Semantic Web}, journal = {J. Chem. Inf & Mod}, volume = {46}, number = {3}, pages = {939-952}, year = {2006} } @misc{tizzard2009-engaging, author = {Tizzard, G.J. and Coles, S.J. and Frey, J.G.}, title = {Engaging Chemists: Making A Useable Lab Blog Book}, year = {2009} } @article{tsipis2005-2849, author = {Tsipis, A. C. and Orpen, A. G. and Harvey, J. N.}, title = {Substituent effects and the mechanism of alkene metathesis catalyzed by ruthenium dichloride catalysts}, journal = {Dalton Trans}, pages = {2849 - 2858}, year = {2005} } @inproceedings{vivek2003-359, author = {Vivek, Sanjay and Tso, Kenneth and De Roure, David}, title = {Mobile Link Services with MQSeries Everyplace}, booktitle = {First IEEE International Conference on Pervasive Computing and Communications (PerCom'03)}, pages = {359}, abstract = {The Open Hypermedia model is based upon the separation of hypertext links from documents and treats them as separate entities. Distributed link services take this approach and implement an open hypermedia system above the infrastructure of the World Wide Web. This paper explores the suitability and applicability of extending the architecture of distributed link services by adding messaging backbone based on secure asynchronous message passing, which provides support for mobile users of distributed hypermedia information systems.}, } @inproceedings{ward2003-208, author = {Ward, S. C. and Hursthouse, M. B. and Woods, D. C. and Lewis, S. M.}, title = {Systematic study into the salt formation of functionalised organic substrates}, booktitle = {UK e-Science All Hands Meeting}, editor = {Cox, S. J.}, pages = {208-211}, } @article{waterhouse2006-design, author = {Waterhouse, T.H. and Woods, D.C. and Eccleston, J.A. and Lewis, S.M.}, title = {Design selection criteria for discrimination/estimation for nested models and a binomial response}, journal = {Journal of Statistical Planning and Inference}, volume = {in press}, year = {2006} } @article{waterhouse2008-132, author = {Waterhouse, T.H. and Woods, D.C. and Eccleston, J.A. and Lewis, S.M.}, title = {Design selection criteria for discrimination/estimation for nested models and a binomial response}, journal = {Journal of Statistical Planning and Inference}, volume = {138}, number = {1}, pages = {132-144}, abstract = {The aim of an experiment is often to enable discrimination between competing forms for a response model. We investigate the selection of a continuous design for a non-sequential strategy when there are two competing generalized linear models for a binomial response, with a common link function and the linear predictor of one model nested within that of the other. A new criterion, TE-optimality, is defined, based on the difference in the deviances from the two models, and comparisons are made with T-, Ds- and D-optimality. Issues are raised through the study of two examples in which designs are assessed using simulation studies of the power to reject the null hypothesis of the smaller model being correct, when the data are generated from the larger model. Parameter estimation for discrimination designs is also discussed and a simple method is investigated of combining designs to form a hybrid design in order to achieve both model discrimination and estimation. This method has a computational advantage over the use of a compound criterion and the similar performance of the designs obtained from the two approaches is illustrated in an example.}, year = {2008} } @article{welsh2005-45, author = {Welsh, A.H. and Mansson, R.A. and Frey, J.G. and Danos, L}, title = {Statistical Analysis of Second Harmonic Generation Experiments: A Phenomenological Model}, journal = {Chemometrics and Intelligent Laboratory Systems}, volume = {75}, pages = {45-54}, year = {2005} } @misc{wilson2009-lego, author = {Wilson, Stephen and Birch, Oliver and Frey, Jeremy G.}, title = {The LEGO laboratory: laser induced fluorescence}, abstract = {Automation of laboratory experiments can save time and energy as well as improve results[1,2]. When automating experiments using high cost equipment such as diffractometers or laser sources it is often useful to prototype the set up; this aims to prevent damage to both the equipment and the users when applied to the actual system. In this project we propose a system of building these prototypes using LEGOTM and controlling it via a standard message brokering system. The message broker used in this project is the IBMTM Microbroker, part of the WebSphere software range[3]. This is a publish/subscribe application; data producers publish a message to the Microbroker on a given topic (the content typically as XML) and data consumers subscribe to a topic, when a message is published the Microbroker determines which subscribers should receive the message. The Microbroker acts as middleware in the system, keeping the producers and consumers independent. As these parts are independent, any software publishing control messages can be used in both the prototyping and deployment stages without modification as it will only be communicating the message broker. Similarly if the software generating the control messages is changed the consumer software will continue to work, this is shown in}, year = {2009} } @misc{wilson2009-smartlab, author = {Wilson, Stephen and Frey, Jeremy}, title = {The smartlab: experimental and environmental control and monitoring of the chemistry laboratory}, abstract = {A suite of software applications was developed in order to provide functionality to monitor and record environmental and experimental data and the associated metadata. A piece of software developed by IBM [1] called the Microbroker was used as middleware to handle the flow of messages containing the monitored data using the MQ telemetry transport [2] (MQTT) format. Methods to send control commands were also employed where allowed by the experimental set up. The software was used to monitor a range of laboratories within the School of Chemistry at the University of Southampton. A number of repository solutions were implemented to build an understanding of what is required for a scalable and interoperable system.}, keywords = {data acquisition, middleware}, year = {2009} } @inproceedings{wilson2010-control, author = {Wilson, S. and Frey, J.}, title = {Control, monitoring, analysis and dissemination of laboratory physical chemistry experiments using semantic web and broker technologies}, booktitle = {ACS RDF Symposium}, } @misc{wilson2010-impact, author = {Wilson, S. and Frey, J.}, title = {The Impact of e-Science o Real Science}, year = {2010} } @misc{wilson2009-critical, author = {Wilson, Stephen and Frey, Jeremy G.}, title = {Critical zone observatories and sensor repositories}, year = {2009} } @misc{wilson2009-critical, author = {Wilson, Stephen and Frey, Jeremy G.}, title = {Critical zone observatories and sensor repositories}, abstract = {The Shale Hills critical zone laboratory in Pennsylvania was one of three critical zones funded by the U.S National Science Foundation[1]. The goal of these areas was to study the complex processes occurring on the Earth's surface, including research into hydrology, geomorphology and biogeochemical systems. Acknowledging that this is a multi-discipline problem the funding promoted interdisciplinary research within these areas. To allow sharing of this data between researchers a standardised approach of storage the data is required. The volume of data and need for automation means that the data must also be accessible through machine to machine interactions.}, year = {2009} } @misc{wilson2009-tools, author = {Wilson, Stephen and Frey, Jeremy G.}, title = {Web tools, mashups and automated lasers}, abstract = {The introduction of software based laboratory information management systems (LIMS) has helped manage many aspects of the laboratory, from movement of samples and people to the experiments being carried out. These management systems have been developed further to interact directly with devices in the laboratory, automating certain experiments (such as auto-samplers). The use of online systems allows for remote management and control of experiments through web browsers and, where possible, through hand held devices such as mobile phones[1]. Allowing remote control and review can benefit the experimenter in a number of ways such as increasing safety where the experimental environment is unsafe to remain in, improving results where small changes in the environment greatly affect the obtained results and can save time through early detection of failures}, year = {2009} } @misc{wilson2009-comment, author = {Wilson, Stephen and Milsted, Andrew J. and Frey, Jeremy G.}, title = {Comment by sketch: a picture says a million words}, year = {2009} } @inproceedings{woods2004-application, author = {Woods, C.J. and Frey, J.G. and J.W.Essex}, title = {The Application of Distributed Computing to the Investigation of Protein Conformational Change}, booktitle = {UK e-Science All Hands Meeting}, } @article{woods2005-designing, author = {Woods, D.C.}, title = {Designing experiments under random contamination with application to polynomial spline regression}, journal = {Statistica Sinica}, volume = {15}, year = {2005} } @article{woods2010-29, author = {Woods, D.C.}, title = {Robust designs for binary data: applications of simulated annealing}, journal = {Journal of Statistical Computation and Simulation}, volume = {80}, number = {1}, pages = {29-41}, abstract = {When the aim of an experiment is the estimation of a generalized linear model (GLM), standard designs from linear model theory may prove inadequate. This paper describes a flexible approach for finding designs for experiments to estimate GLMs through the use of D-optimality and a simulated annealing algorithm. A variety of uncertainties in the model can be incorporated into the design search, including the form of the linear predictor, through use of a robust design-selection criterion and a postulated model space. New methods appropriate for screening experiments and the incorporation of correlations between possible model parameters are described using examples. An updating formula for D-optimality under a GLM is presented, which improves the computational efficiency of the search.}, keywords = {generalized linear models, optimal design, prior information, screening experiments, simulation}, year = {2010} } @inproceedings{woods2006-elearning, author = {Woods, D.C. and Grove, D.M. and Liccardi, I. and Lewis, S.M. and Frey, J.G.}, title = {An eLearning website for the design and analysis of experiments with application to chemical processes}, booktitle = {Compstat 2006}, publisher = {in press}, } @inproceedings{woods2005-designing, author = {Woods, D.C. and Lewis, S.M.}, title = {Designing experiments for binary data using search algorithms}, booktitle = {55th Session of the International Statistical Institute}, } @article{woods2010-continuous, author = {Woods, D.C and Lewis, S.M}, title = {Continuous optimal designs for generalized linear models under model uncertainty}, journal = {Journal of Statistical Theory and Practice}, year = {2010} } @article{woods2005-designs, author = {Woods, D.C. and Lewis, S.M. and Eccleston, J.A. and Russell, K.G.}, title = {Designs for generalized linear models with several variables and model uncertainty}, journal = {Technometrics}, year = {2005} } @techreport{woods2009-block, author = {Woods, D.C. and van de Ven, P.}, title = {Block designs for experiments with non-normal response}, type = {Working Paper}, abstract = {Many experiments measure a response that cannot be adequately described by a linear model with normally distributed errors and are often run in blocks of homogeneous experimental units. We develop the first methods of obtaining efficient block designs for experiments with an exponential family response described by a marginal model fitted via Generalized Estimating Equations. This methodology is appropriate when the blocking factor is a nuisance variable as, for example, occurs in industrial experiments. A D-optimality criterion is developed for finding designs robust to the values of the marginal model parameters and applied using three strategies: unrestricted algorithmic search, use of minimum-support designs, and blocking of an optimal design for the corresponding Generalized Linear Model. Designs obtained from each strategy are critically compared and shown to be much more efficient than designs that ignore the blocking structure. The designs are compared for a range of values of the intra-block working correlation and for exchangeable, autoregressive and nearest neighbor structures. An analysis strategy is developed for a binomial response that allows es- timation from experiments with sparse data, and its efectiveness demonstrated. The design strategies are motivated and demonstrated through the planning of an experiment from the aeronautics industry}, year = {2009} }