PK{H=ԵP.dQdQrefs.MYD?Goble, C.A. De Roure, D.2002,The Grid: an application of the semantic web65-70ACM SIGMOD Record314$http://eprints.ecs.soton.ac.uk/9192/&D֟?Goble, C. De Roure, D.2002#The Semantic Web and Grid Computing$Real World Semantic Web Applications92V. Kashyap L. Shklar IOS Press9http://www.semanticgrid.org/documents/swgc/swgc-final.pdf5Frontiers in Artificial Intelligence and Applications 1 58603 306 9[?9Goble, C.A. De Roure, D. Shadbolt, N.R. Fernandes, A.A.A.2004@Enhancing Services and Applications with Knowledge and Semantics431-458@The Grid: Blueprint for a New Computing Infrastructure (2nd. ed)Foster, I. Kesselman, CMorgan-KaufmannLhttp://www.elsevier.com/wps/find/bookdescription.cws_home/699905/description9?YFrey, Jeremy G.2003+Comb-e-Chem - an e-science research project395-398UEuroQSAR 2002 Designing Drugs and Crop Protectants: processes, problems and solutionsEFord, Martyn Livingstone, David Dearden, John Van der Waterbeemd, Han Oxford, UK Blackwellhttp://eprints.soton.ac.uk/802/ D?ZDe Roure, David Goble, Carole 2005Building the Semantic Grid,Engineering the Grid: status and perspective3J. Dongarra H. Zima A. Hoisie L. Yang B. Di MartinoAmerican Scientific Publishershttp://www.aspbs.com/grid.html 1-58883-038-1&?*De Roure, D. Jennings, N.R. Shadbolt, N.R.20035The Semantic Grid - A future e-Science infrastructure437-470;Grid Computing - Making the Global Infrastructure a Reality Berman, F. Fox, G. Hey, A. J. G.John Wiley and Sons Ltd.$http://eprints.ecs.soton.ac.uk/6869/? 6De Roure, D. Baker, M.A. Jennings, N.R. Shadbolt, N.R.2003The evolution of the Grid65-100;Grid computing - making the global infrastructure a realityBerman, F. Fox, G. Hey, A.J.G.,John Wiley and Sons Ltd$http://eprints.ecs.soton.ac.uk/6871/? De Roure, D. Hendler, J.A.2004(E-Science: the Grid and the Semantic Web65-71IEEE Intelligent Systems191bhttp://eprints.ecs.soton.ac.uk/9977 and http://csdl.computer.org/comp/mags/ex/2004/01/x1065abs.htm:?dT. Gelbrich M.B. Hursthouse2005{A versatile procedure for the identification, description and quantification of structural similarity in molecular crystals324-336Cryst. Eng. Comm7hhttp://eprints.soton.ac.uk/20809/ and http://www.rsc.org/publishing/journals/CE/article.asp?doi=b502484f?[6Stefan W. Christensen Ian Sinclair Philippa A. S. Reed2004JDesigning committees of models through deliberate weighting of data points39-66$Journal of Machine Learning Research41January,http://portal.acm.org/citation.cfm?id=945368D?EBuckingham Shum, S. De Roure, D. Eisenstadt, M. Shadbolt, N. Tate, A.2002CCoAKTinG: Collaborative Advanced Knowledge Technologies in the Grid6Second Workshop on Advanced Collaborative Environments Edinburgh, UK0http://eprints.ecs.soton.ac.uk/archive/00006791/? ,De Roure, D. Jennings, N. R. Shadbolt, N. R.2001IResearch Agenda for the Semantic Grid - A Future e-Science Infrastructure Edinburgh, UKNational e-Science CentreDecember0http://eprints.ecs.soton.ac.uk/archive/00006350/ UKeS-2002-02|?\Stefan W. Christensen20034Ensemble Construction via Designed Output Distortion286-295" Lecture Notes in Computer Science2709 HeidelbergSpringer-Verlag GmbH A new technique for generating regression ensembles is introduced in the present paper. The technique is based on earlier work on promoting model diversity through injection of noise into the outputs; it differs from the earlier methods in its rigorous requirement that the mean displacements applied to any data points output value be exactly zero. It is illustrated how even the introduction of extremely large displacements may lead to prediction accuracy superior to that achieved by bagging. It is demonstrated how ensembles of models with very high bias may have much better prediction accuracy than single models of the same bias-defying the conventional belief that ensembling high bias models is not purposeful. Finally is outlined how the technique may be applied to classification.6http://www.springerlink.com/index/6BLFYULTXDLW7G49.pdf[Proc. 4th Int. Workshop Multiple Classifier Systems, Guildford, Surrey, UK, June 11-13 2003 0302-9743ǟ?XFrey, J. G. Bradley, M. Essex, J.W. Hursthouse, M.B. Lewis, S.M. Luck, M.M. Moreau, L. De Roure, D.C. Surridge, M. Welsh, A.H. 2003$Combinatorial chemistry and the Grid945-962:Grid computing: making the global infrastructure a reality0Berman, Fran Hey, Anthony J.G. Fox, Geoffrey C.Chichester, UKJohn Wiley & Sons Ltd.http://eprints.soton.ac.uk/325/AWiley Series in Communications Networking and Distributed Systems;D?"Frey, J.G. De Roure, D. Carr, L.A.2002UPublication At Source: Scientific Communication from a Publication Web to a Data GridKEuroweb 2002 Conference, The Web and the GRID: from e-science to e-business Oxford, UKBCS17-18 December 20020http://eprints.ecs.soton.ac.uk/archive/00007852/B?Martin Szomszor Luc Moreau2003ERecording and reasoning over data provenance in web and grid services603-620[International Conference on Ontologies, Databases and Applications of SEmantics (ODBASE'03)2888 3-7 November$http://eprints.ecs.soton.ac.uk/9450/!Lecture Notes in Computer Science?yM. Luck P. McBurney C. Preist2004CA Manifesto for Agent Technology: Towards Next Generation Computing203-2524Journal of Autonomous Agents and Multi-Agent Systems93%http://eprints.ecs.soton.ac.uk/10225/?kDe Roure, David2003%Semantic Grid and Pervasive Computing70-76GGF9 Semantic Grid Workshop(David De Roure Carole Goble Geoffrey Fox Chicago, ILOctober)http://www.semanticgrid.org/GGF/ggf9/gpc/*D?jfFrey, J. G. De Roure, D. schraefel, m. c. Mills, H. Fu, H. Peppe, S. Hughes, G. Smith, G. Payne, T. R.2003#Context Slicing the Chemical Aether?First International Workshop on Hypermedia and the Semantic Web Millard, DNottingham, UK$http://eprints.ecs.soton.ac.uk/8790/?# Luc Moreau2002QAgents for the Grid: A Comparison with Web Services (Part 1: the transport layer)220-228WSecond IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID 2002)1Henri E. Bal Klaus-Peter Lohr Alexander ReinefeldBerlin, GermanyIEEE Computer SocietyMay 2002fhttp://eprints.ecs.soton.ac.uk/archive/00007586/ and http://citeseer.ist.psu.edu/moreau2002agents.htmlD?$3Moreau, L Avila-Rosas, A Dialani, V Miles, S Liu, X2002PAgents for the Grid: A Comparison with Web Services (part II: Service Discovery)52-56,Workshop on Challenges in Open Agent SystemsBologna, Italy\http://eprints.ecs.soton.ac.uk/archive/00007598/ and http://citeseer.ist.psu.edu/538865.html?pMichelle Bachler Simon Buckingham Shum Yun-Heh Chen-Burger Jeff Dalton De Roure, David Marc Eisenstadt Jeremy Frey Jiri Komzak Danius Michaelides Kevin Page Stephen Potter Nigel Shadbolt Austin Tate2004:Collaboration in the Semantic Grid: a Basis for e-Learning1-12yGrid Learning Services (GLS'2004) at the 7th International Conference on Intelligent Tutoring Systems Workshop (ITS'2004)Maceio, Brazil%http://eprints.ecs.soton.ac.uk/11164/D?qC.J. Woods J.G. Frey J.W.Essex2004^The Application of Distributed Computing to the Investigation of Protein Conformational ChangeUK e-Science All Hands MeetingNottingham, UK!http://eprints.soton.ac.uk/15881/1-90 4425-21-6?f+De Roure, D. Jennings, N.R. Shadbolt, N.R. 2005,The Semantic Grid: Past, Present, and Future669-681Proceedings of the IEEE933March$http://eprints.ecs.soton.ac.uk/9976/ 0018-9219&DǛ?gwColes, S.J. Frey, J.G. Hursthouse, M.B. Light, M.E. Surridge, M. Meacham, K.E. Marvin, D.J. De Roure, D.C. Mills, H. R.2002vGrid/Web enhancements to the National Crystallographic Service: experiences with an interactive e-Science demonstratorAEuroweb 2002 - the Web and the GRID: from e-Science to e-Business*Hopgood, F.R.A. Matthews, B. Wilson, M.D. Oxford, UKBritish Computer SocietyDecemberUhttp://eprints.soton.ac.uk/346/ and http://www.bcs.org/server.php?show=ConWebDoc.4081 ElectronicWorkshops in Computing?]Mike Hursthouse2004]High-throughput chemical crystallography (HTCC): meeting and greeting the combichem challenge85-96Crystallography Reviews10Phttp://www.ingentaconnect.com/content/tandf/gcrr/2004/00000010/00000001/art000016?^-Welsh, A.H. Mansson, R.A. Frey, J.G. Danos, L2005YStatistical Analysis of Second Harmonic Generation Experiments: A Phenomenological Model 45-54/Chemometrics and Intelligent Laboratory Systems75Vhttp://eprints.soton.ac.uk/20930/ and http://dx.doi.org/10.1016/j.chemolab.2004.05.002?bRThomas Gelbrich Terence L. Threlfall Susanne Huth Eva Seeger Michael B. Hursthouse2004~Investigation of Structural Relationships between Racemic Alkali and Ammonium Hydrogen Tartrates and their Chiral Counterparts 1451-14583Zeitschrift für anorganische und allgemeine Chemie63010Qhttp://eprints.soton.ac.uk/20209/ and http://doi.wiley.com/10.1002/zaac.2004001397c>Stefan Gerber Harald Krautscheid Thomas Gelbrich Heike Vollmer2004Synthesis 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] 1427 - 14323Zeitschrift für anorganische und allgemeine Chemie63010Fhttp://www3.interscience.wiley.com/cgi-bin/abstract/109594385/ABSTRACT10.1002/zaac.200400138,German?1De Roure, David2003*On Self-Organization and the Semantic Grid77-79IEEE Intelligent Systems184July-August 2003-http://www.semanticgrid.org/docs/selforg.htmlTrends & ControversiesxD?4Bachler, M. Buckingham Shum, S. Chen-Burger, J. Dalton, J. De Roure, D. Eisenstadt, M. Komzak, J. Michaelides, D. Page, K. Potter, S. Shadbolt, N. Tate, A.2004(Collaborative Tools in the Semantic Grid&GGF11 - The Eleventh Global Grid Forum Luc MoreauHonolulu, Hawaii, USAGlobal Grid ForumJune 6-10, 2004$http://eprints.ecs.soton.ac.uk/9439/?6Goble, CA De Roure, D.20043The Semantic Grid: Myth Busting and Bridge Building 1129-1135?16th European Conference on Artificial Intelligence (ECAI-2004)Valencia, Spain August 2004Khttp://www.semanticgrid.org/docs/ECAISemanticGrid/ECAISemanticGridFinal.pdf?7 EU Expert Group,2003&Next Generation Grid(s) 2005 – 2010BrusselsEuropean CommissionJune1ftp://ftp.cordis.lu/pub/ist/docs/ngg_eg_final.pdf^?9Bschraefel, m. c. Hughes, G. Mills, H. Smith, G. Payne, T. Frey, J.2004`Breaking the Book: Translating the Chemistry Lab Book into a Pervasive Computing Lab Environment25-326Conference on Human Factors in Computing Systems (CHI)Vienna, Austria ACM Press0http://eprints.ecs.soton.ac.uk/archive/00008780/ 1-58113-702-8 D?:QFrey, J. G. Hughes, G. V. Mills, H. R. schraefel, m. c. Smith, G. M. De Roure, D.2004GLess is More: Lightweight Ontologies and User Interfaces for Smart LabsUK eScience All Hands MeetingNottingham, UK%http://eprints.ecs.soton.ac.uk/10100/l?i+Vivek, Sanjay Tso, Kenneth De Roure, David 2003-Mobile Link Services with MQSeries Everyplace359\First IEEE International Conference on Pervasive Computing and Communications (PerCom'03) Fort Worth, TexasThe Open Hypermedia model is based upon the separation of hypertext links from documents and treats them as separate entities. Distributed link services take this approach and implement an open hypermedia system above the infrastructure of the World Wide Web. This paper explores the suitability and applicability of extending the architecture of distributed link services by adding messaging backbone based on secure asynchronous message passing, which provides support for mobile users of distributed hypermedia information systems.$http://eprints.ecs.soton.ac.uk/7240/>http://doi.ieeecomputersociety.org/10.1109/PERCOM.2003.1192760oF?eOEsther R. Rousay Hongchen Fu Jamie M. Robinson Jonathan W. Essex Jeremy G. Frey2005Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interfacePhil. Trans, Royal Soc.LondonNhttp://eprints.soton.ac.uk/20900/ and http://dx.doi.org/10.1098/rsta.2005.16305?DeGareth Hughes Hugo Mills David De Roure Jeremy G Frey Luc Moreau mc schraefel Graham Smith Ed Zaluska2004NThe Semantic Smart Laboratory: A system for supporting the chemical eScientist1-10Org. Biomol. Chem.2October%http://eprints.ecs.soton.ac.uk/10099/DOI: 10.1039/b410075a?_ J. G. Frey2004JDark Lab or Smart Lab: The Challenges for 21st Century Laboratory Software 1024-1035Org. Proc. Res. Dev.86jhttp://eprints.soton.ac.uk/20201/ and http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/op049895gF?` Woods, D.C.2005aDesigning experiments under random contamination with application to polynomial spline regressionStatistica Sinica15hhttp://eprints.soton.ac.uk/15837/ and http://www3.stat.sinica.edu.tw/statistica/J15N3/J15N32/J15N32.htmlF?a5Woods, D.C. Lewis, S.M. Eccleston, J.A. Russell, K.G.2005RDesigns for generalized linear models with several variables and model uncertainty Technometrics http://eprints.soton.ac.uk/15828F?P'De Roure, David Yolanda Gil Jim Hendler2004E-Science Special IssueIEEE Intelligent Systems191 Jan/Feb 20048http://csdl2.computer.org/comp/mags/ex/2004/01/x1024.pdft?m7Ward, S. C. Hursthouse, M. B. Woods, D. C. Lewis, S. M.2003MSystematic study into the salt formation of functionalised organic substrates208-211UK e-Science All Hands Meeting Cox, S.J.Nottingham, UKhttp://eprints.soton.ac.uk/15855/ and http://www.nesc.ac.uk/events/ahm2003/AHMCD/pdf/040.pdf and http://eprints.soton.ac.uk/15842/ (Poster)8?nSmith, G. M. schraefel, m. c.2004YThe Radial Scroll Tool: Scrolling Support for Stylus- or Touch-Based Document Interaction53-56J17th annual ACM symposium on User interface software and technology (UIST)Santa Fe, New Mexico, USA$http://eprints.ecs.soton.ac.uk/9247/ 1-58113-957-8t?o9schraefel, m. c. Hughes, G. Mills, H. Smith, G. Frey, J. 2004]Making Tea: Iterative Design through Analogy. In Proceedings of Designing Interactive Systems49-58_2004 conference on Designing interactive systems: processes, practices, methods, and techniquesCambridge Mass, USA ACM Press$http://eprints.ecs.soton.ac.uk/8672/ 1-58113-787-7?h1V. Dialani S. Miles L. Moreau D. De Roure M. Luck2002{Transparent, fault tolerance for web services based architectures, Lecture Notes in Computer Science,Springer-Verlag, 2002.889-8984Euro-Par 2002. 8th International Euro-Par Conference2400B. Monien R. Feldman Paderborn, GermanySpringer-Verlag GmbHAugust^http://eprints.ecs.soton.ac.uk/7317/ and http://citeseer.ist.psu.edu/dialani02transparent.html 0302-9743MD?rML. Lyon R. Heery M. Duke S. Coles J. Frey M. Hursthouse L. Carr C. Gutteridge2004FeBank UK: linking research data, scholarly communication and learning UK e-Science All Hands MeetingNottingham, UKZhttp://eprints.soton.ac.uk/8183/ and http://www.allhands.org.uk/proceedings/papers/237.pdf1-90 4425-21-6lD?sM. Bachler S. Buckingham-Shum J. Chen-Burger J. Dalton D. De Roure M. Eisenstadt J. Frey J. Komzak D. Michaelides K. Page S. Potter N. Shadbolt A. Tate2004SChain ReAKTing: Collaborative Advanced Knowledge Technologies in the CombeChem GridUK e-Science All Hands MeetingNottingham, UK!http://eprints.soton.ac.uk/15883/1-90 4425-21-6?t{Rachel Heery Monica Duke Michael Day Liz Lyon Simon Coles Jeremy Frey Michael Hursthouse Leslie Carr Christopher Gutteridge2004IIntegrating research data into the publication workflow: eBank experience135-142bPV-2004: Ensuring the Long-Term Preservation and Adding Value to the Scientific and Technical DataFrascati, ItalyOctober http://eprints.soton.ac.uk/9705/T?uZL. Lyon S. Coles L. Carr R. Heery M. Hursthouse C. Gutteridge M. Duke J. Frey De Roure, D.2004EeBank UK Linking Research Data, Scholarly Communications and Learning61-70,GGF11 Workshop on Semantic Grid ApplicationsDanius Michaelides Luc Moreau Hawaii, USAGGF July 2004!http://eprints.soton.ac.uk/12461/?v H Fu J G Frey2004>Semantic description and tracking of analysis of chemical data140-149ISecond International Workshop on the Knowledge Grid and Grid IntelligenceH Zhuge W K Cheung J LiuBeijing, China!http://eprints.soton.ac.uk/11240/ 0-9734039-8-5D?wWoods, D.C. Lewis, S.M.2005>Designing experiments for binary data using search algorithms 755th Session of the International Statistical InstituteSydney, Australia!http://eprints.soton.ac.uk/15854/57zQK. R. Taylor R. J. Gledhill J. R. Essex J. G. Frey S. W. Harris De Roure, D. C. 2006,Bringing Chemical Data onto the Semantic Web939-952J. Chem. Inf & Mod463jhttp://eprints.soton.ac.uk/32799/ and http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci050378mEnglish 77{CR. Gledhill S. Kent B. Hudson W. G. Richards J. W. Essex J. G. Frey2006=A Computer-Aided Drug Discovery System for Chemistry Teaching960-970J. Chem. Inf & Mod463jhttp://eprints.soton.ac.uk/30135/ and http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci050383qEnglishk7|cNatalie Fey Athanassios C. Tsipis Stephanie E. Harris Jeremy N. Harvey A. Guy Orpen Ralph A. Manson2005fDevelopment of a Ligand Knowldege Base, Part 1: Computational Descriptors for Phosphorus Donor Ligands 291 - 302Chemistry - A European Journal121Ghttp://www3.interscience.wiley.com/cgi-bin/fulltext/112140401/HTMLSTARTEnglish?~LTaylor, K. Gledhill, R. Essex, J.W.; Frey, J.G.; Harris, S.W.; De Roure, D.;2005/A Semantic Datagrid for Combinatorial Chemistry 148 - 155(The 6th IEEE/ACM International Workshop Seattle13-14 Nov. 2005http://eprints.ecs.soton.ac.uk/11778/ and http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1542736 and http://dx.doi.org/doi:10.1109/GRID.2005.1542736Q?*Mansson, RA Frey, JG Essex, JW Welsh, AH2005[Prediction of properties from simulations: A re-examination with modern statistical methods 1791 - 1803-Journal of Chemical Information and Modelling456jhttp://eprints.soton.ac.uk/15866/ and http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci050056iF?9Waterhouse, T.H. Woods, D.C. Eccleston, J.A. Lewis, S.M. 2006aDesign selection criteria for discrimination/estimation for nested models and a binomial response-Journal of Statistical Planning and Inferencein pressD?=Woods, D.C. Grove, D.M. Liccardi, I. Lewis, S.M. Frey, J.G. 2006fAn eLearning website for the design and analysis of experiments with application to chemical processes Compstat 2006in press?1Fey, N. Harris, S. E. Harvey, J. N. Orpen, A. G.2006DAdding Value to Crystallographically-Derived Ligand Knowledge Bases 912-929J. Chem. Inf. Model.46Nhttp://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2006/46/i02/abs/ci0504768.html?&A. C. Tsipis A. G. Orpen J. N. Harvey2005fSubstituent effects and the mechanism of alkene metathesis catalyzed by ruthenium dichloride catalysts 2849 - 2858 Dalton TransBhttp://www.rsc.org/publishing/journals/DT/article.asp?doi=b506929gV?1R. A. Mansson A. H. Welsh Natalie Fey A. G. Orpen2"Statistical Modelling of a Ligand Knowledge Base"J. Chem. Inf. Model. submittedF?Coles, S. J. Frey, J.G. Hursthouse, M.B. Light, M.E. Milsted, A.J. Carr, L.A. De Roure, D., Gutteridge, C.J. Mills, H.R. Meacham, K.E. Surridge, M. Lyon, E. Heery, R. Duke, M. Day, M. 2006XAn E-Science Environment for Service Crystallographys from Submission to Dissemination. ,Journal of Chemical Information and Modelingjhttp://eprints.soton.ac.uk/26845/ and http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci050362w? Woods, D.C. van de Ven, P.20096Block designs for experiments with non-normal response Working PapercMany 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 eps:69903!http://eprints.soton.ac.uk/69903/F? Frey, Jeremy2008NCuration of laboratory experimental data as part of the overall data lifecycle)International Journal of Digital Curation314laboratory data, curation, escience, data life cyclepThe 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. eps:64612!http://eprints.soton.ac.uk/64612/ 1746-8256?bGeldhill, Robert Kent, Sarah Milsted, Andrew Chapman, Richard Essex, Jonathan. W. Frey, Jeremy. G.2008&e-Malaria: the schools Malaria project225-2382Concurrency and Computation: Practice & Experience203Rsites, malaria, grid, genetic algorithm, e-learning, docking, docking, recognitione-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. eps:54457!http://eprints.soton.ac.uk/54457/ 1532-0626F?%Guan, Tao Zaluska, Ed De Roure, David2008\An Autonomic Service Discovery Mechanism to Support Pervasive Device Accessing Semantic Grid,International Journal of Autonomic Computing ecs:16853%http://eprints.ecs.soton.ac.uk/16853/?6de Oliveira Branco, Miguel Zaluska, Ed De Roure, David2008(Managing very-large distributed datasets775-792!Lecture Notes in Computer Science5331In 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. ecs:17323%http://eprints.ecs.soton.ac.uk/17323/$0302-9743 (Print) 1611-3349 (Online)?8Waterhouse, T.H. Woods, D.C. Eccleston, J.A. Lewis, S.M.2008aDesign selection criteria for discrimination/estimation for nested models and a binomial response132-144-Journal of Statistical Planning and Inference1381The 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. eps:54673!http://eprints.soton.ac.uk/54673/ 0378-3758?EBarillari, Caterina Taylor, Justine Viner, Russell Essex, Jonathan W.2007:Classification of water molecules in protein binding sites 2577-2587(Journal of the American Chemical Society1299novo ligand design, free-energy, rational design, am1-bcc model, potent, factor xa, generation, efficient, complexes, selective inhibitors, drug designWater 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. eps:54239!http://eprints.soton.ac.uk/54239/ 0002-7863U?HTaylor, K.R. Essex, J.W. Frey, J.G. Mills, H.R. Hughes, G. Zaluska, E.J.2006;The semantic grid and chemistry: experiences with CombeChem84-101AWeb Semantics: Science, Services and Agents on the World Wide Web42chemical markup, web, xml, communities, triplestores, e-science, units, dissemination, research, chemistry, publication@ source, chemical data, laboratory notebooksThe 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. eps:54225!http://eprints.soton.ac.uk/54225/ 1570-8268P?dTaylor, Kieron R. Gledhill, Robert Essex, Jonathan W. Frey, Jeremy G. Harris, S.W. De Roure, Dave C.2006,Bringing chemical data onto the semantic web939-952,Journal of Chemical Information and Modeling463/CombeChem, e-Science, semantic web, RDF, schemaPresent 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. eps:32799!http://eprints.soton.ac.uk/32799/comebchem project output 1549-9596A?Coles, Simon J. Frey, Jeremy G. Hursthouse, Michel B. Light, Mark E. Milsted, Andrew J. Carr, Leslie A. De Roure, David Gutteridge, Christopher J. Mills, Hogo R. Meacham, Ken E. Surridge, Michael Lyon, Elizabeth Heery, Rachel Duke, Monica Day, Michael2006UAn e-science environment for service crystallographysfrom submission to dissemination 1006-1016,Journal of Chemical Information and Modeling463VThe 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. eps:26845!http://eprints.soton.ac.uk/26845/ 1549-9596h? Woods, D.C.2010CRobust designs for binary data: applications of simulated annealing29-411Journal of Statistical Computation and Simulation801_generalized linear models, optimal design, prior information, screening experiments, simulationWhen 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. eps:151261"http://eprints.soton.ac.uk/151261/ 0094-9655?SFrey, Jeremy De Roure, David Taylor, Kieron Essex, Jonathan Mills, Hugo Zaluska, Ed2006KCombeChem: a case study in provenance and annotation using the Semantic Web270-277!Provenance and Annotation of Data 4145/2006Moreau, Luc Foster, IanSpringerOThe 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. eps:42344!http://eprints.soton.ac.uk/42344/ 9783540463023?aGledhill, Robert Kent, Sarah Hudson, Brian Richards, W. Graham Essex, Jonathan W. Frey, Jeremy G.2006=A computer-aided drug discovery system for chemistry teaching960-970,Journal of Chemical Information and Modeling463dockingThe 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. eps:44452!http://eprints.soton.ac.uk/44452/ 1549-9596? $Biedermann, Stefanie Woods, David C.2009kOptimal designs for generalised nonlinear models with application to second harmonic generation experiments Working Paper eps:69457!http://eprints.soton.ac.uk/69457/?HBandara, Ayomi Payne, Terry De Roure, David Gibbins, Nicholas Lewis, Tim2010UA pragmatic approach for the semantic description and matching of pervasive resources19-46>International Journal of Pervasive Computing and Communication61There 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. ecs:18379%http://eprints.ecs.soton.ac.uk/18379/ 1742-7371F?Woods, D.C Lewis, S.M2010PContinuous optimal designs for generalized linear models under model uncertainty*Journal of Statistical Theory and Practice eps:151267"http://eprints.soton.ac.uk/151267/ 1559-8608N/9Russell, K. G. Eccleston, J. A. Lewis, S. M. Woods, D. C.2009JDesign considerations for small experiments and simple logistic regression81 - 911Journal of Statistical Computation and Simulation7915http://www.informaworld.com/10.1080/00949650701609006 0094-9655%September 29, 2010 %0 Journal Article?aRussell, K.G. Woods, D.C. Lewis, S.M. Eccleston, J.A. Hall, Wendy De Roure, David Shadbolt, Nigel2009gD-optimal designs for Poisson regression models The evolution of the Web and implications for eResearch721-730Statistica Sinica192Dclustering, locally optimal design, log-linear models, robust designWe 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.eps:151269 ecs:17132Hhttp://eprints.soton.ac.uk/151269/ http://eprints.ecs.soton.ac.uk/17132/ 1017-0405D/Frey, Jeremy G.2009 e-MalariaResearch in a Connected World%Voss, A. Vander Meer, E. Ferguson, D.Conexions Web site%http://cnx.org/content/col10677/1.12/ Nov 22, 2009M?Frey, Jeremy G.2009/The value of the semantic web in the laboratory522-561Drug Discovery Today1411-12Csemantic web, chemistry laboratory, electronic laboratory notebooksBThe 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. eps:145173"http://eprints.soton.ac.uk/145173/ 1359-6446?+Hall, Wendy De Roure, David Shadbolt, Nigel20097The evolution of the Web and implications for eResearch991-1001VPhilosophical transactions. Series A, Mathematical, physical, and engineering sciences3671890The 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. ecs:17132%http://eprints.ecs.soton.ac.uk/17132/D?!Wilson, Stephen Frey, Jeremy G.20093Critical zone observatories and sensor repositories Microsoft eScience Workshop 2009 eps:148085"http://eprints.soton.ac.uk/148085/D?!2Wilson, Stephen Milsted, Andrew J. Frey, Jeremy G.20091Comment by sketch: a picture says a million words Microsoft eScience Workshop 2009Other eps:148069"http://eprints.soton.ac.uk/148069/^D?!-Newman, David Bechhofer, Sean De Roure, David2009(myExperiment: An ontology for e-Research1Semantic Web Applications in Scientific DiscourseWashington DC, USpmyExperiment 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. ecs:17787%http://eprints.ecs.soton.ac.uk/17787/D?!Coles, Simon Lyon, Liz2008The eCrystals Federation9Third International Conference on Open Repositories, 2008OR08$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. eps:50902!http://eprints.soton.ac.uk/50902/D?!HBandara, Ayomi Payne, Terry De Roure, David Gibbins, Nicholas Lewis, Tim2008UA Pragmatic Approach for the Semantic Description and Matching of Pervasive ResourcesG3rd International Conference on Grid and Pervasive Computing (GPC 2008)&Semantic Matching, Pervasive ComputingThe 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. ecs:15318%http://eprints.ecs.soton.ac.uk/15318/bD?!rGreenhalgh, Chris Glover, Kevin Humble, Jan Robinson, Jamie Wilson, Steve Frey, Jeremy Page, Kevin De Roure, David2008}Combining System Introspection with User-Provided Description to Support Configuration and Understanding of Pervasive systemsRThird International Conference on Pervasive Computing and Application ( ICPCA2008)Alexandria, Egypt!Pervasive Computing, Semantic WebPervasive 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. ecs:16594%http://eprints.ecs.soton.ac.uk/16594/pD?!Frey, Jeremy G.2007nScience as a collaborative process - the Scholarly Knowledge Cycle and Blogging the Laboratory (Smartlab 2.5?)#Web 2.0 and Grids Workshop at OGF19Open Grid ForumnScience as a collaborative process - the Scholarly Knowledge Cycle and Blogging the Laboratory (Smartlab 2.5?) eps:41795!http://eprints.soton.ac.uk/41795/D?!De Roure, David Frey, Jeremy2007FThree Perspectives on Collaborative Knowledge Acquisition in e-ScienceNWorkshop on Semantic Web for Collaborative Knowledge Acquisition (SWeCKa) 2007Hyderabad, IndiaThrough 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. ecs:13997%http://eprints.ecs.soton.ac.uk/13997/D?! Frey, J. G.2008Blogs, logs and pods-Microsoft Research eScience Workshop at RENCI eps:52013!http://eprints.soton.ac.uk/52013/D?!"Guan, Tao Zaluska, Ed Roure, David2007\An Autonomic Service Discovery Mechanism to Support Pervasive Device Accessing Semantic Grid@Fourth International Conference on Autonomic Computing (ICAC'07) ecs:14488%http://eprints.ecs.soton.ac.uk/14488/.D?!6Bandara, Ayomi Payne, Terry De Roure, David Lewis, Tim2007]A Semantic Approach for Description and Ranked Matching of Services in Pervasive Environments*Applications of Semantic Technologies 2007Germany3service matching, semantic web, pervasive computingWith 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. ecs:14691%http://eprints.ecs.soton.ac.uk/14691/D?!Coles, Simon J.2007aA repository based framework for capture, management, curation and dissemination of research data-The 2007 Microsoft eScience Workshop at RENCIUniversity of Southampton, UKBased 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. eps:49395!http://eprints.soton.ac.uk/49395/ 9D?!Coles, Simon J. Hursthouse, Michael B. Frey, Jeremy G. Milsted, Andrew J. Carr, Leslie A. Koch, Traugott Lyon, Elizabeth Duke, Monica2006KeCrystals: A Route for Open Access to Small Molecule Crystal Structure DataECM 23Felectronic publishing, crystallographic databases, computer networking 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. eps:41257!http://eprints.soton.ac.uk/41257/D?!Frey, Jeremy G.2006RThe curation of laboratory experimental data as part of the overall data lifecycle-2nd International Digital Curation ConferenceDigital Curation CentreXdigital curation, chemistry, laboratory notebooks, semantics, comebchem, metadata, blogsThe 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. eps:44281!http://eprints.soton.ac.uk/44281/?!8Goble, Carole Corcho, Oscar Alper, Pinar De Roure, David20068e-science and the semantic web: A symbiotic relationship1-12Discovery Science 2006LNAI 4Barcelona, SpainSpringer-Verlage-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. ecs:13624%http://eprints.ecs.soton.ac.uk/13624/D?!"Guan, Tao Zaluska, Ed Roure, David2006UExtending Pervasive Devices with the Semantic Grid: A Service Infrastructure ApproachNThe Sixth IEEE International Conference on Computer and Information Technology ecs:14487%http://eprints.ecs.soton.ac.uk/14487/D?!De Roure, David Goble, Carole2010BAnchors in Shifting Sand: the Primacy of Method in the Web of DataWeb Science Conference 2010Raleigh, NC, USA%linked data, myExperiment, versioningIs 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. ecs:20817%http://eprints.ecs.soton.ac.uk/20817/D?!Wilson, Stephen Frey, Jeremy2009_The smartlab: experimental and environmental control and monitoring of the chemistry laboratoryUThe 2009 International Symposium on Collaborative Technologies and Systems (CTS 2009)data acquisition, middlewareA 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. eps:148063"http://eprints.soton.ac.uk/148063/F?De Roure, David2009e-Science and the Web IEEE Computer ecs:17765%http://eprints.ecs.soton.ac.uk/17765/:D?!9Pickering, Adrian Gutteridge, Christopher De Roure, David20097A networked registration scheme to support open science#UK e-Science All Hands Meeting 2009 Oxford, UKFThe 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. ecs:17680%http://eprints.ecs.soton.ac.uk/17680/?LPatel, Manjula Coles, Simon Giaretta, David Rankin, Stephen McIlwrath, Brian2009[The Role of OAIS Representation Information in the Digital Curation of Crystallography Data132-1399e-Science and Grid Computing, International Conference on0Los Alamitos, CA, USAIEEE Computer Society10.1109/e-Science.2009.27<http://doi.ieeecomputersociety.org/10.1109/e-Science.2009.27978-0-7695-3877-8?jMatthews, Brian Duncan, Alastair Jones, Catherine Neylon, Cameron Borkum, Mark Coles, Simon Hunter, Philip2009.A Protocol for Exchanging Scientific Citations171-1779e-Science and Grid Computing, International Conference on0Los Alamitos, CA, USAIEEE Computer Society10.1109/e-Science.2009.32<http://doi.ieeecomputersociety.org/10.1109/e-Science.2009.32978-0-7695-3877-8w?(Borkum, M. Coles, S. Frey, J. Lagoze, C.2010 (accepted)*A Semantic eScience Platform for ChemistryD?2Milsted, A. Frey, J. Michaelides, D. De Roure, D. 2010 (accepted)2"MyExperimentalScience, extending the 'workflow'" Microsoft e-ScienceBerkeleyD?-Milsted, A. Santokhee, A. Frey, J. Blower, J.2010 (accepted)aBlogMyData: A Virtual Research Environment for collobaorative visualization of environmental dataMicrosoft e-ScienceBerkeleyD?(Borkum, M. Lagoze, C. Coles, S. Frey, J.2010 (accepted)<oreChem: Planning and Enacting Chemsitry on the Semantic WebMicrosoft e-ScienceBerkeleyA?!BMonica Duke Michael Day Rachel Heery Leslie A. Carr Simon J. Coles2005CEnhancing access to research data: the challenge of crystallography46-55HProceedings of the 5th ACM/IEEE-CS joint conference on Digital librariesDenver, CO, USAACM1065397*http://doi.acm.org/10.1145/1065385.1065397 D?!&Coles, Simon Carr, Leslie Frey, Jeremy20087Experiences with repositories and blogs in laboratoriesOpen Repositories 2008Jscientific data repositories, e-science, cyberinfrastructure, preservation eps:50901!http://eprints.soton.ac.uk/50901/#?De Roure, David Goble, Carole20083Re-evaluating the Grid: the social life of programs201-2127Danelutto, Marco Fragopoulou, Paraskevi Getov, VladimirSpringer-Verlag New York Inc."Grid, Scientific Workflow, Web 2.0This 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. ecs:15663%http://eprints.ecs.soton.ac.uk/15663/?Robinson, Jamie M. Frey, Jeremy G. De Roure, D. C. Stanford-Clark, Andrew J. Reynolds, Andrew D. Bedi, Bharat V. Conway-Jones, D.2006TThe Combechem MQTT LEGO microscope: a grid enabled scientific apparatus demonstrator393-396*Proceedings of the Fifth All Hands MeetingNational eScience CenterJgrid, message queueing telemetry transport, ibm, broker, publish-subscribeGrid 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. eps:45432!http://eprints.soton.ac.uk/45432/?!)Coles, Simon Frey, Jeremy Milsted, Andrew2006Curation of chemistry from laboratory to publication: “The curation of laboratory experimental data as part of the overall data lifecycle”185-192#UK e-Science All Hands Meeting 2006National e-Science CentreFeprints, data, crystalography, provenance, dissemination, semantic webThe 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”. eps:41794!http://eprints.soton.ac.uk/41794/ vD?!/Stephen, Wilson Frey, Jeremy G. Coles, Simon J.2009)Second Life: The next virtual laboratory?)UK e-Science All Hands Meeting (AHM 2009) 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. eps:148087"http://eprints.soton.ac.uk/148087/D?!Wilson, Stephen Frey, Jeremy G.2009'Web tools, mashups and automated lasers)UK e-Science All Hands Meeting (AHM 2009)]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 eps:148095"http://eprints.soton.ac.uk/148095/fD?!Wilson, Stephen Frey, Jeremy G.20093Critical zone observatories and sensor repositories)UK e-Science All Hands Meeting (AHM 2009)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. eps:148091"http://eprints.soton.ac.uk/148091/D?!-Wilson, Stephen Birch, Oliver Frey, Jeremy G.2009/The LEGO laboratory: laser induced fluorescence)UK e-Science All Hands Meeting (AHM 2009)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 eps:148075"http://eprints.soton.ac.uk/148075/D?!-Blower, J. Santokhee, A. Frey, J. Milsted, A.2010aBlogMyData: A Virtual Research Environment for collobaroative visualization of environmental data AHM 2010 Cardiff, UKlD?!Wilson, S. Frey, J.2010&The Impact of e-Science o Real ScienceAHM 2010 Cardiff, UKD?!Borkum, M. Coles, S. Frey, J.2010HIntegration of oreChem with e-Crystals Repository for Crystal StructuresAHM 201 Cardiff, UKdD?! Taylor, K.R.2009&Blogging Meets Computational ChemistryAHM 2009 Oxford, UKD?!$Tizzard, G.J. Coles, S.J. Frey, J.G.20091Engaging Chemists: Making A Useable Lab Blog BookAll Hands Meeting 2009 Oxford, UKmD?! Taylor, K.R.2006+Semantic Units for Scientific Data ExchangeAHM 2006Nottingham, UK%D?!\Frey, Jeremy G. Gledhill, Robert J. Milsted, Andrew Kent, Sarah Essex, Jon W. Richards, G.W.2006=A computer-aided drug discovery system for chemistry teaching.American Chemical Society 232 National MeetingAmerican Chemical Society$malaria, grid, e-science, e-learningThe 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. eps:41499!http://eprints.soton.ac.uk/41499/D?!Frey, Jeremy G.2006CCombeChem: semantic support for the chemical information life cycle.American Chemical Society 232 National MeetingAmerican Chemical SocietyCombeChem, e-science, RDF, ELN, grid, cyber-infrastructure, crystallography, e-print, dissemination, end-to-end, publication@source, repositories, semanticsX“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”. eps:41498!http://eprints.soton.ac.uk/41498/CombeChem outputD?(Borkum, M. Coles, S. Lagoze, C. Frey, J.2010BUsing oreChemexperiments ontology: Planning and enacting chemistryACS RDF SymposiumBoston, MA, US#http://egonw.github.com/acsrdf2010/D?Wilson, S. Frey, J.2010Control, monitoring, analysis and dissemination of laboratory physical chemistry experiments using semantic web and broker technologiesACS RDF SymposiumBoston, MA, US$http://egongw.github.com/acsrdf2010/? Bicarregui, Juan Boulderstone, Richard Estelle, Lorraine Frey, Jeremy Jacobs, Neil Kilbride, William Matthews, Brian McGreevy, Robert200620/20 Vision: an e-Infrastructure for the next decade. Report of the Data and Information Creation Working Group to the e-Infrastructure Steering GroupOtherWe 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” . eps:42078!http://eprints.soton.ac.uk/42078/ ? Borda, Ann Careless, Jason Dimitrova, Maia Fraser, Michael Frey, Jeremy Hubbard, Paul Goldstein, Stéphane Pung, Caroline Shoebridge, Michele Wiseman, Norman2006gReport of the Working Group on Virtual Research Communities for the OST e-Infrastructure Steering GroupOther' 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). eps:42074!http://eprints.soton.ac.uk/42074/VRC final report`D?Bently, L. Cook, N. Frey, J. Derclaye, E. Donkin, R. Egan, G. Holderness, M. Hudson, L.J. Kelani, R. Korn, N. Mateer, M. Neylon, C. Roberts, D. Smith, V.20107Driving UK Research. Is copyright a help or a hindrance-http://www.bl.uk/ip/pdf/drivingukresearch.pdfThe British Library-http://www.bl.uk/ip/pdf/drivingukresearch.pdf? Coles, S.J.2007/The Repository for the Laboratory (R4L) Project3-4 DLib Magazine135http://www.dlib.org/dlib/march07/03inbrief.html#COLES 1082-9873D?!Frey, Jeremy G.2006Future Lab - "Smart not Dark"*Smart Lab: Laboratory Informatics Exchange4International Quality and Productivity Center (IQPC)ISmart Lab, ELN, Semantic, RDF, Grid, e-Science, HCI, lab journal, contextdDiscussion of the role of Electronic Laboratory Notebooks (ELN) is the future chemistry laboratories eps:20362!http://eprints.soton.ac.uk/20362/CombeChem OutputPK{H=I/**refs.frm 0B< !// !HPRIMARYyearIndex 6ByP/) idreference_type text_stylesauthoryear title pages secondary_title volume numbernumber_of_volumessecondary_authorplace_published publishersubsidiary_authoredition keywords type_of_workdate2)  abstractlabelurltertiary_titletertiary_author notes isbn custom_1 custom_2 custom_3 custom_4alternate_titleaccession_number call_number short_title custom_5 custom_6sectionoriginal_publicationH) reprint_editionreviewed_itemauthor_addressimagecaption custom_7 electronic_resource_number link_to_pdf translated_author translated_titlename_of_databasedatabase_providerresearch_notes language access_datelast_modified_date !! 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