TY - JOUR T1 - Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography JF - Ophthalmic Surg Lasers Imaging Retina Y1 - 2014 A1 - Croft, D.E. A1 - van Hemert, J. A1 - Wykoff, C.C. A1 - Clifton, D. A1 - Verhoek, M. A1 - Fleming, A. A1 - Brown, D.M. KW - medical KW - retinal imaging AB - BACKGROUND AND OBJECTIVE: Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. PATIENTS AND METHODS: Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. RESULTS: Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. CONCLUSION: By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. [Ophthalmic Surg Lasers Imaging Retina. 2014;45:312-317.]. VL - 45 ER - TY - JOUR T1 - Quantification of Ultra-Widefield Retinal Images JF - Retina Today Y1 - 2014 A1 - D.E. Croft A1 - C.C. Wykoff A1 - D.M. Brown A1 - van Hemert, J. A1 - M. Verhoek KW - medical KW - retinal imaging AB - Advances in imaging periodically lead to dramatic changes in the diagnosis, management, and study of retinal disease. For example, the innovation and wide-spread application of fluorescein angiography and optical coherence tomography (OCT) have had tremendous impact on the management of retinal disorders.1,2 Recently, ultra-widefield (UWF) imaging has opened a new window into the retina, allowing the capture of greater than 80% of the fundus with a single shot.3 With montaging, much of the remaining retinal surface area can be captured.4,5 However, to maximize the potential of these new modalities, accurate quantification of the pathology they capture is critical. UR - http://www.bmctoday.net/retinatoday/pdfs/0514RT_imaging_Croft.pdf ER - TY - CONF T1 - Automatic Extraction of the Optic Disc Boundary for Detecting Retinal Diseases T2 - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) Y1 - 2013 A1 - M.S. Haleem A1 - L. Han A1 - B. Li A1 - A. Nisbet A1 - van Hemert, J. A1 - M. Verhoek ED - L. Linsen ED - M. Kampel KW - retinal imaging AB - In this paper, we propose an algorithm based on active shape model for the extraction of Optic Disc boundary. The determination of Optic Disc boundary is fundamental to the automation of retinal eye disease diagnosis because the Optic Disc Center is typically used as a reference point to locate other retinal structures, and any structural change in Optic Disc, whether textural or geometrical, can be used to determine the occurrence of retinal diseases such as Glaucoma. The algorithm is based on determining a model for the Optic Disc boundary by learning patterns of variability from a training set of annotated Optic Discs. The model can be deformed so as to reflect the boundary of Optic Disc in any feasible shape. The algorithm provides some initial steps towards automation of the diagnostic process for retinal eye disease in order that more patients can be screened with consistent diagnoses. The overall accuracy of the algorithm was 92% on a set of 110 images. JF - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM) PB - {ACTA} Press ER - TY - JOUR T1 - The Cloud Paradigm Applied to e-Health JF - BMC Med. Inf. {&} Decision Making Y1 - 2013 A1 - Jordi Vilaplana A1 - Francesc Solsona A1 - Francesc Abella A1 - Rosa Filgueira A1 - Josep Rius Torrento VL - 13 ER - TY - CONF T1 - Towards Addressing CPU-Intensive Seismological Applications in Europe T2 - International Supercomputing Conference Y1 - 2013 A1 - Michele Carpené A1 - I.A. Klampanos A1 - Siew Hoon Leong A1 - Emanuele Casarotti A1 - Peter Danecek A1 - Graziella Ferini A1 - Andre Gemünd A1 - Amrey Krause A1 - Lion Krischer A1 - Federica Magnoni A1 - Marek Simon A1 - Alessandro Spinuso A1 - Luca Trani A1 - Malcolm Atkinson A1 - Giovanni Erbacci A1 - Anton Frank A1 - Heiner Igel A1 - Andreas Rietbrock A1 - Horst Schwichtenberg A1 - Jean-Pierre Vilotte AB - Advanced application environments for seismic analysis help geoscientists to execute complex simulations to predict the behaviour of a geophysical system and potential surface observations. At the same time data collected from seismic stations must be processed comparing recorded signals with predictions. The EU-funded project VERCE (http://verce.eu/) aims to enable specific seismological use-cases and, on the basis of requirements elicited from the seismology community, provide a service-oriented infrastructure to deal with such challenges. In this paper we present VERCE’s architecture, in particular relating to forward and inverse modelling of Earth models and how the, largely file-based, HPC model can be combined with data streaming operations to enhance the scalability of experiments.We posit that the integration of services and HPC resources in an open, collaborative environment is an essential medium for the advancement of sciences of critical importance, such as seismology. JF - International Supercomputing Conference CY - Leipzig, Germany ER - TY - CHAP T1 - Multi-agent Negotiation of Virtual Machine Migration Using the Lightweight Coordination Calculus T2 - Agent and Multi-Agent Systems. Technologies and Applications Y1 - 2012 A1 - Anderson, Paul A1 - Shahriar Bijani A1 - Vichos, Alexandros ED - Jezic, Gordan ED - Kusek, Mario ED - Nguyen, Ngoc-Thanh ED - Howlett, Robert ED - Jain, Lakhmi JF - Agent and Multi-Agent Systems. Technologies and Applications T3 - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 7327 SN - 978-3-642-30946-5 UR - http://dx.doi.org/10.1007/978-3-642-30947-2_16 ER - TY - JOUR T1 - Principles of Provenance (Dagstuhl Seminar 12091) JF - Dagstuhl Reports Y1 - 2012 A1 - James Cheney A1 - Anthony Finkelstein A1 - Bertram Ludäscher A1 - Stijn Vansummeren VL - 2 ER - TY - CONF T1 - Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway T2 - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences Y1 - 2012 A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Jäkel, René A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Dos Santos Vieira, Ines JF - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences PB - IOS Press ER - TY - JOUR T1 - An evaluation of ontology matching in geo-service applications JF - Geoinformatica Y1 - 2011 A1 - Lorenzino Vaccari A1 - Pavel Shvaiko A1 - Juan Pane A1 - Paolo Besana A1 - Maurizio Marchese ER - TY - RPRT T1 - Data-Intensive Research Workshop (15-19 March 2010) Report Y1 - 2010 A1 - Malcolm Atkinson A1 - Roure, David De A1 - van Hemert, Jano A1 - Shantenu Jha A1 - Ruth McNally A1 - Robert Mann A1 - Stratis Viglas A1 - Chris Williams KW - Data-intensive Computing KW - Data-Intensive Machines KW - Machine Learning KW - Scientific Databases AB - We met at the National e-Science Institute in Edinburgh on 15-19 March 2010 to develop our understanding of DIR. Approximately 100 participants (see Appendix A) worked together to develop their own understanding, and we are offering this report as the first step in communicating that to a wider community. We present this in turns of our developing/emerging understanding of "What is DIR?" and "Why it is important?'". We then review the status of the field, report what the workshop achieved and what remains as open questions. JF - National e-Science Centre PB - Data-Intensive Research Group, School of Informatics, University of Edinburgh CY - Edinburgh ER - TY - CONF T1 - Adoption of e-Infrastructure Services: inhibitors, enablers and opportunities T2 - 5th International Conference on e-Social Science Y1 - 2009 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Fragkouli, E. A1 - Anderson, S. A1 - Hughes, L. A1 - Fergusson, D. A1 - Vander Meer, E. A1 - Atkinson, M. AB - Based on more than 100 interviews with respondents from the academic community and information services, we present findings from our study of inhibitors and enablers of adoption of e-Infrastructure services for research. We discuss issues raised and potential ways of addressing them. JF - 5th International Conference on e-Social Science CY - Maternushaus, Cologne ER - TY - JOUR T1 - Distributed Computing Education, Part 1: A Special Case? JF - IEEE Distributed Systems Online Y1 - 2008 A1 - Fergusson, D. A1 - Hopkins, R. A1 - Romano, D. A1 - Vander Meer, E. A1 - Atkinson, M. VL - 9 UR - http://dsonline.computer.org/portal/site/dsonline/menuitem.9ed3d9924aeb0dcd82ccc6716bbe36ec/index.jsp?&pName=dso_level1&path=dsonline/2008/06&file=o6002edu.xml&xsl=article.xsl&;jsessionid=LZ5zjySvc2xPnVv4qTYJXhlvwSnRGGj7S7WvPtrPyv23rJGQdjJr!982319602 IS - 6 ER - TY - JOUR T1 - Distributed Computing Education, Part 2: International Summer Schools JF - IEEE Distributed Systems Online Y1 - 2008 A1 - Fergusson, D. A1 - Hopkins, R. A1 - Romano, D. A1 - Vander Meer, E. A1 - Atkinson, M. VL - 9 UR - http://dsonline.computer.org/portal/site/dsonline/menuitem.9ed3d9924aeb0dcd82ccc6716bbe36ec/index.jsp?&pName=dso_level1&path=dsonline/2008/07&file=o7002edu.xml&xsl=article.xsl& IS - 7 ER - TY - JOUR T1 - Distributed Computing Education, Part 3: The Winter School Online Experience JF - Distributed Systems Online Y1 - 2008 A1 - Low, B. A1 - Cassidy, K. A1 - Fergusson, D. A1 - Atkinson, M. A1 - Vander Meer, E. A1 - McGeever, M. AB - The International Summer Schools in Grid Computing (ISSGC) have provided numerous international students with the opportunity to learn grid systems, as detailed in part 2 of this series (http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.20). The International Winter School on Grid Computing 2008 (IWSGC 08) followed the successful summer schools, opening up the ISSGC experience to a wider range of students because of its online format. The previous summer schools made it clear that many students found the registration and travel costs and the time requirements prohibitive. The EU FP6 ICEAGE project held the first winter school from 6 February to 12 March 2008. The winter school repurposed summer school materials and added resources such as the ICEAGE digital library and summer-school-tested t-Infrastructures such as GILDA (Grid INFN Laboratory for Dissemination Activities). The winter schools shared the goals of the summer school, which emphasized disseminating grid knowledge. The students act as multipliers, spreading the skills and knowledge they acquired at the winter school to their colleagues to build strong and enthusiastic local grid communities. PB - IEEE Computer Society VL - 9 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4659260 IS - 9 ER - TY - JOUR T1 - Distributed Computing Education, Part 4: Training Infrastructure JF - Distributed Systems Online Y1 - 2008 A1 - Fergusson, D. A1 - Barbera, R. A1 - Giorgio, E. A1 - Fargetta, M. A1 - Sipos, G. A1 - Romano, D. A1 - Atkinson, M. A1 - Vander Meer, E. AB - In the first article of this series (see http://doi.ieeecomputersociety.org/10.1109/MDSO.2008.16), we identified the need for teaching environments that provide infrastructure to support education and training in distributed computing. Training infrastructure, or t-infrastructure, is analogous to the teaching laboratory in biology and is a vital tool for educators and students. In practice, t-infrastructure includes the computing equipment, digital communications, software, data, and support staff necessary to teach a course. The International Summer Schools in Grid Computing (ISSGC) series and the first International Winter School on Grid Computing (IWSGC 08) used the Grid INFN Laboratory of Dissemination Activities (GILDA) infrastructure so students could gain hands-on experience with middleware. Here, we describe GILDA, related summer and winter school experiences, multimiddleware integration, t-infrastructure, and academic courses, concluding with an analysis and recommendations. PB - IEEE Computer Society VL - 9 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4752926 IS - 10 ER - TY - RPRT T1 - Education and Training Task Force Report Y1 - 2008 A1 - Atkinson, M. A1 - Vander Meer, E. A1 - Fergusson, D. A1 - Artacho, M. AB - The development of e-Infrastructure, of which grid computing is a fundamental element, will have major economic and social benefits. Online and financial businesses already successfully use grid computing technologies, for instance. There are already demonstrations showing the benefits to engineering, medicine and the creative industries as well. New research methods and technologies generate large data sets that need to be shared in order to ensure continued social and scientific research and innovation. e-Infrastructure provides an environment for coping with these large data sets and for sharing data across regions. An investment in educating people in this technology, then, is an investment that will strengthen our economies and societies. In order to deliver e-Infrastructure education and training successfully in the EU, we must develop a policy framework that will ensure shared responsibility and equivalent training in the field. This document focuses primarily on the current state of grid and e-Science education, introducing key challenges and the opportunities available to educational planners that serve as a starting point for further work. It then proposes strategies and policies to provide a supportive framework for e-Infrastructure education and training. The ETTF Report concludes with policy recommendations to be taken forward by the e-IRG. These recommendations address issues such as the level of Member State investment in e-Infrastructure education, the harmonisation of education in distributed-computation thinking and in the use of e-Infrastructure and the development of standards for student and teacher identification, for the sharing of t-Infrastructure (and training material) and for accreditation. JF - e-Infrastructure Reflection Group UR - http://www.e-irg.eu/index.php?option=com_content&task=view&id=38&Itemid=37 ER - TY - CONF T1 - Fostering e-Infrastructures: from user-designer relations to community engagement T2 - Symposium on Project Management in e-Science Y1 - 2008 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Halfpenny, P. A1 - Procter, R. A1 - Anderson, S. A1 - Dunn, S. A1 - Fragkouli, E. A1 - Hughes, L. A1 - Atkinson, M. A1 - Fergusson, D. A1 - Mineter, M. A1 - Rodden, T. AB - In this paper we discuss how e-Science can draw on the findings, approaches and methods developed in other disciplines to foster e-Infrastructures for research. We also discuss the issue of making user involvement in IT development scale across an open ommunity of researchers and from single systems to distributed e-Infrastructures supporting collaborative research. JF - Symposium on Project Management in e-Science CY - Oxford ER - TY - JOUR T1 - A Grid infrastructure for parallel and interactive applications JF - Computing and Informatics Y1 - 2008 A1 - Gomes, J. A1 - Borges, B. A1 - Montecelo, M. A1 - David, M. A1 - Silva, B. A1 - Dias, N. A1 - Martins, JP A1 - Fernandez, C. A1 - Garcia-Tarres, L. , A1 - Veiga, C. A1 - Cordero, D. A1 - Lopez, J. A1 - J Marco A1 - Campos, I. A1 - Rodríguez, David A1 - Marco, R. A1 - Lopez, A. A1 - Orviz, P. A1 - Hammad, A. VL - 27 IS - 2 ER - TY - CONF T1 - Widening Uptake of e-Infrastructure Services T2 - 4th International Conference on e-Social Science Y1 - 2008 A1 - Voss, A. A1 - Asgari-Targhi, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Dunn, S. A1 - Fragkouli, E. A1 - Anderson, S. A1 - Hughes, L. A1 - Mineter, M. A1 - Fergusson, D. A1 - Atkinson, M. AB - This paper presents findings from the e-Uptake project which aims to widen the uptake of e-Infrastructure Services for research. We focus specifically on the identification of barriers and enablers of uptake and the taxonomy developed to structure our findings. Based on these findings, we describe the development of a number of interventions such as training and outreach events, workshops and the deployment of a UK 'one-stop-shop' for support and event information as well as training material. Finally, we will describe how the project relates to other ongoing community engagement efforts in the UK and worldwide. Introduction Existing investments in e-Science and Grid computing technologies have helped to develop the capacity to build e-Infrastructures for research: distributed, networked, interoperable computing and data resources that are available to underpin a wide range of research activities in all research disciplines. In the UK, the Research Councils and the JISC are funding programmes to support the development of essential components of such infrastructures such as National Grid Service (www.ngs.ac.uk) or the UK Access Management Federation (www.ukfederation.org.uk) as well as discipline-specific efforts to build consistent and accessible instantiations of e-Infrastructures, for example the e- Infrastructure for the Social Sciences (Daw et al. 2007). These investments are complemented by an active programme of community engagement (Voss et al. 2007). As part of the community engagement strand of its e-Infrastructure programme, JISC has funded the e-Uptake project, a collaboration between the ESRC National Centre for e-Social Science at the University of Manchester, the Arts & Humanities e-Science Support Centre at King's College London and the National e-Science Centre at the University of Edinburgh. In this paper we present the project's activities to date to widen the uptake of e-Infrastructure services by eliciting information about the barriers to and enablers of uptake, developing adequate interventions such as training and outreach events, running workshops and the deploying a UK 'one-stop-shop' for support and event information as well as training material. JF - 4th International Conference on e-Social Science CY - Manchester UR - http://www.ncess.ac.uk/events/conference/programme/workshop1/?ref=/programme/thurs/1aVoss.htm ER - TY - CONF T1 - e-Research Infrastructure Development and Community Engagement T2 - All Hands Meeting 2007 Y1 - 2007 A1 - Voss, A. A1 - Mascord, M. A1 - Fraser, M. A1 - Jirotka, M. A1 - Procter, R. A1 - Halfpenny, P. A1 - Fergusson, D. A1 - Atkinson, M. A1 - Dunn, S. A1 - Blanke, T. A1 - Hughes, L. A1 - Anderson, S. AB - The UK and wider international e-Research initiatives are entering a critical phase in which they need to move from the development of the basic underlying technology, demonstrators, prototypes and early applications to wider adoption and the development of stable infrastructures. In this paper we will review existing work on studies of infrastructure and community development, requirements elicitation for existing services as well as work within the arts and humanities and the social sciences to establish e-Research in these communities. We then describe two projects recently funded by JISC to study barriers to adoption and responses to them as well as use cases and service usage models. JF - All Hands Meeting 2007 CY - Nottingham, UK ER - TY - CONF T1 - An Engineering Approach to Evolutionary Art T2 - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) Y1 - 2001 A1 - van Hemert, J. I. A1 - Jansen, M. L. M. ED - Lee Spector ED - Erik D. Goodman ED - Annie Wu ED - W. B. Langdon ED - Hans-Michael Voigt ED - Mitsuo Gen ED - Sandip Sen ED - Marco Dorigo ED - Shahram Pezeshk ED - Max H. Garzon ED - Edmund Burke KW - evolutionary art AB - We present a general system that evolves art on the Internet. The system runs on a server which enables it to collect information about its usage world wide; its core uses operators and representations from genetic program-ming. We show two types of art that can be evolved using this general system. JF - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001) PB - Morgan Kaufmann Publishers, San Francisco ER - TY - CONF T1 - A ``Futurist'' approach to dynamic environments T2 - Proceedings of the Workshops at the Genetic and Evolutionary Computation Conference, Dynamic Optimization Problems Y1 - 2001 A1 - van Hemert, J. I. A1 - Van Hoyweghen, C. A1 - Lukschandl, E. A1 - Verbeeck, K. ED - J. Branke ED - Th. B{\"a}ck KW - dynamic problems AB - The optimization of dynamic environments has proved to be a difficult area for Evolutionary Algorithms. As standard haploid populations find it difficult to track a moving target, diffKerent schemes have been suggested to improve the situation. We study a novel approach by making use of a meta learner which tries to predict the next state of the environment, i.e. the next value of the goal the individuals have to achieve, by making use of the accumulated knowledge from past performance. JF - Proceedings of the Workshops at the Genetic and Evolutionary Computation Conference, Dynamic Optimization Problems PB - Morgan Kaufmann Publishers, San Francisco ER - TY - Generic T1 - VLDB'99, Proceedings of 25th International Conference on Very Large Data Bases, September 7-10, 1999, Edinburgh, Scotland, UK Y1 - 1999 A1 - Atkinson, Malcolm P. A1 - Maria E. Orlowska A1 - Patrick Valduriez A1 - Stanley B. Zdonik A1 - Michael L. Brodie ED - Atkinson, Malcolm P. ED - Maria E. Orlowska ED - Patrick Valduriez ED - Stanley B. Zdonik ED - Michael L. Brodie PB - Morgan Kaufmann SN - 1-55860-615-7 ER -