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Publications

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2009
J. Koetsier, Turner, A., Richardson, P., and van Hemert, J. I., Rapid chemistry portals through engaging researchers, in Fifth IEEE International Conference on e-Science, Oxford, UK, 2009, pp. 284-291.
J. Koetsier and van Hemert, J. I., Rapid development of computational science portals, in Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences, Edinburgh, 2009.
K. Schneeberger, Hagmann, J., Ossowski, S., Warthmann, N., Gesing, S., Kohlbacher, O., and Weigel, D., Simultaneous alignment of short reads against multiple genomes, Genome Biol, vol. 10, p. R98, 2009.
M. Atkinson, Meer, E. V., Fergusson, D., Davenhall, C., and Mehammed, H., Strategies and Policies to Support and Advance Education in e-Science, Computing Now, 2009.
D. ’ F. S. W. e-Science Group, Atkinson, M., Britton, D., Coveney, P., De Roure, D., Garnett, N., Geddes, N., Gurney, R., Haines, K., Hughes, L., Ingram, D., Jeffreys, P., Lyon, L., Osborne, I., Perrott, P., R., P., and Rusbridge, C., A Strategy for Research and Innovation in the Century of Information, Prometheus, vol. 27, pp. 27-45, 2009.
J. D. Armstrong and van Hemert, J. I., Towards a Virtual Fly Brain, Philosophical Transactions A, vol. 367, p. 2387--2397, 2009.
J. Fernández, Han, L., Nuñez, A., Carretero, J., and van Hemert, J., Using architectural simulation models to aid the design of data intensive application, in The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009), Sliema, Malta, 2009, p. 163--168.
G. Wickler, Beckett, G., Han, L., Koo, S. H., Potter, S., Pringle, G., and Tate, A., Using Simulation for Decision Support: Lessons Learned from FireGrid, in Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009), Gothenburg, Sweden, 2009.
J. O’Donoghue and van Hemert, J. I., Using the DCC Lifecycle Model to Curate a Gene Expression Database: A Case Study, International Journal of Digital Curation, vol. 4, no. 3, 2009.
2010
L. Han, Saengngam, T., and van Hemert, J., Accelerating Data-Intensive Applications: a Cloud Computing Approach Image Pattern Recognition Tasks, in The Fourth International Conference on Advanced Engineering Computing and Applications in Sciences, 2010.
R. Filgueira, Singh, D. E., Calderón, A., Carballeira, F. G., and Carretero, J., Adaptive CoMPI: Enhancing MPI based applications performance and scalability by using adaptive compression., International Journal of High Performance Computing and Applications, 2010. Sage, no. 25 (3), 2010.
M. Cuggia, Besana, P., and Glasspool., D., Comparing Clinical Decision Support Systems for Recruitment in Clinical Trials, Journal of Medical Informatics, 2010.
R. R. Kitchen, Sabine, V. S., Sims, A. H., Macaskill, E. J., Renshaw, L., Thomas, J. S., van Hemert, J. I., Dixon, J. M., and Bartlett, J. M. S., Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles, BMC Genomics, vol. 11, no. 134, 2010.
M. Atkinson, Roure, D. D., van Hemert, J., Jha, S., McNally, R., Mann, R., Viglas, S., and Williams, C., Data-Intensive Research Workshop (15-19 March 2010) Report, Data-Intensive Research Group, School of Informatics, University of Edinburgh, Edinburgh, 2010.
R. Filgueira, Carretero, J., Singh, D. E., Calderón, A., and Nunez, A., Dynamic-CoMPI: Dynamic optimization techniques for MPI parallel applications., The Journal of Supercomputing., 2010.
L. Han, Exploiting P2P and Grid Computing Technologies for Resource Sharing to support High Performance Distributed System, in Handbook of Research on P2P and Grid Systems for Service-Oriented Computing: Models, Methodologies and Applications , vol. 1, 2 vol., N. Antonopoulos, Exarchakos, G., Li, M., and Liottac, A. IGI Global publishing, 2010.
G. Yaikhom, Liew, C., Han, L., van Hemert, J., Atkinson, M., and Krause, A., Federated Enactment of Workflow Patterns, Lecture Notes in Computer Science, vol. 6271. Springer Berlin / Heidelberg, pp. 317-328, 2010.
G. Birkenheuer, Breuers, S., Brinkmann, A., Blunk, D., Fels, G., Gesing, S., Herres-Pawlis, S., Kohlbacher, O., Krüger, J., and Packschies, L., Grid-Workflows in Molecular Science, in Software Engineering 2010, Grid Workflow Workshop, 2010.
B. Dobrzelecki, Krause, A., Hume, A. C., Grant, A., Antonioletti, M., Alemu, T. Y., Atkinson, M., Jackson, M., and Theocharopoulos, E., Integrating distributed data sources with OGSA--DAI DQP and Views, Philosophical Transactions A, vol. 368, p. 4133--4145, 2010.
C. A. Morrison, Robertson, N., Turner, A., van Hemert, J., and Koetsier, J., Molecular Orbital Calculations of Inorganic Compounds, in Inorganic Experiments, 3rd ed., D. J. Woollins Wiley-VCH, 2010, p. 261--267.
M. Wewior, Packschies, L., Blunk, D., Wickeroth, D., Warzecha, K., Herres-Pawlis, S., Gesing, S., Breuers, S., Krüger, J., Birkenheuer, G., and Lang, U., The MoSGrid Gaussian Portlet – Technologies for the Implementation of Portlets for Molecular Simulations, in Proceedings of the International Workshop on Science Gateways (IWSG10), 2010.
D. Rodríguez, Carpenter, T. K., van Hemert, J. I., and Wardlaw, J. M., An open source toolkit for medical imaging de-identification, European Radiology, vol. 20, no. 8, p. 1896--1904, 2010.
A. Tichopad, Bar, T., Pecen, L., Kitchen, R. R., Kubista, M., and Pfaffl, M. W., Quality control for quantitative PCR based on amplification compatibility test, Methods, vol. 50, no. 4, pp. 308-312 , 2010.
D. A. Bacigalupo, van Hemert, J., Usmani, A., Dillenberger, D. N., Wills, G. B., and Jarvis, S. A., Resource management of enterprise cloud systems using layered queuing and historical performance models, in IEEE International Symposium on Parallel Distributed Processing, 2010, p. 1--8.
R. R. Kitchen, Kubista, M., and Tichopad, A., Statistical aspects of quantitative real-time PCR experiment design, Methods, vol. 50, no. 4, pp. 231-236, 2010.

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