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Technical report, MUCM Technical Report."},{"key":"ref40","unstructured":"Vernon I, Goldstein M (2014) Bayes linear emulation and history matching of stochastic systems biology models, in preparation."},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1007\/s00382-013-1896-4","article-title":"History matching for exploring and reducing climate model parameter space using observations and a large perturbed physics ensemble","volume":"41","author":"D Williamson","year":"2013","journal-title":"Climate Dynamics"},{"key":"ref42","unstructured":"Brynjarsdottir J, O&apos;Hagan A (2010) Learning about physical parameters: The importance of model discrepancy. Technical report, <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.tonyogahan.co.uk\/academic\/pub.html\" xlink:type=\"simple\">http:\/\/www.tonyogahan.co.uk\/academic\/pub.html<\/ext-link>."},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1198\/016214506000000203","article-title":"Bayes linear calibrated prediction for complex systems","volume":"101","author":"M Goldstein","year":"2006","journal-title":"JASA"},{"key":"ref44","first-page":"239","article-title":"A comparison of three methods for selecting values of input variables in the analysis of output from a computer code","volume":"21","author":"MD McKay","year":"1979","journal-title":"Technometrics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1198\/TECH.2009.08040","article-title":"Choosing the sample size of a computer experiment: a practical guide","volume":"51","author":"JL Loeppky","year":"2009","journal-title":"Technometrics"},{"key":"ref46","unstructured":"Williamson D, Vernon IR (2013) Efficient uniform designs for multi-wave computer experiments."},{"key":"ref47","unstructured":"Vernon I, Goldstein M (2009) Bayes linear analysis of imprecision in computer models, with application to understanding galaxy formation. In: Augustin T, Coolen FPA, editors, ISIPTA&apos;09: Proceedings of the Sixth International Symposium on Imprecise Probability: Theories and Applications. Durham, UK: SIPTA, pp.441\u2013450."},{"key":"ref48","doi-asserted-by":"crossref","unstructured":"Rasmussen CE, Williams CKI (2006) Gaussian Processes for Machine Learning. 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