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The use and treatment of animals in the provision of our food, clothing and other raw materials, as well as in the areas of medical research, sport and entertainment, polarises public opinion and provokes extreme views. Research by Professor Robert Garner on the ethics and politics of animal protection has provided a springboard for political debate and decision making both in the UK and internationally. In particular, Garner's work has impacted upon the debate within the animal protection movement, and has helped to shape aspects of government policy on animal welfare issues in general, most notably on the UK Government's approach to the issue of whaling, and DEFRA's approach to the ethics of using wild animals in circuses.
This case study describes the development, application and commercialisation of an open source tool, BSMBench that enables supercomputer vendors and computing centres to benchmark their system's performance. It comprehensively informs the design and testing of new computing architectures well beyond other benchmarking tools on the market, such as Linpack.
The significance of our code is that, unlike other benchmarking tools, it interpolates from a communication- to a computation-dominated regime simply by varying the (physics) parameters in the code, thus providing a perfect benchmark suite to test the response of modern multi-CPU systems along this axis. The impact of this work has great reach: a start-up company, BSMbench Ltd, has been founded to develop and commercialise the software; adopters have included IBM - one of the giants of the supercomputer world (where it uncovered errors in their compilers); it has been deployed by Fujitsu to validate its systems, by HPC Wales, a multi-site, commercially focussed national computer centre and by Transtec, an HPC company employing over 150 staff; and tutorial articles about BSMBench have appeared in magazines such as Linux Format.
This software tool spawned from our research into "Beyond the Standard Model" (BSM) physics which aims to understand the Higgs mechanism in particle physics at a fundamental level. This involved simulating quantum field theories using bespoke code on some of the fastest supercomputers on the planet.
Knowledge of the three-dimensional structures of macromolecules is a prerequisite for understanding their function at the atomic level, an essential component of modern drug development. Most structures are determined by X-ray crystallography: the majority using molecular replacement (MR, which exploits known structures of related proteins), and about half of the remainder using single-wavelength anomalous diffraction (SAD). The Phaser crystallographic software, developed by Read and colleagues, implements powerful new likelihood-based methods for MR and SAD phasing and has made a large impact, accelerating over the period 2008-2013. At the pharma giant, AstraZeneca, Phaser is considered the "tool of choice" for solving structures by MR.
Novel bioluminescent bacterial biosensors developed at UWE, Bristol, and commercialised by Randox, have been used by a range of companies to demonstrate effectiveness of drugs and decontamination procedures. This has improved development processes at companies including Clavis Pharma, Purest Solutions and Dycem, leading to new manufacturing processes and quality control test methods. The biosensors are used in novel applications to give pharmacodynamic data on effectiveness of drugs and real time in-situ demonstration of effectiveness of decontamination processes. These biosensors, pioneered and developed by Vyv Salisbury's group, have been commercially adopted and used for evaluation by at least six collaborating companies.
The Beazley Archive Online Database enables large and diverse audiences to access and understand ancient art through Oxford research. It allows users around the world to ask and answer their own research questions and to learn about ancient imagery. It is principally dedicated to the study of ancient Athenian figure-decorated pottery and ancient/neo-classical engraved gems. It makes available hundreds of thousands of pictures and information-fields which can be browsed and searched in a variety of ways, according to the level and requirements of the user. The Database is the foremost academic tool for the study of ancient Greek pottery, but its demonstrable impact extends far beyond academia, to an international audience of students, educators, museums, businesses, and private researchers.
Pre-eclampsia is a major contributor to death and disability in pregnancy. Diagnosis, based on accurate blood pressure (BP)/proteinuria determination, is limited by measurement errors and being late features of the disease. In collaboration with industry, King's College London (KCL) researchers have developed an inexpensive, accurate, simple BP device suitable for rural clinics. This device allows intervention to reduce mortality/morbidity and is currently being rolled out in a Gates Foundation project in Africa and Asia. KCL researchers have also helped the company Alere Inc. with the development of a diagnostically accurate test of placental growth factor (PlGF) in women with suspected pre-eclampsia: Alere Triage®PlGF. This demonstrates high sensitivity, superior to current tests, and following commercialisation is being adopted internationally. Their work is additionally reflected in guidelines of international standards for BP device accuracy.
Development of the human cell GADD45a assay enabled accurate identification of carcinogens in vitro, with a low rate of misleading positives. Through the spin-out company Gentronix, this research is reducing costs to industry and decreasing the use of animals in research. Industrial collaboration has enabled commercial adoption of the technology in many sectors. With a 10-fold increase in orders in 2012 versus 2008, Gentronix is a profitable business employing 17 people and with an annual turnover of £1.88m. During 2008-12, Gentronix released a series of new products, established testing services, and signed a product license agreement with GlaxoSmithKline. More than 100 companies worldwide are using Gentronix kits, including pharmaceutical, agricultural and health and beauty companies, along with manufacturers of food flavourings and household goods. The Gentronix assay is currently being reviewed by the European Centre for the Validation of Alternative Methods.
OxCal is the most popular software package world-wide for calibrating and analysing dates within the carbon dating process, enabling the accurate dating of objects from the past. The brainchild of Prof. Christopher Bronk Ramsey, Director of the Oxford Radiocarbon Accelerator Unit (ORAU), OxCal is based on chronologies refined by the use of Bayesian statistical methods, and provides users with access to high-quality calibration of chronological data, now the basis for global chronologies. It is available online and free to download, and has played a highly significant role in establishing the ORAU as one of the pre-eminent international radiocarbon dating facilities. Funded by the NERC, and used widely within professional archaeology as well as other disciplines, OxCal has also played a key role in research projects (within Oxford and beyond) brought to the attention of the general public by the media.
Research in Multi-spectral Imaging (MSI) of manuscripts by researchers in the University of Oxford's Faculty of Classics has led to advances in imaging technology. A series of initiatives by Dr Dirk Obbink that captured images through MSI technology have led to the decipherment of new texts that have made a substantial mark in the public sector. Equity spinout of this technology has resulted in the entry in the market of the first portable multispectral scanning unit in flat-bed desktop format. The scanner, which uses innovative patented LED technology at different levels of the light spectrum, was developed under funding from ISIS, Oxford University's technology transfer division.
The work described here has impacted on European policy and standards concerning energy efficiency in Building Services.
The impact arises from two Welsh School of Architecture led and European Commission funded projects, HARMONAC (focussed on inspection of air-conditioning systems) and iSERV (focussed on automatic system monitoring and feedback). These pan-European projects demonstrate achieved energy savings of up to 33% of total building electricity use in individual buildings, and potential savings up to €60Bn. These projects demonstrably impacted the recast European Energy Performance of Buildings Directive (EPBD) and the revision of EU Standards (European Committee for Standardisation (CEN)).