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Inspired Research Is a Twice-Yearly Newsletter Published Letter from the by the Department of Computer Science at the University of Oxford

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Inspired Research Is a Twice-Yearly Newsletter Published Letter from the by the Department of Computer Science at the University of Oxford InspiredResearch Winter 2015 Issue 7 News from the Department of Computer Science, University of Oxford Resistance is Futile New computational model helps find innovative ways to tackle antibiotic resistance in bacteria – p8 Let’s get physical: embedded systems Royal Society Fellowship to study security issues around the interface between the physical world and embedded systems – p4 Railworker safety: the TrackSafe project Developing magneto-inductive positioning to protect lives on the railways – p16 Organic ‘computers’ made of DNA Processing data inside our bodies – p18 CompSciOxford DepartmentOfComputerScienceUniversityOfOxford Inspired Research is a twice-yearly newsletter published Letter from the by the Department of Computer Science at the University of Oxford. Head of Department If you would like to learn more As I scan through the articles to appear in this edition of Inspired about anything you read in these Research, I find myself struggling with an embarrassment of riches. pages, please get in touch: [email protected] In this issue, you will read about how our research is helping to keep To subscribe to future issues, workers safe on railways, and how it helps to deal with the problem e-mail: [email protected] of bacterial resistance to antibiotics; you will read about how our To download previous issues, visit researchers are helping to build safer buildings, by embedding www.cs.ox.ac.uk/inspiredresearch sensors into structures to monitor them for bending or twisting; you will read about how our security researchers are helping governments to construct IT systems that are safe against malicious attacks, and Editorial board how social media can be managed to prevent digital wildfires… Suzanna Marsh (Editor) What I find remarkable about all this is, apart from the sheer diversity, Kiri Walden (Sub-Editor) how clearly it demonstrates the ever-increasing role that computing Suvarna Designs (Designer) plays in our lives. As these examples clearly show, Oxford remains at the heart of the ongoing digital revolution, and I have no doubt that Jeremy Gibbons we will continue to be surprised and delighted by the innovations of Shoshannah Holdom Oxford’s computer scientists. Peter Jeavons Thomas Lukasiewicz We have just welcomed a new cohort of undergraduates, eager to drink their fill at Oxford’s fountain of knowledge – or possibly at the Martha Lewis Kings Arms. Everyone who gains a place to study at Oxford does so Daniel Marsden against fierce competition, but this year’s intake of Computer Science Benjamin Neal undergraduates has a special distinction: the programmes on which Daniel Neville they will study are now amongst the most competitive and sought after in Oxford, and indeed in the UK. Jason Nurse Dima Pasechnik We now receive 10 applicants for every undergraduate place we Kelly Ryan are able to offer. Most applications we receive are very strong, Helena Webb and the upshot of this is that we end up having to turn away large Frances Wheare numbers of outstanding candidates, simply because we don’t have enough places to offer. I would dearly like us to be able to offer more Maureen York undergraduate places, and this means expanding the number of tutorial fellows in our colleges. Contributors There are very promising signs that more colleges are interested Katherine Fletcher in offering Computer Science, or expanding their student numbers Tim Furche in our subject. I am particularly pleased to be able to welcome David Gavaghan new tutorial fellows at St Catherine’s College (Shimon Whiteson), St Anne’s College (Alex Rogers), and Magdalen College (Rahul David Hobbs Santhanam). It has been many years since our department welcomed Laura Jones three new tutorial fellows in the same year – I very much hope that Marta Kwiatkowska we will welcome more new tutorial fellows in the years to come. Andrew Markham Ursula Martin We hope you enjoy reading this edition of Inspired Research. As ever, we’d be delighted Daniel Nichol to hear from you if there’s anything of Bill Roscoe particular interest that you’d like to explore Julie Sheppard further; do get in touch via Michael Wooldridge [email protected] Professor Michael Wooldridge October 2015 2 Inspired Research: News from the Department of Computer Science, University of Oxford NEWS Not only are we rated highly by the News in brief academic community and industry, but by the student community too. Royal Society Research Professor, In University league tables produced Luca Cardelli has been awarded by The Guardian, for Computer the Programming Languages Science and Information Systems Achievement Award by ACM Oxford was awarded 100/100 for SIGPLAN. The award recognises student satisfaction and scored very individuals who have made a A league of our own well across all other categories. significant and lasting contribution In 2015 Oxford has been recognised to the field of programming as the best UK University for Oxford University is also the top languages. Computer Science. choice for anyone who wants to graduate and continue into a career Blanca Rodriguez and the The latest subject-specific tables in Computer Science or related Computational Cardiovascular produced by higher education data industries. Tech commentator Science Research Group have specialists QS rank Oxford as the website Business Insider has said been nominated for the Lush top University in Europe. In the Oxford is the best University in both Prize, for their work that supports Academic Reputation and Employer the UK and Europe to attend if you the replacement and reduction Reputation categories we surpass want a great job in tech. It identifies of animal testing. The Prize is a any other University in the world for investment from Google as just one collaboration between Lush, the Computer Science. reason for our success. well-known manufacturer and retailer of handmade cosmetics, of such models under different and Ethical Consumer, a research, Assessing models: experimental conditions: both to publishing and campaigning co- Web Lab characterise a model’s behaviours, operative. In September the department hosted and to compare hypotheses by the Cardiac Electrophysiology Web seeing how different models react Lab Workshop. The Web Lab (https:// under the same protocol. chaste.cs.ox.ac.uk/WebLab) is a https://goo.gl/AXjc1a new online system developed in the Computational Biology Group, that supports easy definition of simulated experimental protocols, and allows any heart cell model to be tested under these protocols. This enables examination of the behaviours Fellowship develop techniques to analyse linear dynamical systems for the awarded for purposes of automated verification. Dr Andrew Ker, a University verification of EPSRC Established Career Lecturer in the Department of linear dynamical Fellowships are awarded Computer Science, received an to academics who have an MPLS teaching award in June systems research outstanding track record of 2015. This followed Andrew ’s research, impact delivery, nomination for Most Acclaimed Professor James Worrell has been leadership and innovation. Lecturer in the 2015 Oxford awarded an EPSRC Established Fellowship holders at this level University Student Union (OUSU) Career Fellowship for a research are recognised internationally Teaching Awards. Professor project called Verification of Linear and are known for pushing the Andrew Martin, Director of the Dynamical Systems. Current boundaries of enquiry within their Centre for Doctoral Training in computer-aided design tools field. In addition to their strong Cyber Security, was the second allow engineers to create models academic profile, they show an member of the department and test them, but not to verify on-going commitment to inspire to receive a nomination, for them, ie, to conclusively prove and maximise the potential of future Outstanding Supervisor. that they meet their specification. research leaders. The goal of this project is to www.cs.ox.ac.uk Issue 7 Winter 2015 3 Let’s get physical: embedded systems Kasper Rasmussen has been awarded the Royal Society University Research Fellowship (URF) for 2015. Kasper joined University of Oxford in 2013 as a Lecturer in the Computer Science Department. Before coming to Oxford Kasper completed his PhD at the Department of Computer Science at ETH Zurich, and then worked as a post-doc at University of California, Irvine. Below he discusses the background to his research. The small computers that are The interfaces with embedded Initial experiments have shown automating more and more aspects systems that have most often that it is possible, indeed quite of our lives are collectively called been considered in the past are easy, to induce a current in the ‘embedded systems’ or sometimes radio interfaces, or components wires connecting a microphone cyber-physical systems. An that allow interaction with people, to an embedded system using embedded system consists of a eg buttons, keypads, etc. The an electromagnetic signal. This micro controller, ie a small chip interface that this project aims to means that such an embedded capable of performing calculations, explore is the interface between the system could be fooled into and some form of interaction with embedded system and the sensors believing that sound was present the physical world. Such systems and actuators that are attached to at the microphone, while in permeate every aspect of modern the system. fact the audio signal was being life: they are used in anything from induced using (inaudible) radio modern cars where embedded Any embedded system that wishes waves from (potentially) far away. systems manage braking, power to control or measure something, Due to that lack of authentication steering, engine performance, etc; must have a sensor or an actuator the micro controller has no way to factory control systems where attached as a peripheral element. of differentiating between a such systems control sensors and Sensors come in many different signal generated by the attached actuators as well as the flow of varieties but most are ‘dumb’ microphone and one induced diagnostic information.
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