A warm welcome to the CDT!

1. A warm welcome to the CDT!

2. Welcome Introduction Session Overview • Introduction to Important People • Introduction to Centre for Doctoral Training programme – history and its goals • Overview of 4yr programme • 4yr General Scheme • Year 1 • Today and next week (university-wide induction week, week 0) • Today • Next week

3. Important People • Dr Gari Clifford (me), CDT Director until 31st Dec • Dr Vicente Grau, Incoming Director 1st Jan 2014 • Dr Michael Chappell, Associate Director • Jo Armitage, Administrator of CDT

4. Important People • You! • Let’s make some introductions • Name • College • Education/employment • Any other thing you want to say.....

5. Other Key People at the IBME Biomedical Engineering Academics • Dr Bob Carlisle (Drug delivery) • Dr Michael Chappell (Imaging and physiological modelling) • Professor Robin Cleveland (Ultrasonics) • Dr Gari Clifford (Signal Processing, Machine Learning & mHealth) • Prof. Constantin Coussios (Ultrasonics & drug delivery) • Prof. Zhanfeng Cui (Tissue Engineering) • Prof. Pete Dobson (Begbroke Science Park, Healthcare Innovation) • Dr. Vicente Grau (Biomedical image analysis) • Prof. Alison Noble (Biomedical imaging and image analysis) • Dr. Stephen Payne (Cardiovascular Modelling) • Dr Jens Rittscher (Biological image Analysis and Bioinformatics ) • Dr. Julia Schnabel (Biomedical image analysis) • Dr. Penny Smith (Image Measurement) • Dr Eleanor Stride (Ultrasonics) • Dr. Mark Thompson (Orthopaedic Biomechanics) • Prof. Lionel Tarassenko (Signal Processing & e-Health) • Dr. Cathy Ye (Tissue Engineering) • Dr. Amy Zavatsky (Orthopaedic Biomechanics) IBME Administrative Team • Jo Armitage CDT Administrator • Stacey Churcher PA to Prof Noble, Group AA to Biomedical Image Analysis • Dr Tracey King BUBBL Group Manager & PA to Professor Constantin Coussios • Rosie Perry TempPA to Prof Tarassenko, Group AA to Biosignal analysis faculty • Vernon Bailey IBME IT Team lead • Vanessa Wilkins IBME IT Assistant • Jim Fisk Workshop Manager

6. Other Key People at the IBME Biomedical Engineering Academics • Dr Bob Carlisle (Drug delivery) • Dr Michael Chappell CDT Associate Director • Professor Robin Cleveland (Ultrasonics) • Dr Gari Clifford CDT Director • Prof. Constantin Coussios (Ultrasonics & drug delivery) • Prof. Zhanfeng Cui (Tissue Engineering) • Prof. Pete Dobson (Begbroke Science Park, Healthcare Innovation) • Dr. Vicente Grau Incoming CDT Director • Prof. Alison Noble IBME Director • Dr. Stephen Payne (Cardiovascular Modelling) • Dr Jens Rittscher (Biological image Analysis and Bioinformatics ) • Dr. Julia Schnabel (Biomedical image analysis) • Dr. Penny Smith (Image Measurement) • Dr Eleanor Stride (Ultrasonics) • Dr. Mark Thompson (Orthopaedic Biomechanics) • Prof. Lionel Tarassenko (Signal Processing & e-Health) • Dr. Cathy Ye (Tissue Engineering) • Dr. Amy Zavatsky (Orthopaedic Biomechanics) IBME Administrative Team • Jo Armitage CDT Administrator • Stacey Churcher PA to Prof Noble, Group AA to Biomedical Image Analysis • Dr Tracey King BUBBL Group Manager & PA to Professor Constantin Coussios • Rosie Perry TempPA to Prof Tarassenko, Group AA to Biosignal analysis faculty • Vernon Bailey IBME IT Team lead • Vanessa Wilkins IBME IT Assistant • Jim Fisk Workshop Manager

7. Centres for Doctoral Training Concept In 2008: £250m to create new wave of scientists and engineers for Britain The biggest ever investment in training the scientists and engineers Britain needs for its future was announced today (5th December 2008) by the Engineering and Physical Sciences Research Council – the UK funding body for science and engineering. Minister of State for Science and Innovation, Lord Drayson, announced the £250million initiative which will create 44 training centres across the UK and generate over 2000 PhD students. They will tackle some of the biggest problems currently facing Britain such as climate change, energy, our ageing population, and high-tech crime. Lord Drayson said: “Britain faces many challenges in the 21st Century and needs scientists and engineers with the right skills to find answers to these challenges, build a strong economy and keep us globally competitive. EPSRC’s doctoral training centres will provide a new wave of engineers and scientists to do the job.” He continued: “These new centres will help to develop clean renewable energy, fight high-tech crime, assist in reducing carbon emissions, and discover new healthcare solutions for an ageing population.  This is an exciting, innovative approach to training young researchers and will help build a better future for Britain.

8. Our Centre for Doctoral Training • Associated with and funded by the RCUK Digital Economy Programme (with 6 other training centres), to the value of £7.1m (Nottingham, Southampton, Bath, Lancaster, UCL, QMUL) • We will train 70 full-time students over 5+3 years and expect all IBME postgraduate students to participate in parts of the programme (approx 80 DPhils, 20 taught MSc) • Currently 70 students on the programme including you. • Thus the CDT is providing the core training programme for Oxford’s IBME, and the next generation of biomedical engineers who will go on to be leaders in the BME field. • Engagement with the healthcare industry and clinical partners is key to the success of the programme

9. CDT-HCI Training Goals • To train biomedical engineering (BME) PhD students at the translational interfaces of clinical practice and commercial exploitation • Programme to appeal to applied sciences undergraduates, and particularly those who want to keep career options open; academia vs industry. • “Added value”: Training will lead to greater depth in research and via the breadth of coverage, better prepare graduating PhDs to go on to be global leaders in the BME field in academia or industry

10. The Training Triangle Academia Hospitals/Clinicians Healthcare Industry

11. The Training Triangle

12. The Training Triangle

13. The Training Triangle Innovation Translation Commercialization Better validation of methods and insight into how to develop the next generation of technologies Methods taken further down the commercialization pathway

14. The Training Triangle Innovation Translation Commercialization Better validation of methods and insight into how to develop the next generation of technologies Methods taken further down the commercialization pathway

15. Course Design • 9 months intensive training + 3.25 yr PhD and advanced options

16. CDT Research Themes Address Major Biomedical Engineering Issues in Global Health & are linked to Major Clinical Initiatives at the University Information-driven healthcare - from biomedical signal analysis and machine learning in the ICU, to software-based clinical support systems and mHealth 1 Personalised healthcare - combining advanced modelling and measurement techniques to customize diagnosis or therapeutic management of a patient, e.g. neuro-intervention planning, stroke management, perinatal monitoring 2 Cancer therapeutics and delivery – from molecular imaging, to ultrasound-based methods for detecting early response to cancer therapy, monitoring of high-intensity focused ultrasound, and drug delivery. 3

17. Information Driven Healthcare An compressed course in machine learning Acute Kidney Trauma Mortality Predictor Iris Measurement Database Species Classifier Oxford Centre for Doctoral Training in Healthcare Innovation

18. Modelling for personalised healthcare Computational Modelling Image Registration Predicting stroke outcome How much grey matter can be saved? Oxford Centre for Doctoral Training in Healthcare Innovation

19. Cancer Therapeutics & Drug Delivery Thermal Ablation Targeted Chemotherapy Oxford Centre for Doctoral Training in Healthcare Innovation

20. And much more.... Ethics Hospital placements Oxford Centre for Doctoral Training in Healthcare Innovation Research Skills Entrepreneurship

21. Academic Timetable for 1st Year

22. 1st Year Overview Term 2: • Entrepreneuship • Computational Modelling • Imaging • Machine Learning • Decision Support • Cancer Therapeutics • Personalized Modelling Sept (pre-2nd year) • PhD Proposal • Viva … Then follow traditional Oxford DPhil (PhD) Term 1: • Orientation • Hospital Placement • Particles, Devices & Systems • Computational Methods • BioSignal Processing • Experimental Methods • Research Skills & Ethics Term 3 / Summer: • Clinical Trials • Business Skills • 4-Week Industrial Market Opportunity Project • 12 week summer research project Oxford Centre for Doctoral Training in Healthcare Innovation

23. Boring but important points • During module weeks you are all expected to be at the CDT Mon-Fri, 9am-5pm • You should arrive for classes a few minutes before the scheduled time. • PLEASE do not read emails, texts, etc during lectures. • We have many external speakers. You are our ambassadors for the programme. Respect that they don’t have to say yes to teaching you (or students in future years). • If you are sick contact Jo Armitage. • If you want to be excused from class you need to get permission from myself in advance (and have a good reason). • If you want to see me any time email myself or Jo to arrange a time. I am normally around on Tuesday’s working on CDT business if you want to drop by.

24. Finally • Our goal is to make this the best centre for doctoral training programme in the UK and one that is globally well-recognised. • Selection to get in was highly competitive. • The CDT has already attracted support and interest from industry and overseas institutions who may become partners in due course. • YOU are the ambassadors for this programme - its success depends heavily on the degree of commitment you have to it ...

25. Training Room Conduct Please: • Keep the fridge clean • Wipe the whiteboard at the end of each module • Don’t remove text books without asking the directors • Lock valuables in drawers • Don’t print unnecessarily – go digital. If you must, try 2-up, double sided, draft mode. • Each module we will nominate one of you to thank the module organiser • (We also need a rep to serve on the academic committee – we value your feedback on the course!)

26. In the real world • Don’t volunteer for too much stuff in college the first year • E.g. – don’t join the rowing team until your 2nd year – you can’t compete because it conflicts with lectures • Oxford is safe if you are not a 2-wheeled object: Lock up your bike 7 make it look old • Consider getting a bike? Busses are expensive and irregular, bikes are good for your health • Don’t use Cycle King – they just want your money. • There’s a bike ‘doctor’ here each week. • Get some lights (try the £ store in town) • Don’t be late in the morning!

27. Any questions?

28. Computing things • Laptops – wireless only • Remote Access Account - http://www.oucs.ox.ac.uk/network/remote/index.xml?ID=body.1_div.2 • VPN - http://www.oucs.ox.ac.uk/network/vpn/ • Eduroam - http://www.oucs.ox.ac.uk/network/wireless/services/eduroam/ • Remote access to your machine at IBME – not in 1st 9 months ... Try to take the evenings off, or read! • Check on banned software / settings (e.g. Skype) • http://www.oucs.ox.ac.uk/network/voip/skype.xml • http://www.gtc.ox.ac.uk/college-life/it-information/banned-software.html • Backing up • Network W-drive, USB sticks, Dropbox, Google Drive • NOT your local drives – treat as volatile!

29. Computing things • You will meet Dr Bailey and his team soon – they are by the pigeon holes ... Please respect their opening hours • Please log issues using: cdtsupport@eng.ox.ac.uk • Your computer will follow you around for the rest of your DPhil – please look after it  • Now log on with your username (4 letters + 4 numbers) associated with your college. • scro1234 for example

30. Your user accounts • Username is of the form: abcd1234 • Default password • You have to change it on first log on • This is the same password for all departmental computers Ibme!2013_cdt

31. Now make a bio • Just one paragraph – nothing too long. Add a photo and put it on a one page word document. Talk about your research interests and aims. • Make a CV – see using ONLY this template: http://www.ibme.ox.ac.uk/cdt/scripts/profiles/cdt2009/students • Please send to Jo Armitage by 5.00pm on Friday, 11th October: jo.armitage@eng.ox.ac.uk

32. Any questions?

34. Research Themes • Information-driven healthcare • Modelling for personalized healthcare • Cancer therapeutics and delivery Linked to major clinical initiatives in the University of Oxford All research themes undertaken in the new Oxford Institute of Biomedical Engineering in which the Centre for Doctoral Training is based.

35. Information-driven Healthcare • Clinical informatics can make a major contribution to improving the quality and safety of patient care • IBME activities include • How to integrate and practically deploy active decision support services in the complex, unpredictable and fast-changing context of healthcare delivery (Fox et al). • The development of ultrasound imaging/analysis technologies for monitoring pregnancies and reducing neonatal death in the developing world (Noble) Fig 1 CREDO (www.cossac.org) is a clinical trial of PROForma technology to improve the consistency, quality & safety of cancer patient care (acknowledgement: Fox group) • The CDT will train medical informaticians and software engineers to contribute to this new and important area of informatics. • Developing solutions that enable the delivery of ICU-level monitoring and response, whenever required, to every acute bed in a modern hospital using advanced information fusion techniques (Tarassenko, Clifford et al)

36. Modelling for personalized healthcare Covers areas such as • the personalized management of long-term conditions such as hypertension, diabetes, and asthma using mobile-phone technology • developing technologies and clinical procedures to assess and select therapies for early stroke patients (linked to OxAVIC) • For instance, there is a need to understand how to perform finite-element simulations quickly (ideally real-time), to incorporate automated image measurements in simulations, and to understand how patient-specific parameters can be estimated reliably, bearing in mind work-flow and cost constraints imposed by clinical practice • CDT training will provide a core foundation in software-based skills underpinning this area of research, from modelling processes to grid-based computations.

37. Cancer therapeutics and delivery • The IBME is co-located with Oxford Institute of Cancer Medicine, the UK’s foremost integrated cancer translation cancer research centre, and opposite the new Oxford NHS Cancer Centre • IBME faculty are increasingly involved in a wide range of translational activities including those of the CDT students will learn about the process of nanoparticle design, design of delivery technology, technology clinical assessment/the approval process, work-flow implications of a new technology, technologies for speeding up the drug development process, and the complex world of Intellectual Property in this area and will apply what they have learned during the course of their PhD CRUK/EPSRC Oxford Cancer Imaging Centre and Oxford Biomedical Research Centre